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 TMEM69 51249 broad.mit.edu 36 1 45932007 45932007 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45932007 45932007 TMEM69 1 C C T 25 NEXN 91624 broad.mit.edu 36 1 78156487 78156487 + Nonsense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 78156487 78156487 NEXN 1 G G T 45 RBMXL1 494115 broad.mit.edu 36 1 89221358 89221358 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89221358 89221358 RBMXL1 1 C C G 18 LYST 1130 broad.mit.edu 36 1 234060259 234060259 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 234060259 234060259 LYST 1 C C T 30 ARHGAP21 57584 broad.mit.edu 36 10 24914375 24914375 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24914375 24914375 ARHGAP21 10 C C T 30 PTCHD3 374308 broad.mit.edu 36 10 27742234 27742234 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27742234 27742234 PTCHD3 10 G G A 38 FAM196A 642938 broad.mit.edu 36 10 128864373 128864373 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128864373 128864373 FAM196A 10 G G A 40 CORO1B 57175 broad.mit.edu 36 11 66966579 66966579 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66966579 66966579 CORO1B 11 G G A 39 ARID2 196528 broad.mit.edu 36 12 44516673 44516673 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44516673 44516673 ARID2 12 G G A 40 KRT4 3851 broad.mit.edu 36 12 51494186 51494186 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C G C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 51494186 51494186 KRT4 12 C C G 31 STAT6 6778 broad.mit.edu 36 12 55787774 55787774 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 55787774 55787774 STAT6 12 C C T 31 TPCN1 53373 broad.mit.edu 36 12 112191059 112191059 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112191059 112191059 TPCN1 12 C C T 27 L2HGDH 79944 broad.mit.edu 36 14 49805729 49805729 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 49805729 49805729 L2HGDH 14 T T C 54 PCNX 22990 broad.mit.edu 36 14 70562597 70562597 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G A G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 70562597 70562597 PCNX 14 G G A 40 TDRD9 122402 broad.mit.edu 36 14 103527287 103527287 + Nonsense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 103527287 103527287 TDRD9 14 C C T 27 TRPM7 54822 broad.mit.edu 36 15 48689099 48689099 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 48689099 48689099 TRPM7 15 C C A 25 KIAA0556 23247 broad.mit.edu 36 16 27627607 27627607 + Silent SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G A G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Silent SNP 27627607 27627607 KIAA0556 16 G G A 40 SRSF1 6426 broad.mit.edu 36 17 53439347 53439347 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53439347 53439347 SRSF1 17 G G A 39 RYR1 6261 broad.mit.edu 36 19 43710877 43710877 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43710877 43710877 RYR1 19 C C T 19 HTRA2 27429 broad.mit.edu 36 2 74611552 74611552 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74611552 74611552 HTRA2 2 C C T 32 KCNH7 90134 broad.mit.edu 36 2 163010919 163010919 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 163010919 163010919 KCNH7 2 A A C 9 SCN9A 6335 broad.mit.edu 36 2 166793592 166793592 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 166793592 166793592 SCN9A 2 G G T 48 RAPH1 65059 broad.mit.edu 36 2 204013183 204013183 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G A G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 204013183 204013183 RAPH1 2 G G A 43 TTLL4 9654 broad.mit.edu 36 2 219311967 219311967 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219311967 219311967 TTLL4 2 G G T 45 CAPN10 11132 broad.mit.edu 36 2 241183346 241183346 + Silent SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 241183346 241183346 CAPN10 2 G G A 37 TMC2 117532 broad.mit.edu 36 20 2553002 2553002 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2553002 2553002 TMC2 20 G G A 38 OSBPL2 9885 broad.mit.edu 36 20 60280615 60280615 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60280615 60280615 OSBPL2 20 C C T 26 ADRBK2 157 broad.mit.edu 36 22 24430154 24430154 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C T C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 24430154 24430154 ADRBK2 22 C C T 27 SETD5 55209 broad.mit.edu 36 3 9445678 9445678 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 9445678 9445678 SETD5 3 T T C 51 SNRK 54861 broad.mit.edu 36 3 43363914 43363914 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G T G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 43363914 43363914 SNRK 3 G G T 48 TIPARP 25976 broad.mit.edu 36 3 157904093 157904093 + Silent SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 157904093 157904093 TIPARP 3 C C T 17 YTHDC1 91746 broad.mit.edu 36 4 68867041 68867041 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 68867041 68867041 YTHDC1 4 G G A 40 PCDH10 57575 broad.mit.edu 36 4 134292958 134292958 + Missense_Mutation SNP T T G novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134292958 134292958 PCDH10 4 T T G 59 ACSL1 2180 broad.mit.edu 36 4 185926492 185926492 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G A G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 185926492 185926492 ACSL1 4 G G A 47 PRDM9 56979 broad.mit.edu 36 5 23563434 23563434 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C G C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 23563434 23563434 PRDM9 5 C C G 17 DEPDC1B 55789 broad.mit.edu 36 5 60018679 60018679 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60018679 60018679 DEPDC1B 5 G G T 45 ADAMTS19 171019 broad.mit.edu 36 5 129047834 129047834 + Silent SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 129047834 129047834 ADAMTS19 5 C C T 28 PCDHGB6 56100 broad.mit.edu 36 5 140769188 140769188 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140769188 140769188 PCDHGB6 5 G G A 37 CCDC99 54908 broad.mit.edu 36 5 168958138 168958138 + Silent SNP T T G novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 168958138 168958138 CCDC99 5 T T G 62 HK3 3101 broad.mit.edu 36 5 176249112 176249112 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C T C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 176249112 176249112 HK3 5 C C T 32 TRERF1 55809 broad.mit.edu 36 6 42339057 42339057 + Silent SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42339057 42339057 TRERF1 6 C C T 23 KIAA0240 23506 broad.mit.edu 36 6 42927907 42927907 + Silent SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42927907 42927907 KIAA0240 6 C C T 20 SDK1 221935 broad.mit.edu 36 7 4017140 4017140 + Silent SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 4017140 4017140 SDK1 7 G G T 46 INHBA 3624 broad.mit.edu 36 7 41695796 41695796 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C T C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 41695796 41695796 INHBA 7 C C T 19 CALCR 799 broad.mit.edu 36 7 92946683 92946683 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 92946683 92946683 CALCR 7 C C T 19 RELN 5649 broad.mit.edu 36 7 102966978 102966978 + Silent SNP C C T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 C T C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Silent SNP 102966978 102966978 RELN 7 C C T 23 OR2A12 346525 broad.mit.edu 36 7 143423164 143423164 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 143423164 143423164 OR2A12 7 G G T 36 ZFHX4 79776 broad.mit.edu 36 8 77929104 77929104 + Silent SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77929104 77929104 ZFHX4 8 G G A 39 CDH17 1015 broad.mit.edu 36 8 95255614 95255614 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 95255614 95255614 CDH17 8 G G T 41 MRPL13 28998 broad.mit.edu 36 8 121501290 121501291 + Missense_Mutation DNP GC GC AA novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 121501290 121501291 MRPL13 8 GC GC AA 46 NDUFB9 4715 broad.mit.edu 36 8 125620702 125620702 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125620702 125620702 NDUFB9 8 G G T 40 MAGEB4 4115 broad.mit.edu 36 X 30170960 30170960 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30170960 30170960 MAGEB4 23 A A C 7 SPIN4 139886 broad.mit.edu 36 X 62487129 62487129 + Nonsense_Mutation SNP C C A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 62487129 62487129 SPIN4 23 C C A 32 ARMCX1 51309 broad.mit.edu 36 X 100694882 100694882 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 G C G G Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 100694882 100694882 ARMCX1 23 G G C 33 PLXNA3 55558 broad.mit.edu 36 X 153352653 153352653 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153352653 153352653 PLXNA3 23 G G A 38 TP53 7157 broad.mit.edu 36 17 7518915 7518915 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 T C T T Unknown Valid Somatic Phase_I Capture 454_PCR_WGA Illumina GAIIx Broad Missense_Mutation SNP 7518915 7518915 TP53 17 T T C 49 AQP12B 653437 broad.mit.edu 36 2 241270473 241270473 + Frame_Shift_Del DEL C - C novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 241270473 241270473 AQP12B 2 C - C 28 SLURP1 57152 broad.mit.edu 36 8 143819598 143819600 + In_Frame_Del DEL AGA - AGA novel Unknown TCGA-25-1319-01 TCGA-25-1319-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 143819598 143819600 SLURP1 8 AGA - AGA 7