The mutation patient centric table (PCT) contains the somatic mutation calls for 291 whole exome samples (WES).  This PCT is organized with patients as rows and gene names as columns.  Each cell then represents the worst mutation type seen in the specific patient, for each gene.  Scores are ranked as follows:

Nonsense mutation = 5
Frame shift (deletion or insertion) = 4
Missense mutation = 3
Splice site = 2
Silent = 1
No mutation seen = 0

An individual with both a frame-shift and a silent mutation in EGFR would then be scored a 4 in the EGFR column, an individual with no mutations would be a 0, and an individual with a nonsense mutation would be a 5.  For more resolution, such as the spectrum of mutations in an individual or their exact positions, please consult the associated MAF file that contains extensive information about each call.