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	Case_USI	Data_Type	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	tumor_f	t_ref_count	t_alt_count	Tumor_Verification_Allele1	Tumor_Verification_Allele2	Match_Norm_Verification_Allele1	Match_Norm_Verification_Allele2	Verification_Status	Verification_Method	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	PolyPhen	SIFT	RNAseq
ABL2	27	broadinstitute.org	37	1	179077416	179077416	+	Missense_Mutation	SNP	G	C	C			TARGET-30-PANYGR	"Exome_WGA,Genome_BCCA"	TARGET-30-PANYGR-01A-01W	TARGET-30-PANYGR-10A-01W	0.495575	171	168	C	C	G	G	Valid_somatic	Sequenom	Illumina	g.chr1:179077416G>C	uc001gmj.3	-	12	3273	c.2986C>G	c.(2986-2988)CCG>GCG	p.P996A	ABL2_uc010pnf.1_Missense_Mutation_p.P893A|ABL2_uc010png.1_Missense_Mutation_p.P872A|ABL2_uc010pnh.1_Missense_Mutation_p.P975A|ABL2_uc001gmg.3_Missense_Mutation_p.P878A|ABL2_uc001gmi.3_Missense_Mutation_p.P981A|ABL2_uc001gmh.3_Missense_Mutation_p.P960A|ABL2_uc010pne.1_Missense_Mutation_p.P857A	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b	996	Pro-rich.				axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	CAGATGGACGGATGCTGCAGT	0.567			T	ETV6	AML								possibly_damaging(0.609)	tolerated(0.24)	RNAseq_support
ALK	238	broadinstitute.org	37	2	29445213	29445213	+	Missense_Mutation	SNP	A	T	T			TARGET-30-PAKXDZ	Exome_WGA	TARGET-30-PAKXDZ-01A-01W	TARGET-30-PAKXDZ-10A-01W	0.306122	34	15					Valid_somatic	Sequenom	Illumina	g.chr2:29445213A>T	uc002rmy.2	-	22	4419	c.3512T>A	c.(3511-3513)ATC>AAC	p.I1171N	ALK_uc010ymo.1_Missense_Mutation_p.I103N	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1171	Protein kinase.|Cytoplasmic (Potential).		I -> N (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.I1171N(2)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GCTTTACCTGATGATCAGGGC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.99)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29443697	29443697	+	Missense_Mutation	SNP	A	T	T			TARGET-30-PANRVJ	Exome_Native	TARGET-30-PANRVJ-01A-01D	TARGET-30-PANRVJ-10A-01D	0.230769	50	15	A(224)	T(85)	A(175)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443697A>T	uc002rmy.2	-	23	4427	c.3520T>A	c.(3520-3522)TTC>ATC	p.F1174I	ALK_uc010ymo.1_Missense_Mutation_p.F106I	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TGGTGGTTGAATTTGCTGCAG	0.502			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				possibly_damaging(0.748)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29443697	29443697	+	Missense_Mutation	SNP	A	G	G			TARGET-30-PARKNP	Exome_Native	TARGET-30-PARKNP-01A-01D	TARGET-30-PARKNP-10A-01D	0.487179	20	19	A(213)	G(147)	A(178)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443697A>G	uc002rmy.2	-	23	4427	c.3520T>C	c.(3520-3522)TTC>CTC	p.F1174L	ALK_uc010ymo.1_Missense_Mutation_p.F106L	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TGGTGGTTGAATTTGCTGCAG	0.502			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				benign(0.082)	deleterious(0.02)
ALK	238	broadinstitute.org	37	2	29443696	29443696	+	Missense_Mutation	SNP	A	C	C			TARGET-30-PARLTG	Exome_Native	TARGET-30-PARLTG-01A-01D	TARGET-30-PARLTG-10A-01D	0.176471	28	6	A(254)	C(50)	A(179)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443696A>C	uc002rmy.2	-	23	4428	c.3521T>G	c.(3520-3522)TTC>TGC	p.F1174C	ALK_uc010ymo.1_Missense_Mutation_p.F106C	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	CTGGTGGTTGAATTTGCTGCA	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.993)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29443696	29443696	+	Missense_Mutation	SNP	A	C	C			TARGET-30-PARZIP	Exome_Native	TARGET-30-PARZIP-01A-01D	TARGET-30-PARZIP-10A-01D	0.5	10	10	A(291)	C(157)	A(433)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443696A>C	uc002rmy.2	-	23	4428	c.3521T>G	c.(3520-3522)TTC>TGC	p.F1174C	ALK_uc010ymo.1_Missense_Mutation_p.F106C	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	CTGGTGGTTGAATTTGCTGCA	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.993)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29443695	29443695	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PAPRPR	Exome_Native	TARGET-30-PAPRPR-01A-01D	TARGET-30-PAPRPR-10A-01D	0.363636	42	24	G(252)	T(113)	G(179)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443695G>T	uc002rmy.2	-	23	4429	c.3522C>A	c.(3520-3522)TTC>TTA	p.F1174L	ALK_uc010ymo.1_Missense_Mutation_p.F106L	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TCTGGTGGTTGAATTTGCTGC	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				benign(0.082)	deleterious(0.02)
ALK	238	broadinstitute.org	37	2	29443695	29443695	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PASVRU	Exome_Native	TARGET-30-PASVRU-01A-01D	TARGET-30-PASVRU-10A-01D	0.297872	33	14	G(142)	T(65)	G(508)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443695G>T	uc002rmy.2	-	23	4429	c.3522C>A	c.(3520-3522)TTC>TTA	p.F1174L	ALK_uc010ymo.1_Missense_Mutation_p.F106L	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TCTGGTGGTTGAATTTGCTGC	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				benign(0.082)	deleterious(0.02)
ALK	238	broadinstitute.org	37	2	29443695	29443695	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PATFXV	Exome_Native	TARGET-30-PATFXV-01A-01D	TARGET-30-PATFXV-10A-01D	0.358491	34	19	G(160)	T(100)	G(380)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29443695G>T	uc002rmy.2	-	23	4429	c.3522C>A	c.(3520-3522)TTC>TTA	p.F1174L	ALK_uc010ymo.1_Missense_Mutation_p.F106L	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TCTGGTGGTTGAATTTGCTGC	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				benign(0.082)	deleterious(0.02)
ALK	238	broadinstitute.org	37	2	29443695	29443695	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PALAKE	Exome_WGA	TARGET-30-PALAKE-01A-01W	TARGET-30-PALAKE-10A-01W	0.448276	16	13	G(202)	T(10)	G(240)	T(0)	Valid_somatic	Sequenom	Illumina	g.chr2:29443695G>T	uc002rmy.2	-	23	4429	c.3522C>A	c.(3520-3522)TTC>TTA	p.F1174L	ALK_uc010ymo.1_Missense_Mutation_p.F106L	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TCTGGTGGTTGAATTTGCTGC	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				benign(0.082)	deleterious(0.02)
ALK	238	broadinstitute.org	37	2	29443695	29443695	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PANZVU	Exome_WGA	TARGET-30-PANZVU-01A-01W	TARGET-30-PANZVU-10A-01W	0.375	15	9	G(254)	T(202)	G(240)	T(0)	Valid_somatic	Sequenom	Illumina	g.chr2:29443695G>T	uc002rmy.2	-	23	4429	c.3522C>A	c.(3520-3522)TTC>TTA	p.F1174L	ALK_uc010ymo.1_Missense_Mutation_p.F106L	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1174	Protein kinase.|Cytoplasmic (Potential).		F -> I (in NBLST3; somatic mutation).|F -> C (in NBLST3).|F -> L (in NBLST3; somatic mutation).|F -> V (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1174L(51)|p.F1174?(5)|p.F1174C(3)|p.F1174V(2)|p.F1174I(2)|p.F1174S(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TCTGGTGGTTGAATTTGCTGC	0.507			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				benign(0.082)	deleterious(0.02)
ALK	238	broadinstitute.org	37	2	29436875	29436875	+	Missense_Mutation	SNP	A	C	C			TARGET-30-PATFCY	Exome_Native	TARGET-30-PATFCY-01A-01D	TARGET-30-PATFCY-10A-01D	0.585366	17	24	A(169)	C(288)	A(543)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29436875A>C	uc002rmy.2	-	24	4625	c.3718T>G	c.(3718-3720)TTG>GTG	p.L1240V	ALK_uc010ymo.1_Missense_Mutation_p.L172V	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1240	Protein kinase.|Cytoplasmic (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.L1240V(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TTTTCCTCCAAATACTGACAG	0.582			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.995)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29436860	29436860	+	Missense_Mutation	SNP	A	T	T			TARGET-30-PAINLN	Exome_WGA	TARGET-30-PAINLN-01A-01W	TARGET-30-PAINLN-10A-01W	0.338129	92	47					Valid_somatic	Sequenom	Illumina	g.chr2:29436860A>T	uc002rmy.2	-	24	4640	c.3733T>A	c.(3733-3735)TTC>ATC	p.F1245I	ALK_uc010ymo.1_Missense_Mutation_p.F177I	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1245	Protein kinase.|Cytoplasmic (Potential).		F -> V (in NBLST3; somatic mutation).|F -> C (in NBLST3; somatic mutation).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.F1245V(3)|p.F1245L(2)|p.F1245C(2)|p.F1245I(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	CGGTGGATGAAGTGGTTTTCC	0.567			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.999)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PANWRR	Exome_Native	TARGET-30-PANWRR-01A-01D	TARGET-30-PANWRR-10A-01D	0.268293	60	22	C(134)	T(97)	C(335)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PANXJL	Exome_Native	TARGET-30-PANXJL-01A-01D	TARGET-30-PANXJL-10A-01D	0.263158	56	20	C(265)	T(71)	C(288)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PAPTFZ	Exome_Native	TARGET-30-PAPTFZ-01A-01D	TARGET-30-PAPTFZ-10A-01D	0.513514	36	38	C(238)	T(198)	C(516)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PAPTLV	Exome_Native	TARGET-30-PAPTLV-01A-01D	TARGET-30-PAPTLV-10A-01D	0.36	48	27	C(261)	T(372)	C(594)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PARURB	Exome_Native	TARGET-30-PARURB-01A-01D	TARGET-30-PARURB-10A-01D	0.255319	70	24	C(509)	T(73)	C(458)	T(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PALNLU	Exome_WGA	TARGET-30-PALNLU-01A-01W	TARGET-30-PALNLU-10A-01W	0.257732	72	25					Valid_somatic	Sequenom	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ALK	238	broadinstitute.org	37	2	29432664	29432664	+	Missense_Mutation	SNP	C	T	T	rs113994087		TARGET-30-PANBCI	Exome_WGA	TARGET-30-PANBCI-01A-01W	TARGET-30-PANBCI-10A-01W	0.141935	133	22					Valid_somatic	Sequenom	Illumina	g.chr2:29432664C>T	uc002rmy.2	-	25	4731	c.3824G>A	c.(3823-3825)CGA>CAA	p.R1275Q	ALK_uc010ymo.1_Missense_Mutation_p.R207Q	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1275	Protein kinase.|Cytoplasmic (Potential).		R -> L (observed in neuroblastoma).|R -> Q (in NBLST3).		protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.R1275Q(39)|p.R1275?(10)|p.R1275L(1)	NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTAGATGTCTCGGGCCATCCC	0.557			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				probably_damaging(0.998)	deleterious(0)
ARID1A	8289	broadinstitute.org	37	1	27099000	27099000	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PALNLU	Exome_WGA	TARGET-30-PALNLU-01A-01W	TARGET-30-PALNLU-10A-01W	0.129213	155	23	T	T	G	G	Valid_somatic	Sequenom	Illumina	g.chr1:27099000G>T	uc001bmv.1	+	13	3789	c.3416G>T	c.(3415-3417)GGA>GTA	p.G1139V	ARID1A_uc001bmt.1_Missense_Mutation_p.G1139V|ARID1A_uc001bmu.1_Missense_Mutation_p.G1139V|ARID1A_uc001bmw.1_Missense_Mutation_p.G756V|ARID1A_uc001bmx.1_5'UTR|ARID1A_uc009vsm.1_5'Flank|ARID1A_uc009vsn.1_5'Flank	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1139					"androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent"	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCGGGATCAGGATCTATGCAG	0.517			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC
ARID1A	8289	broadinstitute.org	37	1	27106214	27106214	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PALXHW	Exome_WGA	TARGET-30-PALXHW-01A-01W	TARGET-30-PALXHW-10A-01W	0.344298	299	157	A	A	G	G	Valid_somatic	Sequenom	Illumina	g.chr1:27106214G>A	uc001bmv.1	+	20	6198	c.5825G>A	c.(5824-5826)GGC>GAC	p.G1942D	ARID1A_uc001bmu.1_Missense_Mutation_p.G1725D|ARID1A_uc001bmx.1_Missense_Mutation_p.G788D|ARID1A_uc009vsm.1_Missense_Mutation_p.G270D|ARID1A_uc009vsn.1_Missense_Mutation_p.G184D	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1942					"androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent"	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TTTCCATTTGGCATTAGCCCA	0.527			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC
ARPP21	10777	broadinstitute.org	37	3	35833977	35833977	+	Frame_Shift_Del	DEL	G	-	-			TARGET-30-PASUYG	Exome_Native	TARGET-30-PASUYG-01A-01D	TARGET-30-PASUYG-10A-01D	0.55			271	294	354	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:35833977delG	uc003cgb.2	+	19	2400	c.2136delG	c.(2134-2136)CCGfs	p.P712fs	ARPP21_uc003cga.2_Frame_Shift_Del_p.P693fs|ARPP21_uc011axy.1_Frame_Shift_Del_p.P713fs|ARPP21_uc003cgf.2_Frame_Shift_Del_p.P548fs|ARPP21_uc003cgg.2_Frame_Shift_Del_p.P235fs	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	"cyclic AMP-regulated phosphoprotein, 21 kD"	712	Gln-rich.					cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3
ASPM	259266	broadinstitute.org	37	1	197073553	197073553	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.15	51	9	T	T	C	C	Valid_somatic	Sequenom	Illumina	g.chr1:197073553C>T	uc001gtu.2	-	18	5085	c.4828G>A	c.(4828-4830)GTT>ATT	p.V1610I	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	"asp (abnormal spindle)-like, microcephaly"	1610	IQ 3.				mitosis	cytoplasm|nucleus	calmodulin binding	p.V1610A(1)		ovary(4)|central_nervous_system(2)	6						TGAATTATAACAGCTGCTTTC	0.353													benign(0.011)	tolerated(0.18)
ATRX	546	broadinstitute.org	37	X	76937780	76937780	+	Nonsense_Mutation	SNP	C	A	A			TARGET-30-PARDCK	Exome_Native	TARGET-30-PARDCK-01A-01D	TARGET-30-PARDCK-10A-01D	0.456731	113	95	C(268)	A(52)	C(197)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:76937780C>A	uc004ecp.3	-	9	3200	c.2968G>T	c.(2968-2970)GAA>TAA	p.E990*	ATRX_uc004ecq.3_Nonsense_Mutation_p.E952*|ATRX_uc004eco.3_Nonsense_Mutation_p.E775*|ATRX_uc004ecr.2_Nonsense_Mutation_p.E922*|ATRX_uc010nlx.1_Nonsense_Mutation_p.E961*|ATRX_uc010nly.1_Nonsense_Mutation_p.E935*	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	990					"DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent"	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TTTTTTTCTTCAGTTCCCTTT	0.353			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome
ATRX	546	broadinstitute.org	37	X	76889076	76889076	+	Nonsense_Mutation	SNP	A	C	C			TARGET-30-PASTKW	Exome_Native	TARGET-30-PASTKW-01A-01D	TARGET-30-PASTKW-10A-01D	0.107143	50	6	A(330)	C(30)	A(311)	C(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:76889076A>C	uc004ecp.3	-	18	5166	c.4934T>G	c.(4933-4935)TTA>TGA	p.L1645*	ATRX_uc004ecq.3_Nonsense_Mutation_p.L1607*|ATRX_uc004eco.3_Nonsense_Mutation_p.L1430*	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1645	Helicase ATP-binding.		L -> S (in ATRX).		"DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent"	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATCATCTTTTAATCCCTCTTG	0.299			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome
ATRX	546	broadinstitute.org	37	X	76849227	76849227	+	Missense_Mutation	SNP	A	G	G			TARGET-30-PALXHW	Exome_WGA	TARGET-30-PALXHW-01A-01W	TARGET-30-PALXHW-10A-01W	0.487013	79	75	A(325)	G(302)	A(491)	G(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:76849227A>G	uc004ecp.3	-	26	6281	c.6049T>C	c.(6049-6051)TCT>CCT	p.S2017P	ATRX_uc004ecq.3_Missense_Mutation_p.S1979P|ATRX_uc004eco.3_Missense_Mutation_p.S1802P	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2017					"DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent"	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATTTTCCCAGAATGCTCTAAA	0.358			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome
ATRX	546	broadinstitute.org	37	X	76813058	76813058	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PARFWB	Exome_Native	TARGET-30-PARFWB-01A-01D	TARGET-30-PARFWB-10A-01D	0.847826	7	39	C(120)	T(685)	C(934)	T(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:76813058C>T	uc004ecp.3	-	30	6795	c.6563G>A	c.(6562-6564)CGA>CAA	p.R2188Q	ATRX_uc004ecq.3_Missense_Mutation_p.R2150Q|ATRX_uc004eco.3_Missense_Mutation_p.R1973Q	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2188	Helicase C-terminal.				"DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent"	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATCAACAACTCGAAAAGACAG	0.343			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome
ATRX	546	broadinstitute.org	37	X	76813032	76813032	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PANRVJ	Exome_Native	TARGET-30-PANRVJ-01A-01D	TARGET-30-PANRVJ-10A-01D	0.71875	18	46	G(149)	A(401)	G(349)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:76813032G>A	uc004ecp.3	-	30	6821	c.6589C>T	c.(6589-6591)CGT>TGT	p.R2197C	ATRX_uc004ecq.3_Missense_Mutation_p.R2159C|ATRX_uc004eco.3_Missense_Mutation_p.R1982C	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2197	Helicase C-terminal.				"DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent"	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	GTAAAATGACGCTCCACCTGC	0.388			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome
ATRX	546	broadinstitute.org	37	X	76814303	76814306	+	Frame_Shift_Del	DEL	ATAA	-	-			TARGET-30-PARVLK	Exome_Native	TARGET-30-PARVLK-01A-01D	TARGET-30-PARVLK-14A-01D	0.38			257	82	366	0	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:76814303_76814306delATAA	uc004ecp.3	-	29	6570_6573	c.6338_6341delTTAT	c.(6337-6342)TTTATCfs	p.F2113fs	ATRX_uc004ecq.3_Frame_Shift_Del_p.F2075fs|ATRX_uc004eco.3_Frame_Shift_Del_p.F1898fs	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2113_2114	Helicase C-terminal.				"DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent"	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	p.F2113fs*9(1)		haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)					Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome
CACNA1C	775	broadinstitute.org	37	12	2690946	2690946	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.243243	56	18	C(574)	T(382)	C(577)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:2690946C>T	uc009zdu.1	+	14	2399	c.2086C>T	c.(2086-2088)CTC>TTC	p.L696F	CACNA1C_uc009zdv.1_Missense_Mutation_p.L693F|CACNA1C_uc001qkb.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkc.2_Missense_Mutation_p.L696F|CACNA1C_uc001qke.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkf.2_Missense_Mutation_p.L696F|CACNA1C_uc001qjz.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkd.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkg.2_Missense_Mutation_p.L696F|CACNA1C_uc009zdw.1_Missense_Mutation_p.L696F|CACNA1C_uc001qkh.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkl.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkn.2_Missense_Mutation_p.L696F|CACNA1C_uc001qko.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkp.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkr.2_Missense_Mutation_p.L696F|CACNA1C_uc001qku.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkq.2_Missense_Mutation_p.L696F|CACNA1C_uc001qks.2_Missense_Mutation_p.L696F|CACNA1C_uc001qkt.2_Missense_Mutation_p.L696F|CACNA1C_uc001qka.1_Missense_Mutation_p.L231F|CACNA1C_uc001qki.1_Missense_Mutation_p.L432F|CACNA1C_uc001qkj.1_Missense_Mutation_p.L432F|CACNA1C_uc001qkk.1_Missense_Mutation_p.L432F|CACNA1C_uc001qkm.1_Missense_Mutation_p.L432F|CACNA1C_uc001qkw.2_5'Flank	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	"calcium channel, voltage-dependent, L type,"	696	II.|Extracellular (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CCCCCAGTCCCTCCTCACTGT	0.512													probably_damaging(0.999)	deleterious(0.02)
CACNA1F	778	broadinstitute.org	37	X	49067432	49067432	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PATFXV	Exome_Native	TARGET-30-PATFXV-01A-01D	TARGET-30-PATFXV-10A-01D	0.285714	10	4	C(237)	A(105)	C(472)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:49067432C>A	uc004dnb.2	-	37	4476	c.4414G>T	c.(4414-4416)GGG>TGG	p.G1472W	CACNA1F_uc010nip.2_Missense_Mutation_p.G1461W	NM_005183	NP_005174	O60840	CAC1F_HUMAN	"calcium channel, voltage-dependent, L type,"	1472	By similarity.|Cytoplasmic (Potential).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	TACTTGGCCCCAGGGTCATAT	0.502													probably_damaging(0.994)	deleterious(0)
CACNA1H	8912	broadinstitute.org	37	16	1265063	1265063	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAISSH	Exome_WGA	TARGET-30-PAISSH-01A-01W	TARGET-30-PAISSH-10A-01W	0.428571	8	6	G(214)	A(140)	G(246)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:1265063G>A	uc002cks.2	+	28	5269	c.5021G>A	c.(5020-5022)CGT>CAT	p.R1674H	CACNA1H_uc002ckt.2_Missense_Mutation_p.R1668H|CACNA1H_uc002cku.2_Missense_Mutation_p.R380H|CACNA1H_uc010brj.2_Missense_Mutation_p.R385H|CACNA1H_uc002ckv.2_Missense_Mutation_p.R374H	NM_021098	NP_066921	O95180	CAC1H_HUMAN	"calcium channel, voltage-dependent, T type,"	1674	IV.|Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	TTTGGGTTCCGTCGGTTCTTC	0.622													probably_damaging(0.998)	deleterious(0.01)
CACNA1S	779	broadinstitute.org	37	1	201029824	201029824	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAPBZI	Exome_WGA	TARGET-30-PAPBZI-01A-01W	TARGET-30-PAPBZI-10A-01W	0.166667	340	68	C(424)	A(76)	C(432)	A(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:201029824C>A	uc001gvv.2	-	26	3603	c.3376G>T	c.(3376-3378)GCC>TCC	p.A1126S		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	"calcium channel, voltage-dependent, L type,"	1126	IV.|Helical; Name=S1 of repeat IV; (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	ATGATGAGGGCAAACATCAGG	0.542													possibly_damaging(0.482)	tolerated(0.05)
CACNB3	784	broadinstitute.org	37	12	49220231	49220231	+	Missense_Mutation	SNP	A	T	T			TARGET-30-PAMDAL	Exome_WGA	TARGET-30-PAMDAL-01A-01W	TARGET-30-PAMDAL-10A-01W	0.45098	28	23	A(260)	T(140)	A(663)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:49220231A>T	uc001rsl.1	+	10	1025	c.824A>T	c.(823-825)AAC>ATC	p.N275I	CACNB3_uc010sly.1_Missense_Mutation_p.N262I|CACNB3_uc010slz.1_Missense_Mutation_p.N274I|CACNB3_uc001rsk.1_Missense_Mutation_p.N122I	NM_000725	NP_000716	P54284	CACB3_HUMAN	"calcium channel, voltage-dependent, beta 3"	275					axon guidance|membrane depolarization|synaptic transmission	cytosol|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0					Verapamil(DB00661)	GACACCATCAACCACCCAGCA	0.572													probably_damaging(0.999)	deleterious(0)
CARD11	84433	broadinstitute.org	37	7	2951918	2951918	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAHYWC	Exome_WGA	TARGET-30-PAHYWC-01A-01W	TARGET-30-PAHYWC-10A-01W	0.125	77	11	C(277)	T(46)	C(257)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr7:2951918C>T	uc003smv.2	-	23	3436	c.3032G>A	c.(3031-3033)AGA>AAA	p.R1011K		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	"caspase recruitment domain family, member 11"	1011	Guanylate kinase-like.				positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GAACTCATCTCTTGTGACGAT	0.582			Mis		DLBCL								benign(0)	tolerated(1)
CBL	867	broadinstitute.org	37	11	119142561	119142561	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAMDAL	Exome_WGA	TARGET-30-PAMDAL-01A-01W	TARGET-30-PAMDAL-10A-01W	0.133891	207	32	C(325)	T(86)	C(615)	T(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr11:119142561C>T	uc001pwe.2	+	3	698	c.560C>T	c.(559-561)GCG>GTG	p.A187V		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	187	Cbl-PTB.|EF-hand-like.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GCAGATGCTGCGGAATTTTGG	0.378									CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome
CD247	919	broadinstitute.org	37	1	167409953	167409953	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PARDYU	Exome_Native	TARGET-30-PARDYU-01A-01D	TARGET-30-PARDYU-10A-01D	0.416667	21	15	C(277)	A(134)	C(384)	A(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:167409953C>A	uc001gei.3	-	2	255	c.110G>T	c.(109-111)GGA>GTA	p.G37V	CD247_uc001gej.3_Missense_Mutation_p.G37V|CD247_uc001gek.2_Missense_Mutation_p.G37V	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor	37	Helical; (Potential).				interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			GAAGAGGATTCCATCCAGCAG	0.557													probably_damaging(1)	tolerated(0.14)
CHD8	57680	broadinstitute.org	37	14	21897200	21897200	+	Nonsense_Mutation	SNP	G	A	A			TARGET-30-PANYGR	"Exome_WGA,Genome_BCCA"	TARGET-30-PANYGR-01A-01W	TARGET-30-PANYGR-10A-01W	0.463519	250	216	A	A	G	G	Valid_somatic	"PCR/Sanger, PCR/HiSeq, Sequenom"	Illumina	g.chr14:21897200G>A	uc001was.1	-	3	395	c.301C>T	c.(301-303)CAG>TAG	p.Q101*	CHD8_uc001war.1_5'UTR	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	380	Gln-rich.				"ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent"	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		ATCTGAGCCTGCTGTACAGAG	0.532															RNAseq_support
CHEK2	11200	broadinstitute.org	37	22	29121081	29121081	+	Missense_Mutation	SNP	T	C	C			TARGET-30-PARVLK	Exome_Native	TARGET-30-PARVLK-01A-01D	TARGET-30-PARVLK-14A-01D	0.263158	42	15	T(443)	C(21)	T(456)	C(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr22:29121081T>C	uc003adu.1	-	4	548	c.476A>G	c.(475-477)TAC>TGC	p.Y159C	CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Missense_Mutation_p.Y159C|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Missense_Mutation_p.Y202C|CHEK2_uc003adv.1_Missense_Mutation_p.Y159C|CHEK2_uc003adw.1_Missense_Mutation_p.Y159C|CHEK2_uc003adx.1_Translation_Start_Site|CHEK2_uc003ady.1_Missense_Mutation_p.Y159C|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	159	FHA.				"cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence"	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						ATCTTCTATGTATGCAATGTA	0.353			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				probably_damaging(0.999)	deleterious(0)
CLCN3	1182	broadinstitute.org	37	4	170625278	170625278	+	Frame_Shift_Del	DEL	G	-	-			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.35			1014	323	1068	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr4:170625278delG	uc003isi.2	+	10	2202	c.1693delG	c.(1693-1695)GGGfs	p.G565fs	CLCN3_uc003ish.2_Frame_Shift_Del_p.G565fs|CLCN3_uc011cjz.1_Frame_Shift_Del_p.G548fs|CLCN3_uc011cka.1_Frame_Shift_Del_p.G538fs|CLCN3_uc003isj.1_Frame_Shift_Del_p.G538fs	NM_001829	NP_001820	P51790	CLCN3_HUMAN	chloride channel 3 isoform b	565					endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)
CLTC	1213	broadinstitute.org	37	17	57721820	57721820	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.140673	281	46	G(709)	A(96)	G(530)	A(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr17:57721820G>A	uc002ixq.1	+	2	669	c.226G>A	c.(226-228)GCT>ACT	p.A76T	CLTC_uc002ixp.2_Missense_Mutation_p.A76T|CLTC_uc002ixr.1_Missense_Mutation_p.A76T	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	76	Globular terminal domain.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CATGAATCCAGCTAGCAAAGT	0.328			T	ALK|TFE3	ALCL|renal 								benign(0.027)	tolerated(0.61)
COL1A1	1277	broadinstitute.org	37	17	48268201	48268201	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PATDXG	Exome_Native	TARGET-30-PATDXG-01A-01D	TARGET-30-PATDXG-10A-01D	0.392857	34	22	G(153)	T(118)	G(283)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr17:48268201G>T	uc002iqm.2	-	33	2446	c.2320C>A	c.(2320-2322)CCT>ACT	p.P774T		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	774	Triple-helical region.				"axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception"	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding	p.P774S(1)	COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	GCACCAGCAGGGCCAGGAGGA	0.617			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						unknown(0)	deleterious(0)
COL1A1	1277	broadinstitute.org	37	17	48264420	48264420	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PALHVD	Exome_WGA	TARGET-30-PALHVD-01A-01W	TARGET-30-PALHVD-10A-01W	0.1	27	3	C(427)	G(49)	C(412)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr17:48264420C>G	uc002iqm.2	-	47	3613	c.3487G>C	c.(3487-3489)GGG>CGG	p.G1163R		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	1163	Triple-helical region.				"axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception"	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	CCAGGGGGCCCAATGGGGCCA	0.622			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						unknown(0)	deleterious(0)
COL3A1	1281	broadinstitute.org	37	2	189872235	189872235	+	Frame_Shift_Del	DEL	G	-	-			TARGET-30-PANBSP	Exome_WGA	TARGET-30-PANBSP-01A-01W	TARGET-30-PANBSP-10A-01W	0.32			162	161	243	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:189872235delG	uc002uqj.1	+	45	3382	c.3265delG	c.(3265-3267)GGCfs	p.G1089fs		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	1089	Triple-helical region.		G -> D (in EDS4).		axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)
COL4A1	1282	broadinstitute.org	37	13	110845215	110845215	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PARVLK	Exome_Native	TARGET-30-PARVLK-01A-01D	TARGET-30-PARVLK-14A-01D	0.556818	39	49	C(80)	G(562)	C(457)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr13:110845215C>G	uc001vqw.3	-	23	1549	c.1427G>C	c.(1426-1428)CGG>CCG	p.R476P	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	476	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GGGAGGCCCCCGATATCCGTC	0.498													unknown(0)	tolerated(1)
COL4A1	1282	broadinstitute.org	37	13	110835399	110835399	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PALJPX	Exome_WGA	TARGET-30-PALJPX-01A-01W	TARGET-30-PALJPX-10A-01W	0.333333	6	3	C(235)	A(71)	C(366)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr13:110835399C>A	uc001vqw.3	-	28	2158	c.2036G>T	c.(2035-2037)GGA>GTA	p.G679V	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	679	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GCCCTTCTCTCCTGGCAGGCC	0.622													probably_damaging(1)	deleterious(0)
COL4A1	1282	broadinstitute.org	37	13	110819517	110819517	+	Missense_Mutation	SNP	G	C	C			TARGET-30-PAPBZI	Exome_WGA	TARGET-30-PAPBZI-01A-01W	TARGET-30-PAPBZI-10A-01W	0.3	266	114	G(267)	C(242)	G(465)	C(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr13:110819517G>C	uc001vqw.3	-	44	4059	c.3937C>G	c.(3937-3939)CCA>GCA	p.P1313A	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	1313	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TGAAATCCTGGAACTCCTGGA	0.527													possibly_damaging(0.901)	deleterious(0.01)
COL4A3	1285	broadinstitute.org	37	2	228158027	228158027	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PASGUT	Exome_Native	TARGET-30-PASGUT-01A-01D	TARGET-30-PASGUT-10A-01D	0.405405	22	15	C(358)	T(264)	C(146)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:228158027C>T	uc002vom.1	+	38	3493	c.3331C>T	c.(3331-3333)CTC>TTC	p.L1111F	COL4A3_uc002von.1_Missense_Mutation_p.L1111F|COL4A3_uc002voo.1_Missense_Mutation_p.L1111F|COL4A3_uc002vop.1_Missense_Mutation_p.L1111F|uc002voq.1_Intron|uc002vor.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor	1111	Triple-helical region.				activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AAGTCCTGGCCTCCCAGGTAA	0.488													unknown(0)	tolerated(0.35)
COL4A3	1285	broadinstitute.org	37	2	228169704	228169704	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PAIMDT	Exome_WGA	TARGET-30-PAIMDT-01A-01W	TARGET-30-PAIMDT-10A-01W	0.137255	44	7	C(370)	G(40)	C(346)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:228169704C>G	uc002vom.1	+	47	4319	c.4157C>G	c.(4156-4158)CCC>CGC	p.P1386R	COL4A3_uc002von.1_Missense_Mutation_p.P1386R|COL4A3_uc002voo.1_Missense_Mutation_p.P1386R|COL4A3_uc002vop.1_Missense_Mutation_p.P1386R|uc002voq.1_Intron|uc002vor.1_Intron|COL4A3_uc010fxf.1_5'Flank	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor	1386	Triple-helical region.				activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		TGCCTAGGACCCTGTGGGCCA	0.343													unknown(0)	tolerated(0.39)
COL4A5	1287	broadinstitute.org	37	X	107858222	107858222	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAILNU	Exome_WGA	TARGET-30-PAILNU-01A-01W	TARGET-30-PAILNU-10A-01W	0.566038	46	60	C(147)	A(113)	C(132)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:107858222C>A	uc004enz.1	+	30	2679	c.2477C>A	c.(2476-2478)CCA>CAA	p.P826Q	COL4A5_uc011mso.1_Missense_Mutation_p.P826Q|COL4A5_uc004eob.1_Missense_Mutation_p.P434Q	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	826	Triple-helical region.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						CCACCAGGACCACCAGGGATT	0.438									Alport_syndrome_with_Diffuse_Leiomyomatosis				unknown(0)	tolerated(0.06)
COL5A1	1289	broadinstitute.org	37	9	137703338	137703338	+	Missense_Mutation	SNP	G	C	C			TARGET-30-PARAMT	Exome_Native	TARGET-30-PARAMT-01A-01D	TARGET-30-PARAMT-10A-01D	0.5	14	14	G(253)	C(133)	G(373)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr9:137703338G>C	uc004cfe.2	+	46	3965	c.3583G>C	c.(3583-3585)GGA>CGA	p.G1195R		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1195	Triple-helical region.				"axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells"	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TTCCCTGCAGGGAGCTGACGG	0.637											OREG0019605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	unknown(0)	deleterious(0)
COL5A2	1290	broadinstitute.org	37	2	189901349	189901349	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PASVRU	Exome_Native	TARGET-30-PASVRU-01A-01D	TARGET-30-PASVRU-10A-01D	0.37931	18	11	C(78)	A(87)	C(245)	A(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:189901349C>A	uc002uqk.2	-	52	4381	c.4106G>T	c.(4105-4107)GGG>GTG	p.G1369V	COL5A2_uc010frx.2_Missense_Mutation_p.G945V	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	1369	Fibrillar collagen NC1.				axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TACCTGAGACCCTCTGTTCAT	0.313													unknown(0)	deleterious(0)
COL6A3	1293	broadinstitute.org	37	2	238303725	238303725	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.428571	20	15	C(122)	T(77)	C(132)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:238303725C>T	uc002vwl.2	-	3	499	c.214G>A	c.(214-216)GGA>AGA	p.G72R	COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwq.2_Intron|COL6A3_uc002vwr.2_Intron|COL6A3_uc010znk.1_Missense_Mutation_p.G72R	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	72	VWFA 1.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TCATTTTCTCCCACAGCTAAG	0.383
COL6A6	131873	broadinstitute.org	37	3	130289800	130289800	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PARZMY	Exome_Native	TARGET-30-PARZMY-06A-01D	TARGET-30-PARZMY-10A-01D	0.362319	44	25	G(39)	T(57)	G(170)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:130289800G>T	uc010htl.2	+	6	2571	c.2540G>T	c.(2539-2541)CGG>CTG	p.R847L		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	847	VWFA 5.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						AATCAGGTCCGGTTTGGGGCT	0.418													possibly_damaging(0.531)	deleterious(0.01)
COL6A6	131873	broadinstitute.org	37	3	130368273	130368273	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.133333	39	6	C(506)	T(191)	C(494)	T(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:130368273C>T	uc010htl.2	+	32	5631	c.5600C>T	c.(5599-5601)GCC>GTC	p.A1867V	COL6A6_uc003eni.3_Intron	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1867	VWFA 8.|Nonhelical region.				axon guidance|cell adhesion	collagen		p.A1867A(1)		ovary(6)|central_nervous_system(1)|pancreas(1)	8						AGAAAAATCGCCACATTTTTC	0.557													benign(0.396)	deleterious(0)
COL6A6	131873	broadinstitute.org	37	3	130383893	130383893	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PARHUX	Exome_Native	TARGET-30-PARHUX-01A-01D	TARGET-30-PARHUX-10A-01D	0.428571	12	9	C(343)	A(305)	C(634)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:130383893C>A	uc010htl.2	+	35	6580	c.6549C>A	c.(6547-6549)AAC>AAA	p.N2183K	COL6A6_uc003eni.3_Missense_Mutation_p.N282K	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	2183	Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						TAAAGTGCAACAGACTTAACT	0.338													benign(0.135)	tolerated(0.9)
CREB5	9586	broadinstitute.org	37	7	28610140	28610140	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PASGUT	Exome_Native	TARGET-30-PASGUT-01A-01D	TARGET-30-PASGUT-10A-01D	0.363636	28	16	C(411)	T(272)	C(470)	T(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr7:28610140C>T	uc003szq.2	+	5	839	c.449C>T	c.(448-450)ACC>ATC	p.T150I	CREB5_uc003szo.2_Missense_Mutation_p.T117I|CREB5_uc003szr.2_Missense_Mutation_p.T143I	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	150					"positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter"		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						GCACCTTCCACCAACCGCCAG	0.592													unknown(0)	tolerated(0.1)
CREB5	9586	broadinstitute.org	37	7	28848903	28848903	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAITCI	Exome_WGA	TARGET-30-PAITCI-01A-01W	TARGET-30-PAITCI-10A-01W	0.136986	63	10	G(445)	A(89)	G(608)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr7:28848903G>A	uc003szq.2	+	9	1516	c.1126G>A	c.(1126-1128)GAG>AAG	p.E376K	CREB5_uc003szo.2_Missense_Mutation_p.E343K|CREB5_uc003szr.2_Missense_Mutation_p.E369K|CREB5_uc003szs.2_Missense_Mutation_p.E237K	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	376	Basic motif.				"positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter"		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						GGATCCGGACGAGAGGCGGCG	0.592													possibly_damaging(0.876)	deleterious(0)
CRX	1406	broadinstitute.org	37	19	48343029	48343029	+	Frame_Shift_Del	DEL	C	-	-	rs61748458		TARGET-30-PARVNT	Exome_Native	TARGET-30-PARVNT-01A-01D	TARGET-30-PARVNT-10A-01D	0.36			433	353	377	2	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:48343029delC	uc002phq.3	+	4	909	c.705delC	c.(703-705)AGCfs	p.S235fs		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	235					organ morphogenesis|response to stimulus|visual perception		leucine zipper domain binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)
CYP11A1	1583	broadinstitute.org	37	15	74631979	74631980	+	Frame_Shift_Ins	INS	-	T	T			TARGET-30-PALAKM	Exome_WGA	TARGET-30-PALAKM-01A-01W	TARGET-30-PALAKM-10A-01W	0.33			506	353	702	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr15:74631979_74631980insT	uc002axt.2	-	6	1260_1261	c.1105_1106insA	c.(1105-1107)ACGfs	p.T369fs	CYP11A1_uc002axs.2_Frame_Shift_Ins_p.T211fs|CYP11A1_uc010bjm.1_Frame_Shift_Ins_p.T211fs|CYP11A1_uc010bjn.1_RNA|CYP11A1_uc010bjo.1_Intron|CYP11A1_uc010bjp.1_RNA|CYP11A1_uc010ulj.1_Frame_Shift_Ins_p.T149fs	NM_000781	NP_000772	P05108	CP11A_HUMAN	"cytochrome P450, family 11, subfamily A,"	369					C21-steroid hormone biosynthetic process|cholesterol metabolic process|vitamin D metabolic process|xenobiotic metabolic process	mitochondrial matrix	cholesterol monooxygenase (side-chain-cleaving) activity|electron carrier activity|heme binding			ovary(2)	2					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Clotrimazole(DB00257)|Digitoxin(DB01396)|Digoxin(DB00390)|Medroxyprogesterone(DB00603)|Ouabain(DB01092)|Progesterone(DB00396)|Testosterone(DB00624)|Trilostane(DB01108)
DDB1	1642	broadinstitute.org	37	11	61079358	61079358	+	Nonsense_Mutation	SNP	G	T	T			TARGET-30-PALJPX	Exome_WGA	TARGET-30-PALJPX-01A-01W	TARGET-30-PALJPX-10A-01W	0.427273	63	47					Valid_somatic	Sequenom	Illumina	g.chr11:61079358G>T	uc001nrc.3	-	18	2401	c.2175C>A	c.(2173-2175)TGC>TGA	p.C725*	DDB1_uc010rle.1_Intron|DDB1_uc010rlf.1_Nonsense_Mutation_p.C725*	NM_001923	NP_001914	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1	725	Interaction with CDT1.				"cell cycle checkpoint|interspecies interaction between organisms|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process"	Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytoplasm|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4						CTTCCTGGTAGCAGATCTTCC	0.577								NER
DKK2	27123	broadinstitute.org	37	4	107845226	107845226	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PALIIN	Exome_WGA	TARGET-30-PALIIN-01A-01W	TARGET-30-PALIIN-10A-01W	0.144165	374	63	T	T	G	G	Valid_somatic	Sequenom	Illumina	g.chr4:107845226G>T	uc003hyi.2	-	4	1370	c.665C>A	c.(664-666)TCT>TAT	p.S222Y	DKK2_uc003hyj.1_3'UTR	NM_014421	NP_055236	Q9UBU2	DKK2_HUMAN	dickkopf homolog 2 precursor	222	DKK-type Cys-2.				multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space		p.S222F(1)		ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		CAGCCCATGAGAACCCTTCTT	0.502													possibly_damaging(0.835)	deleterious(0)
DNAH8	1769	broadinstitute.org	37	6	38840517	38840517	+	Frame_Shift_Del	DEL	T	-	-			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.34			852	948	1165	9	Valid_somatic	PCR/MiSeq	Illumina	g.chr6:38840517delT	uc003ooe.1	+	48	7145	c.6545delT	c.(6544-6546)ATTfs	p.I2182fs		NM_001371	NP_001362			"dynein, axonemal, heavy polypeptide 8"											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21
DOCK1	1793	broadinstitute.org	37	10	128829970	128829970	+	Frame_Shift_Del	DEL	G	-	-			TARGET-30-PASWIJ	Exome_Native	TARGET-30-PASWIJ-01A-01D	TARGET-30-PASWIJ-10A-01D	0.34			175	43	175	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr10:128829970delG	uc001ljt.2	+	17	1682	c.1618delG	c.(1618-1620)GATfs	p.D540fs	DOCK1_uc010qun.1_Frame_Shift_Del_p.D561fs	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	540	DHR-1.				"apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction"	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)
EGF	1950	broadinstitute.org	37	4	110908936	110908936	+	Missense_Mutation	SNP	A	G	G			TARGET-30-PATHVK	Exome_Native	TARGET-30-PATHVK-01A-01D	TARGET-30-PATHVK-10A-01D	0.481481	28	26	A(329)	G(233)	A(357)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr4:110908936A>G	uc003hzy.3	+	17	2980	c.2528A>G	c.(2527-2529)TAT>TGT	p.Y843C	EGF_uc011cfu.1_Missense_Mutation_p.Y801C|EGF_uc011cfv.1_Missense_Mutation_p.Y843C|EGF_uc010imk.2_Intron	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	843	EGF-like 6.|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)	TGCAGCATGTATGCTCGGTGT	0.428													benign(0.366)	tolerated(0.07)
EGFR	1956	broadinstitute.org	37	7	55240678	55240678	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PALUDH	Exome_WGA	TARGET-30-PALUDH-01A-01W	TARGET-30-PALUDH-10A-01W	0.189516	201	47					Valid_somatic	Sequenom	Illumina	g.chr7:55240678C>A	uc003tqk.2	+	17	2168	c.1922C>A	c.(1921-1923)CCT>CAT	p.P641H	EGFR_uc010kzg.1_Missense_Mutation_p.P596H|EGFR_uc011kco.1_Missense_Mutation_p.P588H	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	641	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	CATTCCAGGCCTAAGATCCCG	0.597		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			possibly_damaging(0.664)	tolerated(0.11)
EGR1	1958	broadinstitute.org	37	5	137803652	137803652	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PARACR	Exome_Native	TARGET-30-PARACR-01A-01D	TARGET-30-PARACR-10A-01D	0.15847	154	29	C(597)	A(52)	C(578)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr5:137803652C>A	uc003ldb.1	+	2	1784	c.1514C>A	c.(1513-1515)GCT>GAT	p.A505D	EGR1_uc011cyu.1_Missense_Mutation_p.L162I	NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	505					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GTTCCCCCTGCTTTCCCGGCC	0.493													unknown(0)	deleterious(0)
EGR2	1959	broadinstitute.org	37	10	64574184	64574184	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PALXHW	Exome_WGA	TARGET-30-PALXHW-01A-01W	TARGET-30-PALXHW-10A-01W	0.403774	158	107	C(287)	A(215)	C(444)	A(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr10:64574184C>A	uc010qim.1	-	3	368	c.214G>T	c.(214-216)GAT>TAT	p.D72Y	EGR2_uc010qin.1_Missense_Mutation_p.D22Y|EGR2_uc001jmi.2_Missense_Mutation_p.D72Y|EGR2_uc010qio.1_Missense_Mutation_p.D85Y|EGR2_uc009xph.2_Missense_Mutation_p.D72Y	NM_001136177	NP_001129649	P11161	EGR2_HUMAN	early growth response 2 protein isoform a	72					fat cell differentiation|protein export from nucleus|transcription from RNA polymerase II promoter	cytoplasm|nucleus	chromatin binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					TATGGGAGATCCAACGACCTC	0.517													probably_damaging(0.912)	deleterious(0)
EP300	2033	broadinstitute.org	37	22	41546128	41546128	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PANIPC	Exome_WGA	TARGET-30-PANIPC-06A-01W	TARGET-30-PANIPC-10A-01W	0.553191	21	26	T	T	C	C	Valid_somatic	Sequenom	Illumina	g.chr22:41546128C>T	uc003azl.3	+	14	3138	c.2743C>T	c.(2743-2745)CGC>TGC	p.R915C		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	915					"apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia"	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						GCAGCAGCCTCGCTCACAGCA	0.567			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				unknown(0)	tolerated(0.08)
FANCD2	2177	broadinstitute.org	37	3	10084803	10084803	+	Missense_Mutation	SNP	C	A	A	rs121917788		TARGET-30-PASWYR	Exome_Native	TARGET-30-PASWYR-01A-01D	TARGET-30-PASWYR-10A-01D	0.2	40	10	C(332)	A(65)	C(529)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:10084803C>A	uc003buw.2	+	12	1036	c.958C>A	c.(958-960)CAA>AAA	p.Q320K	FANCD2_uc003bux.1_Missense_Mutation_p.Q320K|FANCD2_uc003buy.1_Missense_Mutation_p.Q320K	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform	320	Interaction with BRCA2.				DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		ACAGGCTTCCCAAGTAAAGTT	0.418			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				possibly_damaging(0.85)	tolerated(0.05)
FANCE	2178	broadinstitute.org	37	6	35423873	35423873	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAMBAC	Exome_WGA	TARGET-30-PAMBAC-01A-01W	TARGET-30-PAMBAC-14A-01W	0.285714	10	4	C(258)	T(127)	C(333)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr6:35423873C>T	uc003oko.1	+	2	783	c.598C>T	c.(598-600)CGC>TGC	p.R200C	FANCE_uc010jvw.1_Missense_Mutation_p.R200C	NM_021922	NP_068741	Q9HB96	FANCE_HUMAN	"Fanconi anemia, complementation group E"	200	Interaction with FANCC.				DNA repair	nucleoplasm	protein binding			ovary(1)|lung(1)|skin(1)	3						GCCTGGGAAACGCAGAAAGGA	0.577			N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				possibly_damaging(0.629)	deleterious(0)
FANCG	2189	broadinstitute.org	37	9	35074957	35074957	+	Missense_Mutation	SNP	G	C	C			TARGET-30-PASXNN	Exome_Native	TARGET-30-PASXNN-01A-01D	TARGET-30-PASXNN-10A-01D	0.204082	78	20	G(555)	C(146)	G(703)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr9:35074957G>C	uc003zwb.1	-	12	2095	c.1603C>G	c.(1603-1605)CAG>GAG	p.Q535E	VCP_uc003zvy.2_5'Flank|VCP_uc003zvz.2_5'Flank|VCP_uc010mkh.1_5'Flank|VCP_uc010mki.1_5'Flank|FANCG_uc003zwa.1_Missense_Mutation_p.Q277E|FANCG_uc010mkj.1_Missense_Mutation_p.Q277E	NM_004629	NP_004620	O15287	FANCG_HUMAN	"Fanconi anemia, complementation group G"	535	TPR 4.				cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AGGAAGTCCTGTAAGGCTTTG	0.547			Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				benign(0.082)	tolerated(0.3)
FANCI	55215	broadinstitute.org	37	15	89804018	89804018	+	Missense_Mutation	SNP	T	A	A			TARGET-30-PALWVJ	Exome_WGA	TARGET-30-PALWVJ-01A-01W	TARGET-30-PALWVJ-10A-01W	0.406699	124	85	T(178)	A(134)	T(322)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr15:89804018T>A	uc010bnp.1	+	4	322	c.232T>A	c.(232-234)TCG>ACG	p.S78T	FANCI_uc002bnm.1_Missense_Mutation_p.S78T|FANCI_uc002bnn.1_RNA|FANCI_uc002bno.2_Missense_Mutation_p.S78T|FANCI_uc002bnp.1_5'Flank	NM_001113378	NP_001106849	Q9NVI1	FANCI_HUMAN	"Fanconi anemia, complementation group I isoform"	78					cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					GTTGGTGGAATCGGGGGATTT	0.428								Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				probably_damaging(0.986)	tolerated(0.08)
FANCM	57697	broadinstitute.org	37	14	45646146	45646146	+	Missense_Mutation	SNP	A	C	C			TARGET-30-PASXRG	Exome_Native	TARGET-30-PASXRG-01A-01D	TARGET-30-PASXRG-10A-01D	0.375	45	27	A(368)	C(154)	A(551)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr14:45646146A>C	uc001wwd.3	+	14	4288	c.4189A>C	c.(4189-4191)ATG>CTG	p.M1397L	FANCM_uc010anf.2_Missense_Mutation_p.M1371L|FANCM_uc001wwe.3_Missense_Mutation_p.M933L|FANCM_uc010ang.2_Missense_Mutation_p.M611L	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	"Fanconi anemia, complementation group M"	1397					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						CAGTGGTCCAATGTATCTGCA	0.294								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				benign(0)	tolerated(0.22)
FANCM	57697	broadinstitute.org	37	14	45657091	45657091	+	Splice_Site	SNP	G	A	A			TARGET-30-PARHUX	Exome_Native	TARGET-30-PARHUX-01A-01D	TARGET-30-PARHUX-10A-01D	0.411765	10	7	G(306)	A(297)	G(583)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr14:45657091G>A	uc001wwd.3	+	19	4878	c.4779_splice	c.e19+1	p.Q1593_splice	FANCM_uc010anf.2_Splice_Site_p.Q1567_splice|FANCM_uc001wwe.3_Splice_Site_p.Q1129_splice|FANCM_uc010ang.2_Splice_Site_p.Q807_splice	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	"Fanconi anemia, complementation group M"						DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						TTTCTCGCAGGTATGAACTAT	0.323								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia
FANCM	57697	broadinstitute.org	37	14	45658176	45658176	+	Nonsense_Mutation	SNP	G	T	T			TARGET-30-PARETE	Exome_Native	TARGET-30-PARETE-01A-01D	TARGET-30-PARETE-10A-01D	0.326923	35	17	G(180)	T(114)	G(461)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr14:45658176G>T	uc001wwd.3	+	20	5050	c.4951G>T	c.(4951-4953)GAA>TAA	p.E1651*	FANCM_uc010anf.2_Nonsense_Mutation_p.E1625*|FANCM_uc001wwe.3_Nonsense_Mutation_p.E1187*|FANCM_uc010ang.2_Nonsense_Mutation_p.E865*	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	"Fanconi anemia, complementation group M"	1651					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						AATGCTAAAAGAAATGATGGA	0.294								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia
FBLN2	2199	broadinstitute.org	37	3	13671421	13671421	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAMDAL	Exome_WGA	TARGET-30-PAMDAL-01A-01W	TARGET-30-PAMDAL-10A-01W	0.333333	12	6	A	A	G	G	Valid_somatic	Sequenom	Illumina	g.chr3:13671421G>A	uc011avb.1	+	13	2928	c.2803G>A	c.(2803-2805)GCA>ACA	p.A935T	FBLN2_uc011auz.1_Missense_Mutation_p.A961T|FBLN2_uc011ava.1_Missense_Mutation_p.A982T|FBLN2_uc011avc.1_Missense_Mutation_p.A982T	NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor	935	EGF-like 7; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GTTCCTGCTAGCAGCGGACGG	0.652													possibly_damaging(0.774)	tolerated(0.06)
FGFR1	2260	broadinstitute.org	37	8	38274849	38274849	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PARCRR	Exome_Native	TARGET-30-PARCRR-01A-01D	TARGET-30-PARCRR-10A-01D	0.46988	44	39	G(271)	T(258)	G(267)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr8:38274849G>T	uc003xlp.2	-	13	2580	c.1638C>A	c.(1636-1638)AAC>AAA	p.N546K	FGFR1_uc010lwf.2_RNA|FGFR1_uc011lbo.1_Missense_Mutation_p.N544K|FGFR1_uc011lbp.1_Missense_Mutation_p.N457K|FGFR1_uc011lbq.1_Missense_Mutation_p.N455K|FGFR1_uc010lwk.2_Missense_Mutation_p.N536K	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1	546	Cytoplasmic (Potential).|Protein kinase.				axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity	p.N546K(1)		lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	CCCCCAGCAGGTTGATGATAT	0.542		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						probably_damaging(1)	deleterious(0)
GABRA6	2559	broadinstitute.org	37	5	161115980	161115980	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.252149	261	88	A	A	G	G	Valid_somatic	Sequenom	Illumina	g.chr5:161115980G>A	uc003lyu.2	+	4	589	c.251G>A	c.(250-252)CGC>CAC	p.R84H	GABRA6_uc003lyv.2_5'Flank	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	"gamma-aminobutyric acid A receptor, alpha 6"	84	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	GTTTTTTTCCGCCAGACCTGG	0.403										TCGA Ovarian(5;0.080)			probably_damaging(1)	deleterious(0)
GPR116	221395	broadinstitute.org	37	6	46856083	46856083	+	Frame_Shift_Del	DEL	T	-	-			TARGET-30-PAPTLA	Exome_Native	TARGET-30-PAPTLA-01A-01D	TARGET-30-PAPTLA-10A-01D	0.37			666	310	738	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr6:46856083delT	uc003oyo.3	-	4	606	c.317delA	c.(316-318)AATfs	p.N106fs	GPR116_uc003oyp.3_Frame_Shift_Del_p.N106fs|GPR116_uc003oyq.3_Frame_Shift_Del_p.N106fs|GPR116_uc003oyr.2_Frame_Shift_Del_p.N106fs	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	106	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)
HIST1H2BD	3017	broadinstitute.org	37	6	26158587	26158588	+	Frame_Shift_Ins	INS	-	ATTC	ATTC			TARGET-30-PARKNP	Exome_Native	TARGET-30-PARKNP-01A-01D	TARGET-30-PARKNP-10A-01D	0.3			155	31	194	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr6:26158587_26158588insATTC	uc003ngr.2	+	1	239_240	c.190_191insATTC	c.(190-192)AATfs	p.N64fs	HIST1H2BD_uc003ngs.2_Frame_Shift_Ins_p.N64fs	NM_021063	NP_066407	P58876	H2B1D_HUMAN	"histone cluster 1, H2bd"	64					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|pancreas(1)	2
IGSF11	152404	broadinstitute.org	37	3	118623540	118623540	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PAITCI	Exome_WGA	TARGET-30-PAITCI-01A-01W	TARGET-30-PAITCI-10A-01W	0.292683	232	96	G	G	C	C	Valid_somatic	Sequenom	Illumina	g.chr3:118623540C>G	uc003ebw.2	-	6	1056	c.809G>C	c.(808-810)AGC>ACC	p.S270T	IGSF11_uc011biv.1_Missense_Mutation_p.S242T|IGSF11_uc003ebx.2_Missense_Mutation_p.S246T|IGSF11_uc003eby.2_Missense_Mutation_p.S269T|IGSF11_uc003ebz.2_Missense_Mutation_p.S245T|IGSF11_uc010hqs.2_Missense_Mutation_p.S269T	NM_001015887	NP_001015887	Q5DX21	IGS11_HUMAN	"immunoglobulin superfamily, member 11 isoform b"	270	Cytoplasmic (Potential).				cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0						TTTATTTTTGCTTCTCCAGTA	0.358													benign(0.026)	tolerated(0.52)
IGSF22	283284	broadinstitute.org	37	11	18736075	18736075	+	Frame_Shift_Del	DEL	T	-	-			TARGET-30-PATEPF	Exome_Native	TARGET-30-PATEPF-01A-01D	TARGET-30-PATEPF-10A-01D	0.46			323	369	498	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr11:18736075delT	uc009yht.2	-	12	1818	c.1628delA	c.(1627-1629)GAGfs	p.E543fs	IGSF22_uc001mpa.2_RNA	NM_173588	NP_775859	Q8N9C0	IGS22_HUMAN	"immunoglobulin superfamily, member 22"	543										ovary(4)|large_intestine(2)|kidney(1)	7
IL16	3603	broadinstitute.org	37	15	81561966	81561966	+	Missense_Mutation	SNP	G	C	C			TARGET-30-PAIMDT	Exome_WGA	TARGET-30-PAIMDT-01A-01W	TARGET-30-PAIMDT-10A-01W	0.138365	137	22	C	C	G	G	Valid_somatic	Sequenom	Illumina	g.chr15:81561966G>C	uc002bgh.3	+	5	1028	c.652G>C	c.(652-654)GTG>CTG	p.V218L	IL16_uc002bgc.2_RNA|IL16_uc010blq.1_Missense_Mutation_p.V218L|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.V260L|IL16_uc002bgg.2_Missense_Mutation_p.V218L	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	218	Interaction with GRIN2A.|PDZ 1.				"immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent"	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						CTCCAACATCGTGCTGATGAA	0.592													probably_damaging(0.987)	tolerated(0.09)
INPP5D	3635	broadinstitute.org	37	2	234070424	234070424	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PANUIF	Exome_Native	TARGET-30-PANUIF-01A-01D	TARGET-30-PANUIF-10A-01D	0.178571	23	5	C(177)	A(35)	C(294)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:234070424C>A	uc010zmo.1	+	10	1345	c.1192C>A	c.(1192-1194)CAG>AAG	p.Q398K	INPP5D_uc010zmp.1_Missense_Mutation_p.Q397K	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	398					apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	"inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding"			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		GCACTCAGAGCAGCCGGAGCC	0.592
INPP5D	3635	broadinstitute.org	37	2	234098527	234098527	+	Missense_Mutation	SNP	T	A	A			TARGET-30-PANRVJ	Exome_Native	TARGET-30-PANRVJ-01A-01D	TARGET-30-PANRVJ-10A-01D	0.413223	71	50	T(165)	A(81)	T(178)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:234098527T>A	uc010zmo.1	+	21	2543	c.2390T>A	c.(2389-2391)CTG>CAG	p.L797Q	INPP5D_uc010zmp.1_Missense_Mutation_p.L796Q	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	797					apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	"inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding"			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CCTGAGTACCTGCTAGACCAG	0.572
KEAP1	9817	broadinstitute.org	37	19	10610606	10610607	+	Missense_Mutation	DNP	GA	AT	AT			TARGET-30-PASVRU	Exome_Native	TARGET-30-PASVRU-01A-01D	TARGET-30-PASVRU-10A-01D	0.402778	43	29	G(136)	A(69)	G(436)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:10610606_10610607GA>AT	uc002moq.1	-	2	259_260	c.103_104TC>AT	c.(103-105)TCC>ATC	p.S35I	KEAP1_uc002mor.1_Missense_Mutation_p.S35I	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	35					"regulation of transcription, DNA-dependent|transcription, DNA-dependent"	centrosome|midbody|nucleus	protein binding			lung(12)|breast(3)|ovary(1)|pancreas(1)	17			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)			GCACTCAGTGGAGGCGTACATC	0.649
LILRB1	10859	broadinstitute.org	37	19	55143049	55143049	+	Nonsense_Mutation	SNP	G	T	T			TARGET-30-PALZZV	Exome_WGA	TARGET-30-PALZZV-01A-01W	TARGET-30-PALZZV-10A-01W	0.514019	52	55	T	T	G	G	Valid_somatic	Sequenom	Illumina	g.chr19:55143049G>T	uc002qgj.2	+	5	509	c.169G>T	c.(169-171)GAG>TAG	p.E57*	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Nonsense_Mutation_p.E57*|LILRB1_uc002qgk.2_Nonsense_Mutation_p.E57*|LILRB1_uc002qgm.2_Nonsense_Mutation_p.E57*|LILRB1_uc010erq.2_Nonsense_Mutation_p.E57*|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	"leukocyte immunoglobulin-like receptor,"	57	Ig-like C2-type 1.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		GGAGACCCAGGAGTACCGTCT	0.582										HNSCC(37;0.09)
LILRB1	10859	broadinstitute.org	37	19	55143652	55143652	+	Missense_Mutation	SNP	T	A	A			TARGET-30-PANUKV	Exome_WGA	TARGET-30-PANUKV-01A-01W	TARGET-30-PANUKV-10A-01W	0.769784	32	107	A	A	T	T	Valid_somatic	Sequenom	Illumina	g.chr19:55143652T>A	uc002qgj.2	+	6	965	c.625T>A	c.(625-627)TCT>ACT	p.S209T	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Missense_Mutation_p.S209T|LILRB1_uc002qgk.2_Missense_Mutation_p.S209T|LILRB1_uc002qgm.2_Missense_Mutation_p.S209T|LILRB1_uc010erq.2_Missense_Mutation_p.S209T|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	"leukocyte immunoglobulin-like receptor,"	209	Ig-like C2-type 2.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		CTATGAGTGGTCTCTACCCAG	0.602										HNSCC(37;0.09)			probably_damaging(0.998)	deleterious(0)
LRP1B	53353	broadinstitute.org	37	2	141625771	141625771	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PALWVJ	Exome_WGA	TARGET-30-PALWVJ-01A-01W	TARGET-30-PALWVJ-10A-01W	0.352273	114	62	A	A	C	C	Valid_somatic	Sequenom	Illumina	g.chr2:141625771C>A	uc002tvj.1	-	26	5203	c.4231G>T	c.(4231-4233)GGT>TGT	p.G1411C	LRP1B_uc010fnl.1_Missense_Mutation_p.G593C	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1411	Extracellular (Potential).|LDL-receptor class B 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTCCCAGCACCACTCATAGAG	0.373										TSP Lung(27;0.18)			possibly_damaging(0.437)	deleterious(0)
LRP1B	53353	broadinstitute.org	37	2	140997075	140997075	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PALEVG	Exome_WGA	TARGET-30-PALEVG-01A-01W	TARGET-30-PALEVG-10A-01W	0.135593	204	32	G	G	C	C	Valid_somatic	Sequenom	Illumina	g.chr2:140997075C>G	uc002tvj.1	-	88	14323	c.13351G>C	c.(13351-13353)GTC>CTC	p.V4451L		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4451	Helical; (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACCAAGAGGACGAGAGGCACA	0.289										TSP Lung(27;0.18)			benign(0.204)	tolerated(0.6)
LRRTM4	80059	broadinstitute.org	37	2	77746658	77746659	+	Frame_Shift_Ins	INS	-	T	T			TARGET-30-PATEPF	Exome_Native	TARGET-30-PATEPF-01A-01D	TARGET-30-PATEPF-10A-01D	0.45			506	467	955	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:77746658_77746659insT	uc002snr.2	-	3	751_752	c.336_337insA	c.(334-339)AAAGAAfs	p.K112fs	LRRTM4_uc002snq.2_Frame_Shift_Ins_p.K112fs|LRRTM4_uc002sns.2_Frame_Shift_Ins_p.K112fs|LRRTM4_uc002snt.2_Frame_Shift_Ins_p.K113fs	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	112_113	LRR 3.|Extracellular (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)
MAP2K7	5609	broadinstitute.org	37	19	7975970	7975970	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PARLTG	Exome_Native	TARGET-30-PARLTG-01A-01D	TARGET-30-PARLTG-10A-01D	0.35	13	7	G(274)	A(81)	G(204)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:7975970G>A	uc002mit.2	+	7	846	c.781G>A	c.(781-783)GAC>AAC	p.D261N	MAP2K7_uc002miv.2_Missense_Mutation_p.D261N|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Missense_Mutation_p.D261N|MAP2K7_uc010dvv.2_Missense_Mutation_p.D136N	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	261	Protein kinase.				activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus	ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1)	11					Etoposide(DB00773)	CAAGCTCTGCGACTTCGGCAT	0.662													probably_damaging(1)	deleterious(0)
MAPK3	5595	broadinstitute.org	37	16	30128028	30128028	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PARHUX	Exome_Native	TARGET-30-PARHUX-01A-01D	TARGET-30-PARHUX-10A-01D	0.410959	43	30	C(146)	A(90)	C(210)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:30128028C>A	uc002dws.2	-	8	1201	c.1101G>T	c.(1099-1101)GAG>GAT	p.E367D	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAPK3_uc002dwr.2_Missense_Mutation_p.E253D|MAPK3_uc002dwv.3_Missense_Mutation_p.E323D|MAPK3_uc002dwt.2_3'UTR|MAPK3_uc002dwu.2_RNA|MAPK3_uc010bzp.2_RNA	NM_002746	NP_002737	P27361	MK03_HUMAN	mitogen-activated protein kinase 3 isoform 1	367					activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|cellular response to mechanical stimulus|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|interleukin-1-mediated signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription initiation from RNA polymerase I promoter	cytosol|nucleoplasm	ATP binding|MAP kinase activity|phosphatase binding				0					Arsenic trioxide(DB01169)|Isoproterenol(DB01064)|Simvastatin(DB00641)|Sulindac(DB00605)	AGCGTGCTGTCTCCTGGAAGA	0.627													benign(0.414)	deleterious(0.02)
MBNL3	55796	broadinstitute.org	37	X	131525022	131525023	+	Frame_Shift_Ins	INS	-	G	G			TARGET-30-PARACR	Exome_Native	TARGET-30-PARACR-01A-01D	TARGET-30-PARACR-10A-01D	0.73			389	628	957	0	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:131525022_131525023insG	uc004ewv.3	-	4	702_703	c.623_624insC	c.(622-624)GCGfs	p.A208fs	uc004ewr.1_Intron|MBNL3_uc004eww.2_Frame_Shift_Ins_p.A112fs|MBNL3_uc004ews.2_Frame_Shift_Ins_p.A112fs|MBNL3_uc004ewt.2_Frame_Shift_Ins_p.A158fs|MBNL3_uc011muz.1_Frame_Shift_Ins_p.A112fs|MBNL3_uc004ewu.3_Frame_Shift_Ins_p.A208fs|MBNL3_uc004ewx.1_Frame_Shift_Ins_p.A158fs	NM_018388	NP_060858	Q9NUK0	MBNL3_HUMAN	muscleblind-like 3 isoform G	208					mRNA processing|multicellular organismal development|regulation of RNA splicing|RNA splicing	Golgi apparatus|nucleus	nucleic acid binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)
MET	4233	broadinstitute.org	37	7	116422067	116422067	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PATEPF	Exome_Native	TARGET-30-PATEPF-01A-01D	TARGET-30-PATEPF-10A-01D	0.176471	42	9	G(153)	A(50)	G(137)	A(2)	Valid_somatic	PCR/MiSeq	Illumina	g.chr7:116422067G>A	uc003vij.2	+	18	3735	c.3548G>A	c.(3547-3549)GGC>GAC	p.G1183D	MET_uc010lkh.2_Missense_Mutation_p.G1201D|MET_uc011knj.1_Missense_Mutation_p.G753D	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	1183	Protein kinase.|Cytoplasmic (Potential).				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GATCTTATTGGCTTTGGTCTT	0.353			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				possibly_damaging(0.842)	deleterious(0)
MLH1	4292	broadinstitute.org	37	3	37050322	37050322	+	Nonsense_Mutation	SNP	C	A	A	rs74396541		TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.714286	8	20					Valid_somatic	Sequenom	Illumina	g.chr3:37050322C>A	uc003cgl.2	+	6	531	c.471C>A	c.(469-471)TAC>TAA	p.Y157*	MLH1_uc011aye.1_5'UTR|MLH1_uc011ayb.1_5'UTR|MLH1_uc010hge.2_Nonsense_Mutation_p.Y157*|MLH1_uc003cgn.3_5'UTR|MLH1_uc011ayc.1_Nonsense_Mutation_p.Y59*|MLH1_uc011ayd.1_5'UTR|MLH1_uc003cgo.2_Intron	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1	157					mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						ACCTTTTTTACAACATAGCCA	0.383		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome
MLL5	55904	broadinstitute.org	37	7	104753479	104753479	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PANYGR	"Exome_WGA,Genome_BCCA"	TARGET-30-PANYGR-01A-01W	TARGET-30-PANYGR-10A-01W	0.390093	197	126	A	A	C	C	Valid_somatic	PCR/HiSeq	Illumina	g.chr7:104753479C>A	uc003vcm.2	+	27	5810	c.5276C>A	c.(5275-5277)CCA>CAA	p.P1759Q	MLL5_uc010ljc.2_Missense_Mutation_p.P1759Q|MLL5_uc010ljf.1_Intron|MLL5_uc010ljg.2_Missense_Mutation_p.P493Q	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1759	Pro-rich.				"cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent"	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						CCAACTGTACCACCGTATCCC	0.527															RNAseq_support
MLLT3	4300	broadinstitute.org	37	9	20413868	20413868	+	Nonsense_Mutation	SNP	G	A	A			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.431818	25	19	A	A	G	G	Valid_somatic	Sequenom	Illumina	g.chr9:20413868G>A	uc003zoe.2	-	5	1235	c.976C>T	c.(976-978)CAG>TAG	p.Q326*	MLLT3_uc011lne.1_Nonsense_Mutation_p.Q294*|MLLT3_uc011lnf.1_Nonsense_Mutation_p.Q323*|MLLT3_uc003zof.2_Nonsense_Mutation_p.Q127*	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	326					"regulation of transcription, DNA-dependent|transcription, DNA-dependent"	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TCTTTTATCTGTTTTTTGTCA	0.363			T	MLL	ALL
MSH2	4436	broadinstitute.org	37	2	47693815	47693816	+	Frame_Shift_Del	DEL	AG	-	-			TARGET-30-PARKNP	Exome_Native	TARGET-30-PARKNP-01A-01D	TARGET-30-PARKNP-10A-01D	0.35			329	251	697	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:47693815_47693816delAG	uc002rvy.1	+	10	1597_1598	c.1529_1530delAG	c.(1528-1530)CAGfs	p.Q510fs	MSH2_uc010yoh.1_Frame_Shift_Del_p.Q444fs|MSH2_uc002rvz.2_Frame_Shift_Del_p.Q510fs|MSH2_uc010fbg.2_Frame_Shift_Del_p.Q320fs|MSH2_uc010fbh.1_RNA|MSH2_uc010fbi.1_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2	510					"B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes"	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(2)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)							D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome
MYCN	4613	broadinstitute.org	37	2	16082317	16082317	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPLSD	Exome_Native	TARGET-30-PAPLSD-01A-01D	TARGET-30-PAPLSD-10A-01D	0.488095	43	41	C(169)	T(270)	C(395)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:16082317C>T	uc002rci.2	+	2	431	c.131C>T	c.(130-132)CCC>CTC	p.P44L	MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Missense_Mutation_p.P36L	NM_005378	NP_005369	P04198	MYCN_HUMAN	"v-myc myelocytomatosis viral related oncogene,"	44					regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	p.P44L(1)		central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GACTCGACCCCCCCGGGGGAG	0.652			A		neuroblastoma								probably_damaging(0.971)	deleterious(0)
MYCN	4613	broadinstitute.org	37	2	16082317	16082317	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PARCRR	Exome_Native	TARGET-30-PARCRR-01A-01D	TARGET-30-PARCRR-10A-01D	0.179487	32	7	C(267)	T(92)	C(217)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:16082317C>T	uc002rci.2	+	2	431	c.131C>T	c.(130-132)CCC>CTC	p.P44L	MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Missense_Mutation_p.P36L	NM_005378	NP_005369	P04198	MYCN_HUMAN	"v-myc myelocytomatosis viral related oncogene,"	44					regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	p.P44L(1)		central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GACTCGACCCCCCCGGGGGAG	0.652			A		neuroblastoma								probably_damaging(0.971)	deleterious(0)
MYCN	4613	broadinstitute.org	37	2	16082317	16082317	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PARVNT	Exome_Native	TARGET-30-PARVNT-01A-01D	TARGET-30-PARVNT-10A-01D	0.724138	24	63	C(216)	T(272)	C(332)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:16082317C>T	uc002rci.2	+	2	431	c.131C>T	c.(130-132)CCC>CTC	p.P44L	MYCNOS_uc002rch.1_5'Flank|MYCN_uc010yjr.1_Missense_Mutation_p.P36L	NM_005378	NP_005369	P04198	MYCN_HUMAN	"v-myc myelocytomatosis viral related oncogene,"	44					regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	p.P44L(1)		central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GACTCGACCCCCCCGGGGGAG	0.652			A		neuroblastoma								probably_damaging(0.971)	deleterious(0)
NCAM1	4684	broadinstitute.org	37	11	113130966	113130966	+	Silent	SNP	G	T	T			TARGET-30-PAPZFW	Exome_Native	TARGET-30-PAPZFW-01A-01D	TARGET-30-PAPZFW-10A-01D	0.383562	45	28	G(229)	T(209)	G(262)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr11:113130966G>T	uc001pns.2	+	2	224	c.192G>T	c.(190-192)GTG>GTT	p.V64V				P13591	NCAM1_HUMAN	"SubName: Full=cDNA FLJ52974, highly similar to Neural cell adhesion molecule 1, 140 kDa isoform;"	684	Extracellular (Potential).|Fibronectin type-III 2.				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGGTCTACGTGGTGGCTGAGA	0.567
NCAM1	4684	broadinstitute.org	37	11	113077981	113077982	+	Splice_Site	DNP	AG	TA	TA			TARGET-30-PASGUT	Exome_Native	TARGET-30-PASGUT-01A-01D	TARGET-30-PASGUT-10A-01D	0.62963	10	17	A(262)	T(419)	A(178)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr11:113077981_113077982AG>TA	uc009yyq.1	+	6	969	c.275_splice	c.e6-1	p.V92_splice	NCAM1_uc001pno.2_Splice_Site_p.V92_splice	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		TTTTTCCTTCAGTGCCACCTAC	0.505
NCAN	1463	broadinstitute.org	37	19	19337844	19337844	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PANIPC	Exome_WGA	TARGET-30-PANIPC-06A-01W	TARGET-30-PANIPC-10A-01W	0.25	15	5	G(436)	T(217)	G(576)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:19337844G>T	uc002nlz.2	+	7	1721	c.1622G>T	c.(1621-1623)TGG>TTG	p.W541L	NCAN_uc010ecc.1_Missense_Mutation_p.W105L	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	541					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			CGGAGCCCCTGGGCTGATCTG	0.627													possibly_damaging(0.698)	deleterious(0.04)
NCAN	1463	broadinstitute.org	37	19	19338389	19338389	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAPKXS	Exome_Native	TARGET-30-PAPKXS-01A-01D	TARGET-30-PAPKXS-10A-01D	0.569892	40	53	G(208)	A(266)	G(569)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:19338389G>A	uc002nlz.2	+	8	2059	c.1960G>A	c.(1960-1962)GCC>ACC	p.A654T	NCAN_uc010ecc.1_Missense_Mutation_p.A218T	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	654					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			CTCCACCGAGGCCAATAGAGT	0.612													benign(0.009)	tolerated(0.16)
NCAN	1463	broadinstitute.org	37	19	19359524	19359524	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PANLET	Exome_Native	TARGET-30-PANLET-01A-01D	TARGET-30-PANLET-10A-01D	0.454545	24	20	C(370)	T(276)	C(488)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:19359524C>T	uc002nlz.2	+	14	3752	c.3653C>T	c.(3652-3654)CCT>CTT	p.P1218L	NCAN_uc002nma.2_5'UTR	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	1218	Sushi.				axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			TGTGGTCCCCCTCCGGCAGTG	0.463													probably_damaging(1)	deleterious(0)
NF1	4763	broadinstitute.org	37	17	29677227	29677227	+	Nonsense_Mutation	SNP	C	T	T			TARGET-30-PAPREJ	Exome_Native	TARGET-30-PAPREJ-01A-01D	TARGET-30-PAPREJ-10A-01D	0.185185	66	15	C(35)	T(11)	C(159)	T(3)	Valid_somatic	PCR/MiSeq	Illumina	g.chr17:29677227C>T	uc002hgg.2	+	50	7681	c.7348C>T	c.(7348-7350)CGA>TGA	p.R2450*	NF1_uc002hgh.2_Nonsense_Mutation_p.R2429*|NF1_uc010cso.2_Nonsense_Mutation_p.R638*|NF1_uc010wbt.1_5'UTR|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2450					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.R2450*(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TGAAGAAGTTCGAAGTCGCTG	0.363			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)
NF1	4763	broadinstitute.org	37	17	29679318	29679318	+	Nonsense_Mutation	SNP	G	T	T			TARGET-30-PALJPX	Exome_WGA	TARGET-30-PALJPX-01A-01W	TARGET-30-PALJPX-10A-01W	0.146341	35	6					Valid_somatic	Sequenom	Illumina	g.chr17:29679318G>T	uc002hgg.2	+	51	7834	c.7501G>T	c.(7501-7503)GAA>TAA	p.E2501*	NF1_uc002hgh.2_Nonsense_Mutation_p.E2480*|NF1_uc010cso.2_Nonsense_Mutation_p.E689*|NF1_uc010wbt.1_Intron|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2501					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.E2501fs*22(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CAAAGGTTCTGAAGGATACCT	0.483			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)
NFKB2	4791	broadinstitute.org	37	10	104162112	104162112	+	Frame_Shift_Del	DEL	C	-	-			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.41			21	14	12	1	Valid_somatic	PCR/MiSeq	Illumina	g.chr10:104162112delC	uc001kvb.2	+	23	2947	c.2682delC	c.(2680-2682)CACfs	p.H894fs	NFKB2_uc001kva.2_Frame_Shift_Del_p.H893fs|NFKB2_uc001kvd.2_Frame_Shift_Del_p.H893fs|NFKB2_uc009xxc.2_Frame_Shift_Del_p.H893fs	NM_001077494	NP_001070962	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene	894			Missing (in truncated form p80HT).|Missing (in truncated form LB40).|Missing (in truncated form EB308).		innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	Bcl3/NF-kappaB2 complex|cytosol|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(3)	3		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)						T	IGH@	B-NHL
NOTCH1	4851	broadinstitute.org	37	9	139391625	139391625	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.377358	33	20	T	T	C	C	Valid_somatic	Sequenom	Illumina	g.chr9:139391625C>T	uc004chz.2	-	34	6566	c.6566G>A	c.(6565-6567)TGC>TAC	p.C2189Y		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2189	Cytoplasmic (Potential).				"aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing"	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTCCAGCAGGCAGCCCTTGCC	0.662			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			benign(0.037)	tolerated(0.07)
NRAS	4893	broadinstitute.org	37	1	115258745	115258745	+	Missense_Mutation	SNP	C	G	G	rs121434595		TARGET-30-PANBSP	Exome_WGA	TARGET-30-PANBSP-01A-01W	TARGET-30-PANBSP-10A-01W	0.255892	221	76	C(265)	G(218)	C(506)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:115258745C>G	uc009wgu.2	-	2	291	c.37G>C	c.(37-39)GGT>CGT	p.G13R		NM_002524	NP_002515	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	13	GTP.		G -> D (in a patient with an autoimmune lymphoproliferative disorder).|G -> R (in colorectal cancer).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	p.G13D(174)|p.G13R(59)|p.G13V(55)|p.G13C(21)|p.G13A(16)|p.G13S(5)|p.G13G(3)|p.G13N(1)|p.G13Y(1)		haematopoietic_and_lymphoid_tissue(1008)|skin(956)|thyroid(334)|large_intestine(62)|NS(60)|soft_tissue(32)|lung(31)|upper_aerodigestive_tract(25)|urinary_tract(12)|liver(10)|adrenal_gland(9)|autonomic_ganglia(8)|testis(8)|central_nervous_system(8)|prostate(8)|breast(7)|biliary_tract(6)|ovary(6)|stomach(5)|pancreas(5)|endometrium(2)|kidney(2)|cervix(2)|eye(1)	2607	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCCCAACACCACCTGCTCCA	0.498	G13R(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	50	Mis		melanoma|MM|AML|thyroid				Noonan_syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			probably_damaging(0.986)	deleterious(0)
PALB2	79728	broadinstitute.org	37	16	23646594	23646594	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PANRHJ	Exome_WGA	TARGET-30-PANRHJ-01A-01W	TARGET-30-PANRHJ-10A-01W	0.451977	97	80	C(277)	T(165)	C(229)	T(9)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:23646594C>T	uc002dlx.1	-	4	1473	c.1273G>A	c.(1273-1275)GTG>ATG	p.V425M		NM_024675	NP_078951	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	425					double-strand break repair via homologous recombination	nucleoplasm	DNA binding|protein binding			lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1)	11				GBM - Glioblastoma multiforme(48;0.0167)		ACAGCCTCCACGGCTACTTTC	0.378			F|N|Mis			"Wilms tumor|medulloblastoma|AML ,breast"		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia_type_N|Fanconi_Anemia|PALB2-associated_Familial_Breast_and_Pancreatic_Cancer|Pancreatic_Cancer_Familial_Clustering_of				benign(0.01)	tolerated(0.07)
PBRM1	55193	broadinstitute.org	37	3	52651299	52651299	+	Frame_Shift_Del	DEL	G	-	-			TARGET-30-PASTKC	Exome_Native	TARGET-30-PASTKC-01A-01D	TARGET-30-PASTKC-10A-01D	0.61			193	238	386	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:52651299delG	uc003des.2	-	14	1809	c.1797delC	c.(1795-1797)CACfs	p.H599fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.H599fs|PBRM1_uc003der.2_Frame_Shift_Del_p.H567fs|PBRM1_uc003det.2_Frame_Shift_Del_p.H614fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.H614fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.H599fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.H599fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.H599fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.H599fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.H512fs|PBRM1_uc003dfc.2_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	599	Bromo 4.				"chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent"	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)						Mis|N|F|S|D|O		clear cell renal carcinoma|breast
PDCD1LG2	80380	broadinstitute.org	37	9	5549479	5549479	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.73913	18	51	C(103)	A(622)	C(601)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr9:5549479C>A	uc003zjg.3	+	4	779	c.506C>A	c.(505-507)ACC>AAC	p.T169N	C9orf46_uc003zjd.2_Intron|PDCD1LG2_uc011lmc.1_Missense_Mutation_p.T169N|PDCD1LG2_uc011lmd.1_Missense_Mutation_p.T169N|PDCD1LG2_uc010mhp.1_Intron|PDCD1LG2_uc010mho.1_Intron	NM_025239	NP_079515	Q9BQ51	PD1L2_HUMAN	programmed cell death 1 ligand 2 precursor	169	Ig-like C2-type.|Extracellular (Potential).				immune response|T cell costimulation	endomembrane system|extracellular region|integral to membrane|plasma membrane	receptor activity				0	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)		CACTCCAGGACCCCTGAAGGC	0.557													probably_damaging(0.99)	tolerated(0.06)
PDGFA	5154	broadinstitute.org	37	7	540807	540807	+	Nonsense_Mutation	SNP	C	A	A			TARGET-30-PARGKK	Exome_Native	TARGET-30-PARGKK-01A-01D	TARGET-30-PARGKK-10A-01D	0.157895	320	60	C(401)	A(115)	C(677)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr7:540807C>A	uc003sir.2	-	5	1369	c.526G>T	c.(526-528)GAG>TAG	p.E176*	PDGFA_uc003sis.2_Nonsense_Mutation_p.E176*|PDGFA_uc003sit.1_Nonsense_Mutation_p.E190*	NM_002607	NP_002598	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha isoform 1	176					actin cytoskeleton organization|angiogenesis|cell projection assembly|embryo development|hair follicle development|lung alveolus development|negative chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|organ morphogenesis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of DNA replication|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of MAP kinase activity|positive regulation of mesenchymal cell proliferation|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein kinase B signaling cascade|regulation of actin cytoskeleton organization|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling|regulation of peptidyl-tyrosine phosphorylation|regulation of smooth muscle cell migration|skin development	cell surface|endoplasmic reticulum lumen|extracellular space|Golgi membrane|microvillus|platelet alpha granule lumen	collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		CAGGCGCACTCCAAATGCTCC	0.557
PDGFRA	5156	broadinstitute.org	37	4	54257639	54257639	+	Nonsense_Mutation	SNP	C	T	T			TARGET-30-PARACS	Exome_Native	TARGET-30-PARACS-01A-01D	TARGET-30-PARACS-10A-01D	0.419355	18	13	C(171)	T(211)	C(364)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr4:54257639C>T	uc003haa.2	+	9	865	c.679C>T	c.(679-681)CAA>TAA	p.Q227*	FIP1L1_uc003gzx.3_Nonsense_Mutation_p.Q212*|FIP1L1_uc011bzt.1_Nonsense_Mutation_p.Q227*|FIP1L1_uc003gzy.2_Nonsense_Mutation_p.Q227*|FIP1L1_uc011bzu.1_Nonsense_Mutation_p.Q212*|FIP1L1_uc003gzz.2_Intron|FIP1L1_uc003hab.2_Intron|FIP1L1_uc003hac.2_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	Error:Variant_position_missing_in_P16234_after_alignment					cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TGCAGAGATCCAAGATGGCAG	0.368			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)
PGLYRP3	114771	broadinstitute.org	37	1	153274903	153274903	+	Missense_Mutation	SNP	A	C	C			TARGET-30-PALHVD	Exome_WGA	TARGET-30-PALHVD-01A-01W	TARGET-30-PALHVD-10A-01W	0.142298	657	109	C	C	A	A	Valid_somatic	Sequenom	Illumina	g.chr1:153274903A>C	uc001fbn.1	-	5	763	c.710T>G	c.(709-711)TTT>TGT	p.F237C		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	237					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AATGTCACAAAAGTTCCGTGT	0.478													probably_damaging(0.976)	deleterious(0.01)
PGLYRP3	114771	broadinstitute.org	37	1	153270446	153270446	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PALZSL	Exome_WGA	TARGET-30-PALZSL-01A-01W	TARGET-30-PALZSL-10A-01W	0.161074	625	120	T	T	G	G	Valid_somatic	Sequenom	Illumina	g.chr1:153270446G>T	uc001fbn.1	-	7	1065	c.1012C>A	c.(1012-1014)CAT>AAT	p.H338N		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	338					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCTTGAAATGAGGCCAGGTG	0.582													benign(0.299)	tolerated(0.19)
PIK3C2G	5288	broadinstitute.org	37	12	18534798	18534798	+	Missense_Mutation	SNP	C	T	T	rs66703915		TARGET-30-PAPZFW	Exome_Native	TARGET-30-PAPZFW-01A-01D	TARGET-30-PAPZFW-10A-01D	0.309091	76	34	C(200)	T(86)	C(229)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:18534798C>T	uc001rdt.2	+	13	1972	c.1856C>T	c.(1855-1857)TCC>TTC	p.S619F	PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Missense_Mutation_p.S660F|PIK3C2G_uc010sic.1_Missense_Mutation_p.S438F	NM_004570	NP_004561	O75747	P3C2G_HUMAN	"phosphoinositide-3-kinase, class 2 gamma"	619					cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				AGTCAGCCATCCCCGGTGACC	0.433													possibly_damaging(0.541)	tolerated(0.21)
PIK3CA	5290	broadinstitute.org	37	3	178916946	178916946	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PAIPGU	Exome_WGA	TARGET-30-PAIPGU-01A-01W	TARGET-30-PAIPGU-10A-01W	0.436019	119	92					Valid_somatic	Sequenom	Illumina	g.chr3:178916946G>T	uc003fjk.2	+	2	490	c.333G>T	c.(331-333)AAG>AAT	p.K111N		NM_006218	NP_006209	P42336	PK3CA_HUMAN	"phosphoinositide-3-kinase, catalytic, alpha"	111					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		"1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity"	p.K111N(10)|p.K111E(7)|p.K111R(1)|p.K111del(1)|p.K111_I112>N(1)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			GTGAAGAAAAGATCCTCAATC	0.328		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			probably_damaging(0.947)	tolerated(0.05)
PIK3CA	5290	broadinstitute.org	37	3	178947226	178947226	+	Nonsense_Mutation	SNP	G	T	T			TARGET-30-PASGAP	Exome_Native	TARGET-30-PASGAP-01A-01D	TARGET-30-PASGAP-10A-01D	0.363636	7	4	G(421)	T(151)	G(394)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:178947226G>T	uc003fjk.2	+	18	2819	c.2662G>T	c.(2662-2664)GAA>TAA	p.E888*		NM_006218	NP_006209	P42336	PK3CA_HUMAN	"phosphoinositide-3-kinase, catalytic, alpha"	888	PI3K/PI4K.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		"1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity"			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			GAACAAAGGAGAAATGTGAGT	0.388		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)
PIK3CB	5291	broadinstitute.org	37	3	138431052	138431052	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PATEPF	Exome_Native	TARGET-30-PATEPF-01A-01D	TARGET-30-PATEPF-10A-01D	0.603037	183	278	G(194)	T(325)	G(170)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:138431052G>T	uc011bmq.1	-	8	1397	c.1397C>A	c.(1396-1398)CCT>CAT	p.P466H	PIK3CB_uc011bmo.1_Translation_Start_Site|PIK3CB_uc011bmp.1_Missense_Mutation_p.P70H	NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta	466	C2 PI3K-type.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	"1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity"			breast(2)|ovary(1)|lung(1)|skin(1)	5						AATCTTACCAGGAAATGAAGA	0.338													possibly_damaging(0.499)	deleterious(0)
PIK3CB	5291	broadinstitute.org	37	3	138417785	138417785	+	Silent	SNP	C	A	A			TARGET-30-PAPKXS	Exome_Native	TARGET-30-PAPKXS-01A-01D	TARGET-30-PAPKXS-10A-01D	0.441729	297	235	C(263)	A(318)	C(601)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:138417785C>A	uc011bmq.1	-	11	1734	c.1734G>T	c.(1732-1734)CTG>CTT	p.L578L	PIK3CB_uc011bmn.1_Silent_p.L90L|PIK3CB_uc011bmo.1_Silent_p.L24L|PIK3CB_uc011bmp.1_Silent_p.L165L	NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta	578	PI3K helical.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	"1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity"			breast(2)|ovary(1)|lung(1)|skin(1)	5						ACTTGATTGACAGCAGTAATT	0.383
PLCB1	23236	broadinstitute.org	37	20	8770855	8770855	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PARCRR	Exome_Native	TARGET-30-PARCRR-01A-01D	TARGET-30-PARCRR-10A-01D	0.6	4	6	C(149)	T(146)	C(269)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr20:8770855C>T	uc002wnb.2	+	31	3373	c.3370C>T	c.(3370-3372)CTC>TTC	p.L1124F	PLCB1_uc002wna.2_Missense_Mutation_p.L1124F	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	1124					"activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission"	cytosol|nuclear chromatin|nuclear speck	"calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity"			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						GCAAGAAAAACTCGTAGAGAA	0.328													probably_damaging(1)	deleterious(0)
PLCG1	5335	broadinstitute.org	37	20	39802312	39802312	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PASTKC	Exome_Native	TARGET-30-PASTKC-01A-01D	TARGET-30-PASTKC-10A-01D	0.244681	71	23	G(471)	T(291)	G(651)	T(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr20:39802312G>T	uc002xjp.1	+	29	3536	c.3415G>T	c.(3415-3417)GTA>TTA	p.V1139L	PLCG1_uc002xjo.1_Missense_Mutation_p.V1139L|PLCG1_uc010zwe.1_Missense_Mutation_p.V804L	NM_182811	NP_877963	P19174	PLCG1_HUMAN	"phospholipase C, gamma 1 isoform b"	1139	C2.				activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)				ACTCAACCCTGTATGGCCAGC	0.527											OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	benign(0.056)	tolerated(0.08)
PLK4	10733	broadinstitute.org	37	4	128811211	128811211	+	Frame_Shift_Del	DEL	C	-	-			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.35			749	590	803	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr4:128811211delC	uc003ifo.2	+	7	1895	c.1650delC	c.(1648-1650)CACfs	p.H550fs	PLK4_uc011cgs.1_Frame_Shift_Del_p.H518fs|PLK4_uc011cgt.1_Frame_Shift_Del_p.H509fs	NM_014264	NP_055079	O00444	PLK4_HUMAN	polo-like kinase 4	550					G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation	centriole|cleavage furrow|cytosol|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0
PMFBP1	83449	broadinstitute.org	37	16	72174339	72174339	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PARBLH	Exome_Native	TARGET-30-PARBLH-01A-01D	TARGET-30-PARBLH-10A-01D	0.337209	171	87	C(310)	A(84)	C(326)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:72174339C>A	uc002fcc.3	-	6	951	c.779G>T	c.(778-780)CGA>CTA	p.R260L	PMFBP1_uc002fcd.2_Missense_Mutation_p.R260L|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Missense_Mutation_p.R115L	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	260										ovary(2)	2		Ovarian(137;0.179)				CAGCTTATTTCGAAGTTCTTG	0.463													possibly_damaging(0.592)	tolerated(0.15)
PMFBP1	83449	broadinstitute.org	37	16	72166776	72166776	+	Nonsense_Mutation	SNP	C	A	A			TARGET-30-PASAJU	Exome_Native	TARGET-30-PASAJU-01A-01D	TARGET-30-PASAJU-10A-01D	0.28	90	35	C(441)	A(87)	C(519)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:72166776C>A	uc002fcc.3	-	10	1490	c.1318G>T	c.(1318-1320)GAA>TAA	p.E440*	PMFBP1_uc002fcd.2_Nonsense_Mutation_p.E440*|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Nonsense_Mutation_p.E295*	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	440	Potential.									ovary(2)	2		Ovarian(137;0.179)				ATTTCAAGTTCTGTGGCCATG	0.527
PMFBP1	83449	broadinstitute.org	37	16	72162663	72162663	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PANUIF	Exome_Native	TARGET-30-PANUIF-01A-01D	TARGET-30-PANUIF-10A-01D	0.333333	26	13	C(582)	G(136)	C(302)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:72162663C>G	uc002fcc.3	-	14	2168	c.1996G>C	c.(1996-1998)GAA>CAA	p.E666Q	PMFBP1_uc002fcd.2_Missense_Mutation_p.E661Q|PMFBP1_uc002fce.2_Intron|PMFBP1_uc002fcf.2_Missense_Mutation_p.E516Q|PMFBP1_uc010cgo.1_5'UTR	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	666	Potential.									ovary(2)	2		Ovarian(137;0.179)				TTCTCATTTTCTTCCTCCAAC	0.413													possibly_damaging(0.627)	deleterious(0.05)
PMFBP1	83449	broadinstitute.org	37	16	72158716	72158716	+	Nonsense_Mutation	SNP	G	A	A			TARGET-30-PASXHE	Exome_Native	TARGET-30-PASXHE-01A-01D	TARGET-30-PASXHE-10A-01D	0.583333	75	105	G(78)	A(170)	G(192)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr16:72158716G>A	uc002fcc.3	-	17	2726	c.2554C>T	c.(2554-2556)CAG>TAG	p.Q852*	PMFBP1_uc002fcd.2_Nonsense_Mutation_p.Q847*|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Nonsense_Mutation_p.Q702*|PMFBP1_uc010cgo.1_Nonsense_Mutation_p.Q143*	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	852	Potential.									ovary(2)	2		Ovarian(137;0.179)				ATCTCCTCCTGGAACTCCCTG	0.572											OREG0023927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
PPP2CB	5516	broadinstitute.org	37	8	30655140	30655140	+	Missense_Mutation	SNP	T	C	C			TARGET-30-PAIVHE	Exome_WGA	TARGET-30-PAIVHE-01A-01W	TARGET-30-PAIVHE-10A-01W	0.312849	123	56	T(344)	C(129)	T(265)	C(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr8:30655140T>C	uc003xik.2	-	4	678	c.443A>G	c.(442-444)GAT>GGT	p.D148G		NM_004156	NP_004147	P62714	PP2AB_HUMAN	"protein phosphatase 2, catalytic subunit, beta"	148					protein dephosphorylation	"chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex|spindle pole"	metal ion binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	ATCAAAGAGATCTGTAAAATA	0.383													benign(0.333)	deleterious(0)
PRIM2	5558	broadinstitute.org	37	6	57190802	57190802	+	Missense_Mutation	SNP	A	C	C			TARGET-30-PAKFUY	Exome_WGA	TARGET-30-PAKFUY-01A-01W	TARGET-30-PAKFUY-10A-01W	0.280255	113	44	C	C	A	A	Valid_somatic	Sequenom	Illumina	g.chr6:57190802A>C	uc003pdx.2	+	5	505	c.418A>C	c.(418-420)ATT>CTT	p.I140L	PRIM2_uc003pdv.1_Missense_Mutation_p.I140L|PRIM2_uc003pdw.2_Missense_Mutation_p.I140L	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	140					"DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication"	alpha DNA polymerase:primase complex|nucleoplasm	"4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding"				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CAAGGATAAAATTCAGGATTT	0.328
PRKACG	5568	broadinstitute.org	37	9	71627974	71627974	+	Frame_Shift_Del	DEL	G	-	-			TARGET-30-PAPBZI	Exome_WGA	TARGET-30-PAPBZI-01A-01W	TARGET-30-PAPBZI-10A-01W	0.34			1189	621	1326	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr9:71627974delG	uc004agy.2	-	1	1066	c.1035delC	c.(1033-1035)GCCfs	p.A345fs		NM_002732	NP_002723	P22612	KAPCG_HUMAN	"protein kinase, cAMP-dependent, catalytic,"	345	AGC-kinase C-terminal.			A -> P (in Ref. 5; AAH39888).	activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|gluconeogenesis|intracellular protein kinase cascade|male gonad development|nerve growth factor receptor signaling pathway|regulation of insulin secretion|spermatogenesis|transmembrane transport|triglyceride catabolic process|water transport	cytosol|nucleoplasm	ATP binding|cAMP-dependent protein kinase activity			ovary(1)|pancreas(1)|skin(1)	3
PRKCQ	5588	broadinstitute.org	37	10	6470274	6470274	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PARDVT	Exome_Native	TARGET-30-PARDVT-01A-01D	TARGET-30-PARDVT-14A-01D	0.302041	171	74	C(481)	A(87)	C(576)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr10:6470274C>A	uc001ijj.1	-	18	2091	c.2016G>T	c.(2014-2016)AAG>AAT	p.K672N	PRKCQ_uc009xim.1_Missense_Mutation_p.K609N|PRKCQ_uc001iji.1_Missense_Mutation_p.K705N|PRKCQ_uc009xin.1_Missense_Mutation_p.K636N|PRKCQ_uc010qax.1_Missense_Mutation_p.K547N	NM_006257	NP_006248	Q04759	KPCT_HUMAN	"protein kinase C, theta"	672	AGC-kinase C-terminal.				axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						ACAGCCGGGGCTTCTCGTTTA	0.433													benign(0.211)	deleterious(0.01)
PTK2	5747	broadinstitute.org	37	8	141900755	141900755	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PARASL	Exome_Native	TARGET-30-PARASL-01A-01D	TARGET-30-PARASL-10A-01D	0.414414	65	46	G(329)	A(179)	G(282)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr8:141900755G>A	uc003yvu.2	-	3	312	c.82C>T	c.(82-84)CGT>TGT	p.R28C	PTK2_uc003yvs.2_Missense_Mutation_p.R28C|PTK2_uc003yvt.2_Missense_Mutation_p.R50C|PTK2_uc003yvv.2_Translation_Start_Site|PTK2_uc011ljr.1_Missense_Mutation_p.R28C	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a	28					axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CCAGGAGAACGTTCCATACCA	0.453													probably_damaging(0.997)	deleterious(0)
PTPN11	5781	broadinstitute.org	37	12	112888165	112888165	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PATGWT	Exome_Native	TARGET-30-PATGWT-01A-01D	TARGET-30-PATGWT-10A-01D	0.430233	49	37	G(80)	T(92)	G(163)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:112888165G>T	uc001ttx.2	+	3	561	c.181G>T	c.(181-183)GAT>TAT	p.D61Y	PTPN11_uc001ttw.1_Missense_Mutation_p.D61Y	NM_002834	NP_002825	Q06124	PTN11_HUMAN	"protein tyrosine phosphatase, non-receptor type"	61	SH2 1.		D -> Y (in JMML).|D -> V (in JMML; also in myelodysplastic syndrome).|D -> N (in NS1).|D -> G (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.D61Y(28)|p.D61V(26)|p.D61H(3)|p.D61N(3)|p.D61G(2)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						GAACACTGGTGATTACTATGA	0.423			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				probably_damaging(0.998)	deleterious(0)
PTPN11	5781	broadinstitute.org	37	12	112888198	112888198	+	Missense_Mutation	SNP	G	A	A	rs121918453		TARGET-30-PATFIN	Exome_Native	TARGET-30-PATFIN-01A-01D	TARGET-30-PATFIN-10A-01D	0.370787	56	33	G(178)	A(115)	G(96)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:112888198G>A	uc001ttx.2	+	3	594	c.214G>A	c.(214-216)GCC>ACC	p.A72T	PTPN11_uc001ttw.1_Missense_Mutation_p.A72T	NM_002834	NP_002825	Q06124	PTN11_HUMAN	"protein tyrosine phosphatase, non-receptor type"	72	SH2 1.		A -> T (in JMML).|A -> V (in JMML).|A -> S (in NS1).|A -> G (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.A72V(34)|p.A72T(31)|p.A72D(3)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						GGAGAAATTTGCCACTTTGGC	0.418			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				probably_damaging(0.97)	deleterious(0.03)
PTPN11	5781	broadinstitute.org	37	12	112888198	112888198	+	Missense_Mutation	SNP	G	A	A	rs121918453		TARGET-30-PAPBZI	Exome_WGA	TARGET-30-PAPBZI-01A-01W	TARGET-30-PAPBZI-10A-01W	0.338902	277	142	G(394)	A(163)	G(490)	A(1)	Valid_somatic	"PCR/MiSeq, "	Illumina	g.chr12:112888198G>A	uc001ttx.2	+	3	594	c.214G>A	c.(214-216)GCC>ACC	p.A72T	PTPN11_uc001ttw.1_Missense_Mutation_p.A72T	NM_002834	NP_002825	Q06124	PTN11_HUMAN	"protein tyrosine phosphatase, non-receptor type"	72	SH2 1.		A -> T (in JMML).|A -> V (in JMML).|A -> S (in NS1).|A -> G (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.A72V(34)|p.A72T(31)|p.A72D(3)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						GGAGAAATTTGCCACTTTGGC	0.418			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				probably_damaging(0.97)	deleterious(0.03)
PTPN11	5781	broadinstitute.org	37	12	112888199	112888199	+	Missense_Mutation	SNP	C	A	A	rs121918454		TARGET-30-PAPRXW	Exome_Native	TARGET-30-PAPRXW-01A-01D	TARGET-30-PAPRXW-10A-01D	0.44	70	55	C(215)	A(150)	C(393)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:112888199C>A	uc001ttx.2	+	3	595	c.215C>A	c.(214-216)GCC>GAC	p.A72D	PTPN11_uc001ttw.1_Missense_Mutation_p.A72D	NM_002834	NP_002825	Q06124	PTN11_HUMAN	"protein tyrosine phosphatase, non-receptor type"	72	SH2 1.		A -> T (in JMML).|A -> V (in JMML).|A -> S (in NS1).|A -> G (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.A72V(34)|p.A72T(31)|p.A72D(3)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						GAGAAATTTGCCACTTTGGCT	0.418			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				probably_damaging(0.979)	deleterious(0.02)
PTPN11	5781	broadinstitute.org	37	12	112888211	112888211	+	Missense_Mutation	SNP	A	C	C	rs121918465		TARGET-30-PALHVD	Exome_WGA	TARGET-30-PALHVD-01A-01W	TARGET-30-PALHVD-10A-01W	0.158273	234	44	A(380)	C(38)	A(363)	C(1)	Valid_somatic	"PCR/MiSeq, "	Illumina	g.chr12:112888211A>C	uc001ttx.2	+	3	607	c.227A>C	c.(226-228)GAG>GCG	p.E76A	PTPN11_uc001ttw.1_Missense_Mutation_p.E76A	NM_002834	NP_002825	Q06124	PTN11_HUMAN	"protein tyrosine phosphatase, non-receptor type"	76	SH2 1.		E -> D (in NS1).|E -> V (in JMML).|E -> A (in JMML; also in myelodysplastic syndrome).|E -> G (in JMML).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.E76K(68)|p.E76G(31)|p.E76Q(11)|p.E76V(10)|p.E76A(7)|p.E76M(1)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						ACTTTGGCTGAGTTGGTCCAG	0.418			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				probably_damaging(0.977)	deleterious(0)
PTPN11	5781	broadinstitute.org	37	12	112926248	112926248	+	Missense_Mutation	SNP	G	A	A	rs121918468		TARGET-30-PASAAN	Exome_Native	TARGET-30-PASAAN-01A-01D	TARGET-30-PASAAN-10A-01D	0.153846	77	14	G(215)	A(10)	G(439)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:112926248G>A	uc001ttx.2	+	12	1761	c.1381G>A	c.(1381-1383)GCT>ACT	p.A461T		NM_002834	NP_002825	Q06124	PTN11_HUMAN	"protein tyrosine phosphatase, non-receptor type"	465	Tyrosine-protein phosphatase.|Substrate binding (By similarity).		A -> T (in LEOPARD1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						TGCCCGCAGTGCTGGAATTGG	0.453			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				probably_damaging(0.999)	deleterious(0)
PTPN6	5777	broadinstitute.org	37	12	7067233	7067233	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PASYPX	Exome_Native	TARGET-30-PASYPX-01A-01D	TARGET-30-PASYPX-10A-01D	0.296296	19	8	G(230)	T(32)	G(302)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr12:7067233G>T	uc001qsb.2	+	11	1600	c.1358G>T	c.(1357-1359)TGC>TTC	p.C453F	PTPN6_uc001qsa.1_Missense_Mutation_p.C455F|PTPN6_uc010sfr.1_Missense_Mutation_p.C414F|PTPN6_uc009zfl.1_Missense_Mutation_p.C453F|PTPN6_uc010sfs.1_Missense_Mutation_p.C441F	NM_002831	NP_002822	P29350	PTN6_HUMAN	"protein tyrosine phosphatase, non-receptor type"	453	Tyrosine-protein phosphatase.|Substrate binding (By similarity).	Phosphocysteine intermediate.			apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity			breast(1)	1						ATCGTGCACTGCAGGTGAGGA	0.527													probably_damaging(0.997)	tolerated(0.08)
RAD54B	25788	broadinstitute.org	37	8	95423526	95423526	+	Frame_Shift_Del	DEL	C	-	-			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.45			278	170	452	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr8:95423526delC	uc003ygk.2	-	4	420	c.322delG	c.(322-324)GAAfs	p.E108fs	RAD54B_uc010may.1_5'UTR|RAD54B_uc003ygl.1_RNA	NM_012415	NP_036547	O95073	FSBP_HUMAN	RAD54 homolog B	Error:Variant_position_missing_in_O95073_after_alignment					"double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent"	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)												Direct_reversal_of_damage|Homologous_recombination
RAF1	5894	broadinstitute.org	37	3	12633211	12633211	+	Missense_Mutation	SNP	G	C	C			TARGET-30-PARBGP	Exome_Native	TARGET-30-PARBGP-01A-01D	TARGET-30-PARBGP-10A-01D	0.894737	4	34	G(79)	C(562)	G(681)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:12633211G>C	uc003bxf.3	-	11	1604	c.1189C>G	c.(1189-1191)CTG>GTG	p.L397V	RAF1_uc011aut.1_Missense_Mutation_p.L182V|RAF1_uc011auu.1_Missense_Mutation_p.L315V	NM_002880	NP_002871	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog	397	Protein kinase.				activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)	ACTCACCGCAGAACAGCCACC	0.542			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				probably_damaging(0.993)	deleterious(0)
RMI1	80010	broadinstitute.org	37	9	86617024	86617025	+	Frame_Shift_Ins	INS	-	A	A			TARGET-30-PAPKXS	Exome_Native	TARGET-30-PAPKXS-01A-01D	TARGET-30-PAPKXS-10A-01D	0.31			361	254	654	14	Valid_somatic	PCR/MiSeq	Illumina	g.chr9:86617024_86617025insA	uc004anq.3	+	3	1531_1532	c.1123_1124insA	c.(1123-1125)GAAfs	p.E375fs	RMI1_uc004anr.3_Frame_Shift_Ins_p.E375fs|RMI1_uc004anp.3_Frame_Shift_Ins_p.E375fs|RMI1_uc004ans.3_Frame_Shift_Ins_p.E375fs	NM_024945	NP_079221	Q9H9A7	RMI1_HUMAN	"RMI1, RecQ mediated genome instability 1,"	375					DNA replication	nucleus					0
RPL7L1	285855	broadinstitute.org	37	6	42852437	42852437	+	Frame_Shift_Del	DEL	C	-	-			TARGET-30-PARDYU	Exome_Native	TARGET-30-PARDYU-01A-01D	TARGET-30-PARDYU-10A-01D	0.38			389	191	693	3	Valid_somatic	PCR/MiSeq	Illumina	g.chr6:42852437delC	uc003osq.1	+	4	376	c.371delC	c.(370-372)ACCfs	p.T124fs	RPL7L1_uc011dux.1_Frame_Shift_Del_p.T124fs|RPL7L1_uc010jxw.1_5'UTR|RPL7L1_uc003osr.1_5'UTR|RPL7L1_uc011duy.1_Frame_Shift_Del_p.T124fs|RPL7L1_uc003oss.1_5'UTR|RPL7L1_uc003ost.2_Frame_Shift_Del_p.T124fs|RPL7L1_uc003osu.2_RNA	NM_198486	NP_940888	Q6DKI1	RL7L_HUMAN	ribosomal protein L7-like 1	124					translation	large ribosomal subunit	protein binding|structural constituent of ribosome				0	Colorectal(47;0.196)		Colorectal(64;0.00237)|all cancers(41;0.00288)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.088)
RPS6KA3	6197	broadinstitute.org	37	X	20193326	20193326	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPBZI	Exome_WGA	TARGET-30-PAPBZI-01A-01W	TARGET-30-PAPBZI-10A-01W	0.52459	58	64	C(470)	T(252)	C(647)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chrX:20193326C>T	uc004czu.2	-	14	1183	c.1183G>A	c.(1183-1185)GAA>AAA	p.E395K	RPS6KA3_uc011mjk.1_Missense_Mutation_p.E366K|RPS6KA3_uc004czv.2_Missense_Mutation_p.E383K|RPS6KA3_uc011mjl.1_Missense_Mutation_p.E367K|RPS6KA3_uc011mjm.1_Missense_Mutation_p.E367K	NM_004586	NP_004577	P51812	KS6A3_HUMAN	"ribosomal protein S6 kinase, 90kDa, polypeptide"	395	AGC-kinase C-terminal.				axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8						GCTTGGCTTTCATCATCTGAG	0.378													benign(0.001)	tolerated(0.39)
S100A14	57402	broadinstitute.org	37	1	153587858	153587858	+	Splice_Site	SNP	C	G	G			TARGET-30-PARRLH	Exome_Native	TARGET-30-PARRLH-01A-01D	TARGET-30-PARRLH-10A-01D	0.375	15	9	C(113)	G(74)	C(208)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:153587858C>G	uc001fce.2	-	3	129	c.31_splice	c.e3-1	p.D11_splice	S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723	Q9HCY8	S10AE_HUMAN	S100 calcium binding protein A14						calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTGAGCATCCTGAGGGCAGG	0.567
S100A14	57402	broadinstitute.org	37	1	153587431	153587431	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAPREJ	Exome_Native	TARGET-30-PAPREJ-01A-01D	TARGET-30-PAPREJ-10A-01D	0.33871	41	21	C(124)	A(20)	C(261)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:153587431C>A	uc001fce.2	-	4	343	c.245G>T	c.(244-246)AGG>ATG	p.R82M	S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723	Q9HCY8	S10AE_HUMAN	S100 calcium binding protein A14	82	2; high affinity (Potential).				calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAGAAACTCCTGAACTCCAG	0.547													benign(0)	deleterious(0.01)
SH3GL2	6456	broadinstitute.org	37	9	17795686	17795686	+	Missense_Mutation	SNP	A	T	T			TARGET-30-PANLET	Exome_Native	TARGET-30-PANLET-01A-01D	TARGET-30-PANLET-10A-01D	0.5625	14	18	A(555)	T(243)	A(400)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr9:17795686A>T	uc003zna.2	+	9	1292	c.1004A>T	c.(1003-1005)CAT>CTT	p.H335L	SH3GL2_uc011lmy.1_Missense_Mutation_p.H288L	NM_003026	NP_003017	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	335	SH3.				axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		CTGCATGGCCATTCAGGCTTC	0.478													benign(0.005)	deleterious(0.01)
SHC1	6464	broadinstitute.org	37	1	154938948	154938948	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAPRXW	Exome_Native	TARGET-30-PAPRXW-01A-01D	TARGET-30-PAPRXW-10A-01D	0.409091	13	9	C(229)	A(213)	C(464)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:154938948C>A	uc001ffv.2	-	8	1250	c.1029G>T	c.(1027-1029)GAG>GAT	p.E343D	SHC1_uc001ffu.2_5'Flank|SHC1_uc001ffz.1_Missense_Mutation_p.E114D|SHC1_uc001ffw.2_Missense_Mutation_p.E343D|SHC1_uc001ffx.2_Missense_Mutation_p.E233D|SHC1_uc001ffy.2_Missense_Mutation_p.E233D	NM_183001	NP_892113	P29353	SHC1_HUMAN	SHC-transforming protein 1 isoform 1	343	CH1.				activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth	cytosol|mitochondrial matrix|Shc-EGFR complex	epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(1)|skin(1)	2	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGTCAGGTGGCTCTTCCTCCT	0.597													benign(0.013)	tolerated(0.35)
SMAD4	4089	broadinstitute.org	37	18	48591850	48591850	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PALJPX	Exome_WGA	TARGET-30-PALJPX-01A-01W	TARGET-30-PALJPX-10A-01W	0.178344	129	28	A	A	C	C	Valid_somatic	Sequenom	Illumina	g.chr18:48591850C>A	uc010xdp.1	+	9	1551	c.1013C>A	c.(1012-1014)ACA>AAA	p.T338K	SMAD4_uc002lfb.3_Missense_Mutation_p.T183K	NM_005359	NP_005350	Q13485	SMAD4_HUMAN	mothers against decapentaplegic homolog 4	338	MH2.				"BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway"	activin responsive factor complex|centrosome|cytosol	"I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity"	p.0?(35)|p.?(2)		pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GTAGGAGAGACATTTAAGGTT	0.433									Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				probably_damaging(0.906)	deleterious(0)
SPHKAP	80309	broadinstitute.org	37	2	228883487	228883487	+	Missense_Mutation	SNP	T	G	G			TARGET-30-PAILNU	Exome_WGA	TARGET-30-PAILNU-01A-01W	TARGET-30-PAILNU-10A-01W	0.197248	350	86	T(404)	G(125)	T(523)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:228883487T>G	uc002vpq.2	-	7	2130	c.2083A>C	c.(2083-2085)AAC>CAC	p.N695H	SPHKAP_uc002vpp.2_Missense_Mutation_p.N695H|SPHKAP_uc010zlx.1_Missense_Mutation_p.N695H	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	695						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GAATGCCTGTTGTCATTGGGG	0.393													benign(0.081)	deleterious(0.04)
SPHKAP	80309	broadinstitute.org	37	2	228883380	228883380	+	Silent	SNP	A	G	G			TARGET-30-PALHVD	Exome_WGA	TARGET-30-PALHVD-01A-01W	TARGET-30-PALHVD-10A-01W	0.756522	56	174	A(108)	G(319)	A(518)	G(43)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:228883380A>G	uc002vpq.2	-	7	2237	c.2190T>C	c.(2188-2190)CTT>CTC	p.L730L	SPHKAP_uc002vpp.2_Silent_p.L730L|SPHKAP_uc010zlx.1_Silent_p.L730L	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	730						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GACATTCACCAAGCCGTACAA	0.443
SPHKAP	80309	broadinstitute.org	37	2	228881991	228881991	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PATDWN	Exome_Native	TARGET-30-PATDWN-01A-01D	TARGET-30-PATDWN-10A-01D	0.397849	56	37	C(406)	G(290)	C(758)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:228881991C>G	uc002vpq.2	-	7	3626	c.3579G>C	c.(3577-3579)GAG>GAC	p.E1193D	SPHKAP_uc002vpp.2_Missense_Mutation_p.E1193D|SPHKAP_uc010zlx.1_Missense_Mutation_p.E1193D	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1193						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ACCTGTAGAACTCCTCAGTGA	0.562													probably_damaging(0.998)	deleterious(0.03)
SPRR1A	6698	broadinstitute.org	37	1	152957731	152957731	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAIMDT	Exome_WGA	TARGET-30-PAIMDT-01A-01W	TARGET-30-PAIMDT-10A-01W	0.4375	144	112	C(135)	A(85)	C(219)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:152957731C>A	uc009wnu.1	+	2	103	c.25C>A	c.(25-27)CCT>ACT	p.P9T	SPRR1A_uc001faw.2_Missense_Mutation_p.P9T	NM_005987	NP_005978	P35321	SPR1A_HUMAN	small proline-rich protein 1A	9	1.|2 X 12 AA approximate repeats.				keratinization|peptide cross-linking	cornified envelope|cytoplasm	"protein binding, bridging|structural molecule activity"				0	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCAGAAGCAGCCTTGCACCCC	0.488													unknown(0)	deleterious(0.01)
SPRR1A	6698	broadinstitute.org	37	1	152957948	152957948	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PASMNT	Exome_Native	TARGET-30-PASMNT-01A-01D	TARGET-30-PASMNT-10A-01D	0.358209	43	24	C(65)	A(54)	C(110)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:152957948C>A	uc009wnu.1	+	2	320	c.242C>A	c.(241-243)CCA>CAA	p.P81Q	SPRR1A_uc001faw.2_Missense_Mutation_p.P81Q	NM_005987	NP_005978	P35321	SPR1A_HUMAN	small proline-rich protein 1A	81					keratinization|peptide cross-linking	cornified envelope|cytoplasm	"protein binding, bridging|structural molecule activity"				0	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACTCCAGCACCAGCCCAGCAG	0.597													probably_damaging(0.986)	deleterious(0.02)
SPTA1	6708	broadinstitute.org	37	1	158655069	158655069	+	Silent	SNP	C	G	G			TARGET-30-PASEGA	Exome_Native	TARGET-30-PASEGA-01A-01D	TARGET-30-PASEGA-10A-01D	0.179775	146	32	C(556)	G(79)	C(303)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:158655069C>G	uc001fst.1	-	2	292	c.93G>C	c.(91-93)GTG>GTC	p.V31V		NM_003126	NP_003117	P02549	SPTA1_HUMAN	"spectrin, alpha, erythrocytic 1"	31	Spectrin 1.		V -> A (in EL2; Marseille).		actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					ACCGAGTCAACACTTCCTGAC	0.338
SPTA1	6708	broadinstitute.org	37	1	158653184	158653184	+	Missense_Mutation	SNP	G	T	T			TARGET-30-PAPVXS	Exome_Native	TARGET-30-PAPVXS-01A-01D	TARGET-30-PAPVXS-10A-01D	0.12037	95	13	G(117)	T(26)	G(558)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:158653184G>T	uc001fst.1	-	3	566	c.367C>A	c.(367-369)CAT>AAT	p.H123N		NM_003126	NP_003117	P02549	SPTA1_HUMAN	"spectrin, alpha, erythrocytic 1"	123	Spectrin 2.			Missing (in Ref. 3; AAA60575).	actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TGGGCAGAATGACCCATGGTA	0.373													probably_damaging(0.999)	deleterious(0)
SPTA1	6708	broadinstitute.org	37	1	158621164	158621164	+	Missense_Mutation	SNP	A	G	G			TARGET-30-PAPRMJ	Exome_Native	TARGET-30-PAPRMJ-01A-01D	TARGET-30-PAPRMJ-10A-01D	0.256881	243	84	A(78)	G(18)	A(97)	G(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:158621164A>G	uc001fst.1	-	24	3669	c.3470T>C	c.(3469-3471)ATC>ACC	p.I1157T		NM_003126	NP_003117	P02549	SPTA1_HUMAN	"spectrin, alpha, erythrocytic 1"	1157	Spectrin 11.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TACCTGCCGGATTTGAGCTCC	0.453													benign(0.27)	tolerated(0.06)
SPTA1	6708	broadinstitute.org	37	1	158619701	158619701	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PASRFS	Exome_Native	TARGET-30-PASRFS-01A-01D	TARGET-30-PASRFS-10A-01D	0.340909	29	15	C(499)	A(154)	C(790)	A(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:158619701C>A	uc001fst.1	-	25	3713	c.3514G>T	c.(3514-3516)GCA>TCA	p.A1172S		NM_003126	NP_003117	P02549	SPTA1_HUMAN	"spectrin, alpha, erythrocytic 1"	1172	Spectrin 11.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TGTTCATCTGCAAGCCTCTGC	0.463													probably_damaging(0.997)	tolerated(0.12)
SPTA1	6708	broadinstitute.org	37	1	158607958	158607958	+	Missense_Mutation	SNP	A	T	T			TARGET-30-PASSRS	Exome_Native	TARGET-30-PASSRS-01A-01D	TARGET-30-PASSRS-10A-01D	0.166667	65	13	A(429)	T(94)	A(426)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:158607958A>T	uc001fst.1	-	36	5253	c.5054T>A	c.(5053-5055)GTG>GAG	p.V1685E		NM_003126	NP_003117	P02549	SPTA1_HUMAN	"spectrin, alpha, erythrocytic 1"	1685	Spectrin 16.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TTTTTTCTTCACAATCTGATC	0.438													benign(0.002)	tolerated(0.4)
SPTA1	6708	broadinstitute.org	37	1	158589073	158589073	+	Nonsense_Mutation	SNP	C	A	A			TARGET-30-PASEGA	Exome_Native	TARGET-30-PASEGA-01A-01D	TARGET-30-PASEGA-10A-01D	0.189573	171	40	C(541)	A(68)	C(302)	A(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:158589073C>A	uc001fst.1	-	45	6668	c.6469G>T	c.(6469-6471)GAG>TAG	p.E2157*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	"spectrin, alpha, erythrocytic 1"	2157	Spectrin 21.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TGACACATCTCAAAGTTCTTG	0.488
SPTBN1	6711	broadinstitute.org	37	2	54753679	54753679	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPTJB	Exome_Native	TARGET-30-PAPTJB-01A-01D	TARGET-30-PAPTJB-14A-01D	0.216867	65	18	C(418)	T(103)	C(650)	T(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:54753679C>T	uc002rxu.2	+	2	373	c.124C>T	c.(124-126)CGG>TGG	p.R42W	SPTBN1_uc002rxv.1_Missense_Mutation_p.R42W|RPL23AP32_uc010yot.1_5'Flank	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	"spectrin, beta, non-erythrocytic 1 isoform 1"	42	Actin-binding.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			GCTTTTTGAGCGGTCCCGCAT	0.532													probably_damaging(0.999)	deleterious(0)
SPTBN4	57731	broadinstitute.org	37	19	41029377	41029377	+	Missense_Mutation	SNP	A	G	G			TARGET-30-PANZVU	Exome_WGA	TARGET-30-PANZVU-01A-01W	TARGET-30-PANZVU-10A-01W	0.447368	21	17	A(279)	G(116)	A(604)	G(6)	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:41029377A>G	uc002ony.2	+	17	3774	c.3688A>G	c.(3688-3690)ACA>GCA	p.T1230A	SPTBN4_uc002onx.2_Missense_Mutation_p.T1230A|SPTBN4_uc002onz.2_Missense_Mutation_p.T1230A|SPTBN4_uc010egx.2_5'UTR	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	"spectrin, beta, non-erythrocytic 4 isoform"	1230	Spectrin 10.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCTCCCGGGCACAGTGGAATC	0.617													benign(0.38)	deleterious(0)
STAG1	10274	broadinstitute.org	37	3	136057265	136057265	+	Frame_Shift_Del	DEL	C	-	-			TARGET-30-PAPZFW	Exome_Native	TARGET-30-PAPZFW-01A-01D	TARGET-30-PAPZFW-10A-01D	0.36			969	434	1060	2	Valid_somatic	PCR/MiSeq	Illumina	g.chr3:136057265delC	uc003era.1	-	33	3992	c.3700delG	c.(3700-3702)GCTfs	p.A1234fs	STAG1_uc003erb.1_Frame_Shift_Del_p.A1197fs	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1234					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	"cell junction|chromatin|chromosome, centromeric region|nucleoplasm"	protein binding			ovary(2)	2
STAM2	10254	broadinstitute.org	37	2	153000443	153000443	+	Missense_Mutation	SNP	T	C	C			TARGET-30-PAPVFD	Exome_Native	TARGET-30-PAPVFD-01A-01D	TARGET-30-PAPVFD-10A-01D	0.532258	29	33	T(73)	C(72)	T(126)	C(0)	Valid_somatic	PCR/MiSeq	Illumina	g.chr2:153000443T>C	uc002tyc.3	-	7	952	c.602A>G	c.(601-603)AAT>AGT	p.N201S	STAM2_uc010foa.1_Missense_Mutation_p.N201S|STAM2_uc002tyd.2_Missense_Mutation_p.N201S	NM_005843	NP_005834	O75886	STAM2_HUMAN	signal transducing adaptor molecule 2	201					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.22)		TGCAACCTTATTATTTAACTG	0.323													benign(0.006)	tolerated(0.37)
SUCLG2	8801	broadinstitute.org	37	3	67579512	67579512	+	Missense_Mutation	SNP	C	G	G			TARGET-30-PAICGF	Exome_WGA	TARGET-30-PAICGF-01A-01W	TARGET-30-PAICGF-10A-01W	0.165242	293	58	G	G	C	C	Valid_somatic	Sequenom	Illumina	g.chr3:67579512C>G	uc003dna.3	-	3	353	c.325G>C	c.(325-327)GAC>CAC	p.D109H	SUCLG2_uc010hob.2_5'Flank	NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	"succinate-CoA ligase, GDP-forming beta subunit"	109	ATP-grasp.				succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	CAGACTTACTCTTTTGTTAAA	0.408													possibly_damaging(0.891)	deleterious(0.01)
TP53	7157	broadinstitute.org	37	17	7577097	7577097	+	Missense_Mutation	SNP	C	T	T			TARGET-30-PAPUWY	Exome_Native	TARGET-30-PAPUWY-01A-01D	TARGET-30-PAPUWY-10A-01D	0.302326	30	13	C(88)	T(57)	C(142)	T(1)	Valid_somatic	PCR/MiSeq	Illumina	g.chr17:7577097C>T	uc002gim.2	-	8	1035	c.841G>A	c.(841-843)GAC>AAC	p.D281N	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.D281N|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.D149N|TP53_uc010cng.1_Missense_Mutation_p.D149N|TP53_uc002gii.1_Missense_Mutation_p.D149N|TP53_uc010cnh.1_Missense_Mutation_p.D281N|TP53_uc010cni.1_Missense_Mutation_p.D281N|TP53_uc002gij.2_Missense_Mutation_p.D281N	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	281	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		D -> Y (in sporadic cancers; somatic mutation).|D -> E (in sporadic cancers; somatic mutation).|D -> V (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).|D -> R (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|D -> G (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).|D -> A (in sporadic cancers; somatic mutation).|D -> N (in LFS; germline mutation and in sporadic cancers; somatic mutation).|D -> H (in sporadic cancers; somatic mutation).		"activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray"	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.D281E(25)|p.D281H(19)|p.D281N(18)|p.D281G(10)|p.0?(7)|p.D281Y(6)|p.D281D(5)|p.D281V(3)|p.D281fs*63(2)|p.?(2)|p.R280_D281delRD(2)|p.D281A(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.A276fs*64(1)|p.D281fs*24(1)|p.R280fs*62(1)|p.G279fs*59(1)|p.F270_D281del12(1)|p.C275_R283delCACPGRDRR(1)|p.D281_R282insXX(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.V272_K292del21(1)|p.C275fs*20(1)|p.D281R(1)|p.D281_R282delDR(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GTGCGCCGGTCTCTCCCAGGA	0.547		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			probably_damaging(0.991)	deleterious(0)
USP48	84196	broadinstitute.org	37	1	22047628	22047630	+	In_Frame_Del	DEL	AGG	-	-			TARGET-30-PAIXNC	Exome_WGA	TARGET-30-PAIXNC-01A-01W	TARGET-30-PAIXNC-10A-01W	0.34			343	286	530	0	Valid_somatic	PCR/MiSeq	Illumina	g.chr1:22047628_22047630delAGG	uc001bfb.2	-	14	2031_2033	c.1793_1795delCCT	c.(1792-1797)TCCTTG>TTG	p.S598del	USP48_uc001bfa.2_In_Frame_Del_p.S136del|USP48_uc010odq.1_In_Frame_Del_p.S597del|USP48_uc009vqc.2_In_Frame_Del_p.S532del|USP48_uc001bfc.2_In_Frame_Del_p.S598del|USP48_uc001bfe.1_In_Frame_Del_p.S596del	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	598	DUSP 2.				ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)
ZNF44	51710	broadinstitute.org	37	19	12384448	12384448	+	Frame_Shift_Del	DEL	A	-	-			TARGET-30-PAPPKJ	Exome_WGA	TARGET-30-PAPPKJ-01A-01W	TARGET-30-PAPPKJ-10A-01W	0.47			299	293	422	14	Valid_somatic	PCR/MiSeq	Illumina	g.chr19:12384448delA	uc010xmj.1	-	5	971	c.766delT	c.(766-768)TGGfs	p.W256fs	ZNF44_uc002mtl.2_Intron|ZNF44_uc010dyr.1_Intron|ZNF44_uc010xmi.1_RNA|ZNF44_uc002mtn.3_RNA|ZNF44_uc010dys.2_Frame_Shift_Del_p.W208fs	NM_001164276	NP_001157748	P15621	ZNF44_HUMAN	zinc finger protein 44 isoform 1	256	C2H2-type 3.				"regulation of transcription, DNA-dependent|transcription, DNA-dependent"	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)
ZNF529	57711	broadinstitute.org	37	19	37038544	37038544	+	Missense_Mutation	SNP	C	A	A			TARGET-30-PAPBZI	Exome_WGA	TARGET-30-PAPBZI-01A-01W	TARGET-30-PAPBZI-10A-01W	0.464286	165	143	A	A	C	C	Valid_somatic	Sequenom	Illumina	g.chr19:37038544C>A	uc002oeh.3	-	5	1118	c.916G>T	c.(916-918)GAT>TAT	p.D306Y	ZNF529_uc010xth.1_Missense_Mutation_p.D306Y|ZNF529_uc010xti.1_Missense_Mutation_p.D288Y|ZNF529_uc002oeg.3_Missense_Mutation_p.D201Y	NM_020951	NP_066002	Q6P280	ZN529_HUMAN	zinc finger protein 529 isoform a	273					"regulation of transcription, DNA-dependent|transcription, DNA-dependent"	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)					GTTTTCTCATCAGTATGGATT	0.388													possibly_damaging(0.891)	deleterious(0)
ZNF529	57711	broadinstitute.org	37	19	37037970	37037970	+	Missense_Mutation	SNP	T	C	C			TARGET-30-PAMZGT	Exome_WGA	TARGET-30-PAMZGT-01A-01W	TARGET-30-PAMZGT-10A-01W	0.197917	154	38	C	C	T	T	Valid_somatic	Sequenom	Illumina	g.chr19:37037970T>C	uc002oeh.3	-	5	1692	c.1490A>G	c.(1489-1491)CAG>CGG	p.Q497R	ZNF529_uc010xth.1_Missense_Mutation_p.Q497R|ZNF529_uc010xti.1_Missense_Mutation_p.Q479R|ZNF529_uc002oeg.3_Missense_Mutation_p.Q392R	NM_020951	NP_066002	Q6P280	ZN529_HUMAN	zinc finger protein 529 isoform a	464	C2H2-type 10.				"regulation of transcription, DNA-dependent|transcription, DNA-dependent"	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)					ATGAATTCTCTGATGTTCTGT	0.403													benign(0.116)	deleterious(0.03)
ZNF780B	163131	broadinstitute.org	37	19	40542140	40542140	+	Missense_Mutation	SNP	G	A	A			TARGET-30-PAISSH	Exome_WGA	TARGET-30-PAISSH-01A-01W	TARGET-30-PAISSH-10A-01W	0.198473	105	26	A	A	G	G	Valid_somatic	Sequenom	Illumina	g.chr19:40542140G>A	uc002omu.2	-	5	691	c.626C>T	c.(625-627)ACT>ATT	p.T209I	ZNF780B_uc002omv.2_Missense_Mutation_p.T61I	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	209	C2H2-type 2.				"regulation of transcription, DNA-dependent|transcription, DNA-dependent"	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTGATGTCGAGTAAGTTGTAT	0.368													benign(0.123)	tolerated(0.65)
