Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context C1orf201 90529 broad.mit.edu 36 1 24572784 24572784 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24572784 24572784 C1orf201 1 G G A 43 SLC1A7 6512 broad.mit.edu 36 1 53328074 53328074 + Silent SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 53328074 53328074 SLC1A7 1 G G C 39 S1PR1 1901 broad.mit.edu 36 1 101477260 101477260 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C A C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 101477260 101477260 S1PR1 1 C C A 25 CELSR2 1952 broad.mit.edu 36 1 109594631 109594631 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109594631 109594631 CELSR2 1 C C A 23 ADAM30 11085 broad.mit.edu 36 1 120239173 120239173 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 120239173 120239173 ADAM30 1 G G C 42 C1orf56 54964 broad.mit.edu 36 1 149287040 149287040 + Silent SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 149287040 149287040 C1orf56 1 C C G 23 FLG2 388698 broad.mit.edu 36 1 150590300 150590300 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150590300 150590300 FLG2 1 G G T 48 FLAD1 80308 broad.mit.edu 36 1 153229299 153229299 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 A C A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 153229299 153229299 FLAD1 1 A A C 16 FAM189B 10712 broad.mit.edu 36 1 153484651 153484651 + Silent SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 153484651 153484651 FAM189B 1 C C G 18 GON4L 54856 broad.mit.edu 36 1 154002179 154002179 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154002179 154002179 GON4L 1 C C T 29 NTRK1 4914 broad.mit.edu 36 1 155115677 155115677 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 155115677 155115677 NTRK1 1 C C T 23 NUAK2 81788 broad.mit.edu 36 1 203539966 203539966 + Silent SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 203539966 203539966 NUAK2 1 G G C 45 MIA3 375056 broad.mit.edu 36 1 220905509 220905509 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 220905509 220905509 MIA3 1 C C T 28 URB2 9816 broad.mit.edu 36 1 227839846 227839846 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 227839846 227839846 URB2 1 G G A 43 LYST 1130 broad.mit.edu 36 1 234038960 234038960 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 234038960 234038960 LYST 1 G G T 35 PLD5 200150 broad.mit.edu 36 1 240330665 240330665 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 240330665 240330665 PLD5 1 C C G 32 OR2T12 127064 broad.mit.edu 36 1 246525061 246525061 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 246525061 246525061 OR2T12 1 A A T 11 ZNF25 219749 broad.mit.edu 36 10 38281644 38281644 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38281644 38281644 ZNF25 10 C C G 17 RET 5979 broad.mit.edu 36 10 42926708 42926708 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 42926708 42926708 RET 10 C C T 19 PRKG1 5592 broad.mit.edu 36 10 53492301 53492301 + Splice_Site_SNP SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Splice_Site_SNP SNP 53492301 53492301 PRKG1 10 A A T 7 EGR2 1959 broad.mit.edu 36 10 64243747 64243747 + Silent SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 64243747 64243747 EGR2 10 G G C 33 MGEA5 10724 broad.mit.edu 36 10 103540644 103540644 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 103540644 103540644 MGEA5 10 T T A 54 DHX32 55760 broad.mit.edu 36 10 127516868 127516868 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 127516868 127516868 DHX32 10 C C A 21 MUC2 4583 broad.mit.edu 36 11 1082891 1082891 + Silent SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1082891 1082891 MUC2 11 C C A 22 PAX6 5080 broad.mit.edu 36 11 31772909 31772909 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31772909 31772909 PAX6 11 C C A 26 OR5T1 390155 broad.mit.edu 36 11 55800656 55800656 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 55800656 55800656 OR5T1 11 C C T 29 FAM111B 374393 broad.mit.edu 36 11 58649831 58649831 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 58649831 58649831 FAM111B 11 G G A 47 MS4A5 64232 broad.mit.edu 36 11 59957856 59957856 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59957856 59957856 MS4A5 11 G G A 34 GANAB 23193 broad.mit.edu 36 11 62154461 62154461 + Silent SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 62154461 62154461 GANAB 11 C C G 22 LGALS12 85329 broad.mit.edu 36 11 63032877 63032877 + Silent SNP C C A rs12289952 byHapMap TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 63032877 63032877 LGALS12 11 C C A 31 CDC42BPG 55561 broad.mit.edu 36 11 64358982 64358982 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64358982 64358982 CDC42BPG 11 T T C 57 SF3B2 10992 broad.mit.edu 36 11 65584674 65584674 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65584674 65584674 SF3B2 11 C C T 26 SYTL2 54843 broad.mit.edu 36 11 85123119 85123119 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 85123119 85123119 SYTL2 11 C C G 17 DYNC2H1 79659 broad.mit.edu 36 11 102575379 102575379 + Silent SNP A A G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 102575379 102575379 DYNC2H1 11 A A G 12 DCPS 28960 broad.mit.edu 36 11 125720539 125720539 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125720539 125720539 DCPS 11 C C A 25 NCAPD2 9918 broad.mit.edu 36 12 6505594 6505594 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6505594 6505594 NCAPD2 12 C C T 26 APOLD1 81575 broad.mit.edu 36 12 12831529 12831529 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 12831529 12831529 APOLD1 12 C C G 32 PIK3C2G 5288 broad.mit.edu 36 12 18549513 18549513 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 18549513 18549513 PIK3C2G 12 C C T 20 IRAK4 51135 broad.mit.edu 36 12 42448338 42448338 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 42448338 42448338 IRAK4 12 A A G 8 C12orf51 283450 broad.mit.edu 36 12 111090030 111090030 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 111090030 111090030 C12orf51 12 A A C 6 TBX5 6910 broad.mit.edu 36 12 113278154 113278154 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113278154 113278154 TBX5 12 G G A 38 CIT 11113 broad.mit.edu 36 12 118619990 118619990 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 118619990 118619990 CIT 12 C C T 27 UBAC2 337867 broad.mit.edu 36 13 98764371 98764371 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 98764371 98764371 UBAC2 13 C C G 32 G2E3 55632 broad.mit.edu 36 14 30151266 30151266 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30151266 30151266 G2E3 14 G G A 45 ITPK1 3705 broad.mit.edu 36 14 92494301 92494301 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 92494301 92494301 ITPK1 14 G G A 45 EVL 51466 broad.mit.edu 36 14 99673694 99673694 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99673694 99673694 EVL 14 A A T 11 PLA2G4F 255189 broad.mit.edu 36 15 40229338 40229338 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40229338 40229338 PLA2G4F 15 G G T 34 FOXB1 27023 broad.mit.edu 36 15 58084968 58084968 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58084968 58084968 FOXB1 15 A A T 8 UBE2Q2 92912 broad.mit.edu 36 15 73978838 73978838 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73978838 73978838 UBE2Q2 15 C C G 21 UNC45A 55898 broad.mit.edu 36 15 89293649 89293649 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89293649 89293649 UNC45A 15 A A G 10 KIFC3 3801 broad.mit.edu 36 16 56357032 56357032 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56357032 56357032 KIFC3 16 C C T 19 PLEKHG4 25894 broad.mit.edu 36 16 65871480 65871480 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65871480 65871480 PLEKHG4 16 C C T 30 ZFP1 162239 broad.mit.edu 36 16 73761359 73761359 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73761359 73761359 ZFP1 16 A A T 6 TP53 7157 broad.mit.edu 36 17 7519221 7519221 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7519221 7519221 TP53 17 A A C 7 GLP2R 9340 broad.mit.edu 36 17 9731991 9731991 + Silent SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 9731991 9731991 GLP2R 17 G G A 46 KIAA0100 9703 broad.mit.edu 36 17 23986322 23986322 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 23986322 23986322 KIAA0100 17 T T A 62 ITGB3 3690 broad.mit.edu 36 17 42724773 42724773 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 42724773 42724773 ITGB3 17 C C T 19 BZRAP1 9256 broad.mit.edu 36 17 53737957 53737957 + Silent SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 53737957 53737957 BZRAP1 17 G G C 47 EPB41L3 23136 broad.mit.edu 36 18 5396870 5396870 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 5396870 5396870 EPB41L3 18 G G A 40 TRAPPC8 22878 broad.mit.edu 36 18 27689653 27689653 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27689653 27689653 TRAPPC8 18 G G C 34 SOCS6 9306 broad.mit.edu 36 18 66143303 66143303 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 66143303 66143303 SOCS6 18 G G A 39 REEP6 92840 broad.mit.edu 36 19 1447361 1447361 + Silent SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1447361 1447361 REEP6 19 G G T 38 MAP2K2 5605 broad.mit.edu 36 19 4068604 4068604 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4068604 4068604 MAP2K2 19 T T A 56 DOCK6 57572 broad.mit.edu 36 19 11172116 11172116 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11172116 11172116 DOCK6 19 G G T 42 ASF1B 55723 broad.mit.edu 36 19 14093358 14093358 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 14093358 14093358 ASF1B 19 G G A 42 COPE 11316 broad.mit.edu 36 19 18891111 18891111 + Missense_Mutation SNP A A C rs11537888 Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 18891111 18891111 COPE 19 A A C 14 HPN 3249 broad.mit.edu 36 19 40248371 40248371 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 40248371 40248371 HPN 19 C C G 29 THAP8 199745 broad.mit.edu 36 19 41222196 41222196 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41222196 41222196 THAP8 19 G G T 46 SPTBN4 57731 broad.mit.edu 36 19 45695272 45695272 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45695272 45695272 SPTBN4 19 C C T 21 SCAF1 58506 broad.mit.edu 36 19 54846138 54846138 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54846138 54846138 SCAF1 19 T T A 50 FPR3 2359 broad.mit.edu 36 19 57019316 57019316 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57019316 57019316 FPR3 19 G G T 36 ZNF132 7691 broad.mit.edu 36 19 63636598 63636598 + Missense_Mutation SNP T T G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63636598 63636598 ZNF132 19 T T G 56 VSNL1 7447 broad.mit.edu 36 2 17636864 17636864 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 17636864 17636864 VSNL1 2 G G T 35 LAPTM4A 9741 broad.mit.edu 36 2 20104232 20104232 + Missense_Mutation SNP T T G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20104232 20104232 LAPTM4A 2 T T G 52 DPYSL5 56896 broad.mit.edu 36 2 27003805 27003805 + Splice_Site_SNP SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 27003805 27003805 DPYSL5 2 G G A 42 ALK 238 broad.mit.edu 36 2 29299735 29299735 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 29299735 29299735 ALK 2 C C T 27 USP34 9736 broad.mit.edu 36 2 61392182 61392182 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 61392182 61392182 USP34 2 G G A 41 ADRA2B 151 broad.mit.edu 36 2 96145134 96145134 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 96145134 96145134 ADRA2B 2 C C T 27 CSRNP3 80034 broad.mit.edu 36 2 166222658 166222658 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166222658 166222658 CSRNP3 2 G G A 38 TTN 7273 broad.mit.edu 36 2 179205742 179205742 + Silent SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 179205742 179205742 TTN 2 T T C 59 TTN 7273 broad.mit.edu 36 2 179320783 179320783 + Silent SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 179320783 179320783 TTN 2 A A T 9 NBEAL1 65065 broad.mit.edu 36 2 203709031 203709031 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 203709031 203709031 NBEAL1 2 G G C 45 C2orf67 151050 broad.mit.edu 36 2 210601925 210601925 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 210601925 210601925 C2orf67 2 C C T 23 PROKR2 128674 broad.mit.edu 36 20 5242763 5242763 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5242763 5242763 PROKR2 20 G G A 38 PLCB1 23236 broad.mit.edu 36 20 8653336 8653336 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8653336 8653336 PLCB1 20 G G A 33 ZGPAT 84619 broad.mit.edu 36 20 61810451 61810451 + Silent SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 61810451 61810451 ZGPAT 20 C C A 27 TMPRSS15 5651 broad.mit.edu 36 21 18647201 18647201 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 18647201 18647201 TMPRSS15 21 C C A 17 MORC3 23515 broad.mit.edu 36 21 36658405 36658405 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36658405 36658405 MORC3 21 C C G 29 CRYAA 1409 broad.mit.edu 36 21 43462450 43462450 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43462450 43462450 CRYAA 21 G G C 41 GAB4 128954 broad.mit.edu 36 22 15825730 15825730 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15825730 15825730 GAB4 22 A A T 11 PI4KA 5297 broad.mit.edu 36 22 19412084 19412084 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 19412084 19412084 PI4KA 22 C C T 20 RAB36 9609 broad.mit.edu 36 22 21822252 21822252 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 21822252 21822252 RAB36 22 G G A 44 GRAMD1C 54762 broad.mit.edu 36 3 115117258 115117258 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 115117258 115117258 GRAMD1C 3 C C G 32 ARHGAP31 57514 broad.mit.edu 36 3 120595050 120595050 + Silent SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 120595050 120595050 ARHGAP31 3 C C T 24 C3orf15 89876 broad.mit.edu 36 3 120917218 120917218 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 120917218 120917218 C3orf15 3 C C T 25 CASR 846 broad.mit.edu 36 3 123485524 123485524 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 123485524 123485524 CASR 3 G G A 38 MCM2 4171 broad.mit.edu 36 3 128807766 128807766 + Silent SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 128807766 128807766 MCM2 3 C C A 22 AMOTL2 51421 broad.mit.edu 36 3 135572745 135572745 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135572745 135572745 AMOTL2 3 G G T 43 SLC9A9 285195 broad.mit.edu 36 3 144468407 144468407 + Missense_Mutation SNP T T G rs2289491 byCluster;byFrequency;bySubmitter;byHapMap TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 144468407 144468407 SLC9A9 3 T T G 51 MUC4 4585 broad.mit.edu 36 3 196977572 196977572 + Nonsense_Mutation SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 196977572 196977572 MUC4 3 C C A 29 TADA2B 93624 broad.mit.edu 36 4 7107290 7107291 + Missense_Mutation DNP CT CT AG novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 7107290 7107291 TADA2B 4 CT CT AG 20 COL25A1 84570 broad.mit.edu 36 4 110003986 110003986 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 110003986 110003986 COL25A1 4 G G A 40 ADAMTS12 81792 broad.mit.edu 36 5 33679330 33679330 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33679330 33679330 ADAMTS12 5 G G C 40 PCDHB2 56133 broad.mit.edu 36 5 140454591 140454591 + Silent SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 140454591 140454591 PCDHB2 5 G G T 37 FAT2 2196 broad.mit.edu 36 5 150900507 150900507 + Silent SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 150900507 150900507 FAT2 5 G G T 43 SH3PXD2B 285590 broad.mit.edu 36 5 171698702 171698702 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 171698702 171698702 SH3PXD2B 5 C C G 24 HIST1H3C 8352 broad.mit.edu 36 6 26153624 26153624 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26153624 26153624 HIST1H3C 6 C C G 31 HIST1H1C 3006 broad.mit.edu 36 6 26164309 26164309 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26164309 26164309 HIST1H1C 6 C C G 32 ZKSCAN4 387032 broad.mit.edu 36 6 28320943 28320943 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28320943 28320943 ZKSCAN4 6 C C G 18 MRPS18B 28973 broad.mit.edu 36 6 30698627 30698627 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30698627 30698627 MRPS18B 6 G G T 43 C6orf48 50854 broad.mit.edu 36 6 31913162 31913162 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31913162 31913162 C6orf48 6 G G C 33 TCTE1 202500 broad.mit.edu 36 6 44362100 44362100 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44362100 44362100 TCTE1 6 C C T 25 GPR110 266977 broad.mit.edu 36 6 47085986 47085986 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47085986 47085986 GPR110 6 G G A 35 TINAG 27283 broad.mit.edu 36 6 54320270 54320270 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54320270 54320270 TINAG 6 C C T 19 ZNF292 23036 broad.mit.edu 36 6 88023857 88023857 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88023857 88023857 ZNF292 6 C C T 24 MDN1 23195 broad.mit.edu 36 6 90442620 90442620 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90442620 90442620 MDN1 6 C C G 22 TNRC18B 84629 broad.mit.edu 36 7 5383118 5383118 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5383118 5383118 TNRC18B 7 C C T 26 RSPH10B 222967 broad.mit.edu 36 7 5949590 5949590 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5949590 5949590 RSPH10B 7 A A C 8 OGDH 4967 broad.mit.edu 36 7 44702654 44702654 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44702654 44702654 OGDH 7 C C T 26 ADAM22 53616 broad.mit.edu 36 7 87598675 87598675 + Silent SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 87598675 87598675 ADAM22 7 T T C 62 MOSPD3 64598 broad.mit.edu 36 7 100050739 100050739 + Silent SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 100050739 100050739 MOSPD3 7 C C G 24 ZAN 7455 broad.mit.edu 36 7 100215053 100215053 + Nonsense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 100215053 100215053 ZAN 7 G G T 41 MGAM 8972 broad.mit.edu 36 7 141368668 141368668 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 141368668 141368668 MGAM 7 A A G 3 KRBA1 84626 broad.mit.edu 36 7 149049527 149049527 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 149049527 149049527 KRBA1 7 G G C 44 BIN3 55909 broad.mit.edu 36 8 22537732 22537732 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22537732 22537732 BIN3 8 T T C 54 PURG 29942 broad.mit.edu 36 8 31009036 31009036 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31009036 31009036 PURG 8 C C G 20 SNTG1 54212 broad.mit.edu 36 8 51611798 51611798 + Nonsense_Mutation SNP T T A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 51611798 51611798 SNTG1 8 T T A 61 RGS20 8601 broad.mit.edu 36 8 55033562 55033562 + Silent SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 55033562 55033562 RGS20 8 T T C 63 PRDM14 63978 broad.mit.edu 36 8 71141225 71141225 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71141225 71141225 PRDM14 8 C C T 17 KCNB2 9312 broad.mit.edu 36 8 74011716 74011716 + Silent SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 74011716 74011716 KCNB2 8 G G T 45 RGS22 26166 broad.mit.edu 36 8 101144951 101144951 + Nonsense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 101144951 101144951 RGS22 8 A A T 8 DMRT3 58524 broad.mit.edu 36 9 980347 980347 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 980347 980347 DMRT3 9 T T A 59 ARID3C 138715 broad.mit.edu 36 9 34612527 34612527 + Splice_Site_SNP SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 34612527 34612527 ARID3C 9 C C G 32 CA9 768 broad.mit.edu 36 9 35669329 35669329 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 35669329 35669329 CA9 9 G G T 36 FRMPD1 22844 broad.mit.edu 36 9 37722367 37722367 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37722367 37722367 FRMPD1 9 G G C 38 PRUNE2 158471 broad.mit.edu 36 9 78514633 78514633 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 78514633 78514633 PRUNE2 9 C C T 28 C9orf21 195827 broad.mit.edu 36 9 98453761 98453761 + Splice_Site_SNP SNP C C A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 98453761 98453761 C9orf21 9 C C A 18 SVEP1 79987 broad.mit.edu 36 9 112316053 112316053 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112316053 112316053 SVEP1 9 A A C 6 PAPPA 5069 broad.mit.edu 36 9 118179697 118179697 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 118179697 118179697 PAPPA 9 C C G 32 PPP6C 5537 broad.mit.edu 36 9 126956018 126956018 + Silent SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 126956018 126956018 PPP6C 9 G G A 45 FAM102A 399665 broad.mit.edu 36 9 129750189 129750190 + Missense_Mutation DNP GC GC AG novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 129750189 129750190 FAM102A 9 GC GC AG 42 SLC27A4 10999 broad.mit.edu 36 9 130162578 130162578 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130162578 130162578 SLC27A4 9 A A G 11 C9orf116 138162 broad.mit.edu 36 9 137527258 137527258 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 137527258 137527258 C9orf116 9 T T C 61 EGFL7 51162 broad.mit.edu 36 9 138686547 138686547 + Silent SNP G G A novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 138686547 138686547 EGFL7 9 G G A 33 TUBB2C 10383 broad.mit.edu 36 9 139257542 139257542 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 139257542 139257542 TUBB2C 9 A A T 2 APOOL 139322 broad.mit.edu 36 X 84197550 84197550 + Silent SNP A A G novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 84197550 84197550 APOOL 23 A A G 7 MORC4 79710 broad.mit.edu 36 X 106116087 106116087 + Splice_Site_SNP SNP C C T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 106116087 106116087 MORC4 23 C C T 28 PAK3 5063 broad.mit.edu 36 X 110346422 110346422 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 110346422 110346422 PAK3 23 T T C 50 TKTL1 8277 broad.mit.edu 36 X 153202398 153202398 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153202398 153202398 TKTL1 23 G G C 41 F8 2157 broad.mit.edu 36 X 153880954 153880954 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 153880954 153880954 F8 23 A A T 7 CD163L1 283316 broad.mit.edu 36 12 7418493 7418512 + Frame_Shift_Del DEL CACACCACGTGGGCATCGCT - CACACCACGTGGGCATCGCT novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 7418493 7418512 CD163L1 12 CACACCACGTGGGCATCGCT - CACACCACGTGGGCATCGCT 17 MPRIP 23164 broad.mit.edu 36 17 17002754 17002786 + In_Frame_Del DEL CGGAGGCGGGAGGAGCGCCGCAAGCGCTTCGGG - CGGAGGCGGGAGGAGCGCCGCAAGCGCTTCGGG novel Unknown TCGA-25-1313-01 TCGA-25-1313-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 17002754 17002786 MPRIP 17 CGGAGGCGGGAGGAGCGCCGCAAGCGCTTCGGG - CGGAGGCGGGAGGAGCGCCGCAAGCGCTTCGGG 19