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 ECE1 1889 broad.mit.edu 36 1 21444134 21444134 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21444134 21444134 ECE1 1 A A C 3 PTPRU 10076 broad.mit.edu 36 1 29504461 29504461 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 29504461 29504461 PTPRU 1 C C A 18 PODN 127435 broad.mit.edu 36 1 53312904 53312904 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53312904 53312904 PODN 1 A A C 5 LPPR4 9890 broad.mit.edu 36 1 99544192 99544192 + Missense_Mutation SNP T T A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99544192 99544192 LPPR4 1 T T A 50 SHE 126669 broad.mit.edu 36 1 152728203 152728203 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152728203 152728203 SHE 1 C C A 20 INSRR 3645 broad.mit.edu 36 1 155090390 155090390 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 155090390 155090390 INSRR 1 C C G 17 SPTA1 6708 broad.mit.edu 36 1 156917982 156917982 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156917982 156917982 SPTA1 1 C C G 17 AIM2 9447 broad.mit.edu 36 1 157302731 157302731 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 157302731 157302731 AIM2 1 G G T 48 HMCN1 83872 broad.mit.edu 36 1 184101573 184101573 + Silent SNP A A C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 184101573 184101573 HMCN1 1 A A C 5 CACNA1S 779 broad.mit.edu 36 1 199306144 199306144 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 199306144 199306144 CACNA1S 1 C C T 30 PFKFB3 5209 broad.mit.edu 36 10 6302685 6302685 + Nonsense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 6302685 6302685 PFKFB3 10 C C T 25 KRTAP5-3 387266 broad.mit.edu 36 11 1586141 1586141 + Silent SNP A A G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 1586141 1586141 KRTAP5-3 11 A A G 6 ACCSL 390110 broad.mit.edu 36 11 44031588 44031588 + Silent SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 44031588 44031588 ACCSL 11 C C A 32 NUP160 23279 broad.mit.edu 36 11 47826395 47826395 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47826395 47826395 NUP160 11 C C G 29 FADD 8772 broad.mit.edu 36 11 69729942 69729942 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 69729942 69729942 FADD 11 G G C 42 RSF1 51773 broad.mit.edu 36 11 77055836 77055836 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77055836 77055836 RSF1 11 T T C 58 CARD18 59082 broad.mit.edu 36 11 104514961 104514961 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 104514961 104514961 CARD18 11 G G T 48 VWF 7450 broad.mit.edu 36 12 5998813 5998813 + Silent SNP G G A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 5998813 5998813 VWF 12 G G A 47 RBP5 83758 broad.mit.edu 36 12 7172153 7172153 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7172153 7172153 RBP5 12 C C G 22 CD163L1 283316 broad.mit.edu 36 12 7419173 7419173 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7419173 7419173 CD163L1 12 T T C 51 PXN 5829 broad.mit.edu 36 12 119136393 119136393 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119136393 119136393 PXN 12 G G C 48 RNF31 55072 broad.mit.edu 36 14 23689492 23689492 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 23689492 23689492 RNF31 14 C C A 24 SHC4 399694 broad.mit.edu 36 15 46947314 46947314 + Silent SNP A A G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 46947314 46947314 SHC4 15 A A G 12 HCN4 10021 broad.mit.edu 36 15 71404475 71404475 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71404475 71404475 HCN4 15 G G T 42 PPL 5493 broad.mit.edu 36 16 4880198 4880198 + Silent SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 4880198 4880198 PPL 16 C C T 29 DCUN1D3 123879 broad.mit.edu 36 16 20781014 20781014 + Silent SNP A A G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 20781014 20781014 DCUN1D3 16 A A G 8 PRSS36 146547 broad.mit.edu 36 16 31062194 31062194 + Nonsense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 31062194 31062194 PRSS36 16 C C T 21 ARMC5 79798 broad.mit.edu 36 16 31383762 31383762 + Silent SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 31383762 31383762 ARMC5 16 C C A 22 CNOT1 23019 broad.mit.edu 36 16 57133879 57133879 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57133879 57133879 CNOT1 16 G G C 36 DNAH17 8632 broad.mit.edu 36 17 74034652 74034652 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74034652 74034652 DNAH17 17 T T G 64 NFATC1 4772 broad.mit.edu 36 18 75312053 75312053 + Silent SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 75312053 75312053 NFATC1 18 C C T 19 PPAN-P2RY11 692312 broad.mit.edu 36 19 10086200 10086200 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10086200 10086200 PPAN-P2RY11 19 A A C 7 APLP1 333 broad.mit.edu 36 19 41061911 41061911 + Silent SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 41061911 41061911 APLP1 19 C C G 30 ZNF224 7767 broad.mit.edu 36 19 49302639 49302639 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 49302639 49302639 ZNF224 19 C C G 20 PPP1R13L 10848 broad.mit.edu 36 19 50593124 50593124 + Silent SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 50593124 50593124 PPP1R13L 19 C C A 27 GRLF1 2909 broad.mit.edu 36 19 52115784 52115784 + Missense_Mutation SNP T T A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52115784 52115784 GRLF1 19 T T A 53 ABCG5 64240 broad.mit.edu 36 2 43904698 43904698 + Silent SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 43904698 43904698 ABCG5 2 C C A 29 PAPOLG 64895 broad.mit.edu 36 2 60852164 60852164 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60852164 60852164 PAPOLG 2 C C G 32 BMP10 27302 broad.mit.edu 36 2 68946356 68946356 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 68946356 68946356 BMP10 2 G G A 42 LRRTM1 347730 broad.mit.edu 36 2 80383703 80383703 + Silent SNP C C A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 80383703 80383703 LRRTM1 2 C C A 27 ZSWIM2 151112 broad.mit.edu 36 2 187401221 187401221 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 187401221 187401221 ZSWIM2 2 T T C 64 SEL1L2 80343 broad.mit.edu 36 20 13815034 13815034 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13815034 13815034 SEL1L2 20 G G A 40 BOC 91653 broad.mit.edu 36 3 114452142 114452142 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 114452142 114452142 BOC 3 G G A 39 HERC6 55008 broad.mit.edu 36 4 89533744 89533744 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89533744 89533744 HERC6 4 C C T 27 LARP7 51574 broad.mit.edu 36 4 113790234 113790234 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113790234 113790234 LARP7 4 T T G 58 TNIP1 10318 broad.mit.edu 36 5 150421932 150421932 + Silent SNP G G C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 150421932 150421932 TNIP1 5 G G C 43 SERPINB1 1992 broad.mit.edu 36 6 2779179 2779179 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2779179 2779179 SERPINB1 6 C C T 29 AIF1 199 broad.mit.edu 36 6 31692100 31692100 + Missense_Mutation SNP A A T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31692100 31692100 AIF1 6 A A T 12 LRFN2 57497 broad.mit.edu 36 6 40508130 40508130 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40508130 40508130 LRFN2 6 G G T 43 PRPH2 5961 broad.mit.edu 36 6 42797589 42797589 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42797589 42797589 PRPH2 6 C C G 32 EPHA1 2041 broad.mit.edu 36 7 142804789 142804789 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 142804789 142804789 EPHA1 7 C C T 19 CNBD1 168975 broad.mit.edu 36 8 88318266 88318266 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88318266 88318266 CNBD1 8 T T G 60 PKHD1L1 93035 broad.mit.edu 36 8 110604253 110604253 + Silent SNP G G A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 110604253 110604253 PKHD1L1 8 G G A 34 RFX3 5991 broad.mit.edu 36 9 3291562 3291562 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3291562 3291562 RFX3 9 G G C 33 FCN1 2219 broad.mit.edu 36 9 136949470 136949470 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 136949470 136949470 FCN1 9 C C G 32 SCML1 6322 broad.mit.edu 36 X 17678068 17678068 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17678068 17678068 SCML1 23 G G A 40 HUWE1 10075 broad.mit.edu 36 X 53612533 53612533 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53612533 53612533 HUWE1 23 C C T 20 DRP2 1821 broad.mit.edu 36 X 100380655 100380655 + Silent SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 100380655 100380655 DRP2 23 C C T 26 ARMCX3 51566 broad.mit.edu 36 X 100767422 100767422 + Missense_Mutation SNP T T A novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100767422 100767422 ARMCX3 23 T T A 54 BEX4 56271 broad.mit.edu 36 X 102357839 102357839 + Silent SNP A A G novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 102357839 102357839 BEX4 23 A A G 4 L1CAM 3897 broad.mit.edu 36 X 152784144 152784144 + Silent SNP C C T novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 152784144 152784144 L1CAM 23 C C T 19 TJP1 7082 broad.mit.edu 36 15 27798088 27798104 + Frame_Shift_Del DEL TGGGCCCTGCTGAAGGG - TGGGCCCTGCTGAAGGG novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 27798088 27798104 TJP1 15 TGGGCCCTGCTGAAGGG - TGGGCCCTGCTGAAGGG 63 MYADM 91663 broad.mit.edu 36 19 59069058 59069089 + Frame_Shift_Del DEL GTGGCCTGGACCCGGGCCCGGCCCGGCGAGAT - GTGGCCTGGACCCGGGCCCGGCCCGGCGAGAT novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 59069058 59069089 MYADM 19 GTGGCCTGGACCCGGGCCCGGCCCGGCGAGAT - GTGGCCTGGACCCGGGCCCGGCCCGGCGAGAT 36 USP40 55230 broad.mit.edu 36 2 234054656 234054658 + In_Frame_Del DEL ATC - ATC novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 234054656 234054658 USP40 2 ATC - ATC 4 ABCF1 23 broad.mit.edu 36 6 30658158 30658172 + In_Frame_Del DEL GGAAGAAGGAGAAGG - GGAAGAAGGAGAAGG novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 30658158 30658172 ABCF1 6 GGAAGAAGGAGAAGG - GGAAGAAGGAGAAGG 35 FAM86B2 653333 broad.mit.edu 36 8 12335964 12335966 + In_Frame_Del DEL CTG - CTG novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 12335964 12335966 FAM86B2 8 CTG - CTG 32 CYHR1 50626 broad.mit.edu 36 8 145660466 145660467 + Frame_Shift_Ins INS - C - novel Unknown TCGA-04-1356-01 TCGA-04-1356-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 145660466 145660467 CYHR1 8 - C - 38