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 Tumor_Sample_UUID Matched_Norm_Sample_UUID COSMIC_Codon COSMIC_Gene Transcript_Id Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq COSMIC_Site_Freq TVarRat NVarRat dbSNP_Strength dbSNP_AF dbSNP_PopFreq Confidence Algorithm PLOD1 5351 hgsc.bcm.edu hg19 1 12030830 12030830 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PLOD1 NM_000302 exon17 c.T1859G p.I620S AGTACATTGCGCC . 70.0 13.0 151.0 0.0 . 75 . . . none . . PASS Atlas-SNP PTPRU 10076 hgsc.bcm.edu hg19 1 29585229 29585229 + Missense_Mutation SNP G G T rs145487041 bycluster;by1000genomes;alternate_allele TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PTPRU NM_001195001 exon3 c.G418T p.G140C TCCCACGGCCGTC . 107.0 6.0 130.0 0.0 . 374 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP B4GALT2 8704 hgsc.bcm.edu hg19 1 44447485 44447485 + Silent SNP G G T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed B4GALT2,pharynx,carcinoma,0,1 B4GALT2 NM_030587 exon3 c.G525T p.A175A GGTGGCGGTCATC . 139.0 31.0 235.0 0.0 . 35 . . . none . . PASS Atlas-SNP DOCK7 85440 hgsc.bcm.edu hg19 1 63096983 63096983 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . DOCK7 NM_001271999 exon11 c.C1210A p.H404N TTAAATGGATTGC . 259.0 66.0 344.0 0.0 . 184 . . . none . . PASS Atlas-SNP RBM8A 9939 hgsc.bcm.edu hg19 1 145507671 145507671 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . RBM8A NM_005105 exon1 c.C5T p.A2V AGATGGCGGACGT . 81.0 20.0 140.0 0.0 . 18 . . . none . . PASS Atlas-SNP CACNA1E 777 hgsc.bcm.edu hg19 1 181727893 181727893 + Splice_Site SNP G G T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CACNA1E NM_001205293 exon32 c.4495-1G>T . CTGGCAGTATTAT . 56.0 4.0 85.0 0.0 . 778 . . . none . . PASS Atlas-SNP ZNF648 127665 hgsc.bcm.edu hg19 1 182027010 182027010 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ZNF648 NM_001009992 exon2 c.G136C p.E46Q TGCCCTCTTTTTC . 85.0 22.0 142.0 0.0 . 111 . . . none . . PASS Atlas-SNP PRG4 10216 hgsc.bcm.edu hg19 1 186276990 186276990 + Silent SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PRG4 NM_005807 exon7 c.T2139A p.A713A GACTGCTCCAACT . 96.0 29.0 114.0 0.0 . 259 . . . none . . PASS Atlas-SNP SLC30A10 55532 hgsc.bcm.edu hg19 1 220101416 220101416 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SLC30A10 NM_018713 exon1 c.G367C p.G123R ACAGCCCCAGGAC . 207.0 50.0 378.0 0.0 . 58 . . . none . . PASS Atlas-SNP CEP170 9859 hgsc.bcm.edu hg19 1 243329104 243329104 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CEP170 NM_014812 exon13 c.C2158T p.L720F AGTGAAGTAGGGT . 97.0 18.0 33.0 0.0 . 153 . . . none . . PASS Atlas-SNP CGREF1 10669 hgsc.bcm.edu hg19 2 27324530 27324530 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CGREF1 NM_001166239 exon6 c.A569C p.E190A TTTGCTTCTTCTC . 48.0 8.0 76.0 0.0 . 31 . . . none . . PASS Atlas-SNP SULT1C4 27233 hgsc.bcm.edu hg19 2 108998295 108998295 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SULT1C4 NM_006588 exon2 c.C247T p.H83Y CCGACTCATCAAC . 166.0 38.0 192.0 0.0 . 41 . . . none . . PASS Atlas-SNP CNTNAP5 129684 hgsc.bcm.edu hg19 2 125192134 125192134 + Silent SNP C C G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CNTNAP5 NM_130773 exon5 c.C603G p.L201L TACTCTCAAAGAT . 92.0 25.0 121.0 0.0 . 405 . . . none . . PASS Atlas-SNP CCDC115 84317 hgsc.bcm.edu hg19 2 131099478 131099478 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CCDC115 NM_032357 exon2 c.G151A p.A51T ACTTGGCGCCCAT . 94.0 4.0 131.0 0.0 . 19 . . . none . . PASS Atlas-SNP XRN1 54464 hgsc.bcm.edu hg19 3 142137718 142137718 + Silent SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . XRN1 NM_001042604 exon11 c.G1179A p.Q393Q ATTTTCCTGGCCC . 155.0 25.0 189.0 0.0 . 138 . . . none . . PASS Atlas-SNP PPARGC1A 10891 hgsc.bcm.edu hg19 4 23886468 23886468 + Silent SNP A A G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PPARGC1A NM_013261 exon2 c.T141C p.D47D GTCTGTATCCAAG . 84.0 19.0 68.0 0.0 . 129 . . . none . . PASS Atlas-SNP TMPRSS11D 9407 hgsc.bcm.edu hg19 4 68699085 68699085 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TMPRSS11D NM_004262 exon7 c.C529G p.P177A GGTCTGGACCGGC . 56.0 10.0 78.0 0.0 . 68 . . . none . . PASS Atlas-SNP C4orf3 401152 hgsc.bcm.edu hg19 4 120221611 120221611 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . C4orf3 NM_001170330 exon2 c.A479C p.N160T TCGAAGTTCTGCC . 85.0 19.0 130.0 0.0 . 16 . . . none . . PASS Atlas-SNP PCSK1 5122 hgsc.bcm.edu hg19 5 95768715 95768715 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PCSK1 NM_000439 exon1 c.C32T p.T11I AAAGCAGTGCACT . 136.0 39.0 241.0 0.0 . 93 . . . none . . PASS Atlas-SNP CEP120 153241 hgsc.bcm.edu hg19 5 122682287 122682287 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CEP120 NM_153223 exon21 c.C2887T p.H963Y CCTCGTGATTATA . 95.0 19.0 57.0 0.0 . 72 . . . none . . PASS Atlas-SNP DOCK2 1794 hgsc.bcm.edu hg19 5 169463523 169463523 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . DOCK2 NM_004946 exon36 c.T3629A p.F1210Y AGAATTTCTACAA . 72.0 32.0 97.0 0.0 . 389 . . . none . . PASS Atlas-SNP GPR116 221395 hgsc.bcm.edu hg19 6 46836697 46836697 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed GPR116,colon,carcinoma,0,2 GPR116 NM_015234 exon12 c.G1544T p.R515I TAAAATCTTTGGT . 72.0 16.0 76.0 0.0 . 133 . . . none . . PASS Atlas-SNP KATNA1 11104 hgsc.bcm.edu hg19 6 149922828 149922828 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . KATNA1 NM_007044 exon7 c.A790T p.T264S ATTCTGTAGCTAC . 97.0 25.0 138.0 0.0 . 34 . . . none . . PASS Atlas-SNP TIAM2 26230 hgsc.bcm.edu hg19 6 155572110 155572110 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed TIAM2,mouth,carcinoma,0,1 TIAM2 NM_012454 exon21 c.C4015A p.L1339M CCATTTCTGTCTC . 90.0 29.0 97.0 0.0 . 161 . . . none . . PASS Atlas-SNP TMEM106B 54664 hgsc.bcm.edu hg19 7 12254528 12254528 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TMEM106B NM_001134232 exon2 c.T92G p.V31G GACTGGTTAATAG . 85.0 16.0 66.0 0.0 . 34 . . . none . . PASS Atlas-SNP MFHAS1 9258 hgsc.bcm.edu hg19 8 8747815 8747815 + Silent SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . MFHAS1 NM_004225 exon1 c.C2754T p.A918A TCTATAGGCAAAG . 120.0 29.0 118.0 0.0 . 58 . . . none . . PASS Atlas-SNP PDLIM2 64236 hgsc.bcm.edu hg19 8 22442384 22442384 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PDLIM2 NM_021630 exon4 c.T1046C p.V349A TGGAAGTGCTGGC . 67.0 7.0 106.0 0.0 . 42 . . . none . . PASS Atlas-SNP RP1 6101 hgsc.bcm.edu hg19 8 55538963 55538963 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . RP1 NM_006269 exon4 c.G2521A p.E841K CAAGCAGAAGTGG . 181.0 60.0 115.0 0.0 . 429 . . . none . . PASS Atlas-SNP LAPTM4B 55353 hgsc.bcm.edu hg19 8 98788210 98788210 + Silent SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . LAPTM4B NM_018407 exon1 c.G246A p.A82A TTGCGCGCGCGCT . 38.0 10.0 63.0 0.0 . 26 . . . none . . PASS Atlas-SNP SMC2 10592 hgsc.bcm.edu hg19 9 106882315 106882315 + Silent SNP A A T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SMC2 NM_006444 exon16 c.A2004T p.R668R TGCTCGATCCCAG . 84.0 17.0 75.0 0.0 . 127 . . . none . . PASS Atlas-SNP SH2D3C 10044 hgsc.bcm.edu hg19 9 130511796 130511796 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SH2D3C NM_170600 exon5 c.A833G p.Y278C TGTGTGTAGCTCT . 73.0 25.0 89.0 0.0 . 102 . . . none . . PASS Atlas-SNP HERC4 26091 hgsc.bcm.edu hg19 10 69749982 69749982 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . HERC4 NM_022079 exon14 c.C1619T p.P540L TTCAGTGGTGCCT . 47.0 11.0 30.0 0.0 . 78 . . . none . . PASS Atlas-SNP PPA1 5464 hgsc.bcm.edu hg19 10 71974287 71974287 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PPA1 NM_021129 exon5 c.A353G p.D118G ATTGGGTCATTGT . 46.0 11.0 65.0 0.0 . 24 . . . none . . PASS Atlas-SNP CDH23 64072 hgsc.bcm.edu hg19 10 73572275 73572275 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CDH23 NM_022124 exon65 c.T9419A p.L3140Q GGAACCTGGAGCT . 57.0 20.0 101.0 0.0 . 365 . . . none . . PASS Atlas-SNP TNKS2 80351 hgsc.bcm.edu hg19 10 93588096 93588096 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed TNKS2,rectum,carcinoma,0,1 TNKS2 NM_025235 exon9 c.G1037A p.R346Q TTACTCGAATCAA . 213.0 53.0 132.0 2.0 . 103 . . . none . . PASS Atlas-SNP LCOR 84458 hgsc.bcm.edu hg19 10 98715299 98715299 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . LCOR NM_001170766 exon8 c.G922C p.G308R GATGCTGGACCCG . 142.0 33.0 116.0 0.0 . 32 . . . none . . PASS Atlas-SNP TRIM8 81603 hgsc.bcm.edu hg19 10 104404444 104404444 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TRIM8 NM_030912 exon1 c.G70A p.E24K TTCGTGGAGCCAG . 153.0 33.0 231.0 0.0 . 35 . . . none . . PASS Atlas-SNP OR51E2 81285 hgsc.bcm.edu hg19 11 4703309 4703309 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . OR51E2 NM_030774 exon2 c.G633A p.M211I GATGAACATTACG . 88.0 18.0 140.0 0.0 . 77 . . . none . . PASS Atlas-SNP TUT1 64852 hgsc.bcm.edu hg19 11 62346467 62346467 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TUT1 NM_022830 exon5 c.C840A p.D280E GGCCGAGTCCAGC . 108.0 23.0 135.0 0.0 . 122 . . . none . . PASS Atlas-SNP CTSF 8722 hgsc.bcm.edu hg19 11 66332038 66332038 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CTSF NM_003793 exon11 c.T1312C p.Y438H TGCCGTAGCCCAC . 104.0 19.0 148.0 0.0 . 42 . . . none . . PASS Atlas-SNP ATM 472 hgsc.bcm.edu hg19 11 108178695 108178695 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed ATM_ENST00000278616,colon,carcinoma,0,4 ATM NM_000051 exon38 c.A5746G p.M1916V GACTACATGAGAA . 57.0 4.0 70.0 0.0 . 1657 . . . none . . PASS Atlas-SNP ALG9 79796 hgsc.bcm.edu hg19 11 111707006 111707006 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ALG9 NM_024740 exon14 c.A1484T p.Q495L ATGAACTGAAGCT . 51.0 10.0 70.0 0.0 . 77 . . . none . . PASS Atlas-SNP CACNA1C 775 hgsc.bcm.edu hg19 12 2602503 2602503 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CACNA1C NM_001129831 exon7 c.C1064T p.T355M TGCTCACGGTGTT . 96.0 21.0 137.0 0.0 . 1023 . . . none . . PASS Atlas-SNP TAS2R31 259290 hgsc.bcm.edu hg19 12 11183487 11183487 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TAS2R31 NM_176885 exon1 c.A448G p.K150E TCTCTTTCATGTT . 173.0 37.0 174.0 0.0 . 24 . . . none . . PASS Atlas-SNP LRRK2 120892 hgsc.bcm.edu hg19 12 40757356 40757356 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . LRRK2 NM_198578 exon48 c.G7181T p.R2394M TTTTAAGGTAAAT . 73.0 4.0 38.0 0.0 . 763 . . . none . . PASS Atlas-SNP ADCY6 112 hgsc.bcm.edu hg19 12 49171000 49171000 + Silent SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ADCY6 NM_020983 exon6 c.G1263A p.L421L GATCCTCAGGCAG . 37.0 6.0 68.0 0.0 . 81 . . . none . . PASS Atlas-SNP XPOT 11260 hgsc.bcm.edu hg19 12 64825465 64825465 + Silent SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . XPOT NM_007235 exon18 c.T2124A p.L708L TTTCCTTCATCGA . 108.0 27.0 90.0 0.0 . 105 . . . none . . PASS Atlas-SNP TPH2 121278 hgsc.bcm.edu hg19 12 72335374 72335374 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TPH2 NM_173353 exon2 c.C116G p.P39R ATAAACCTAACTC . 62.0 16.0 43.0 0.0 . 81 . . . none . . PASS Atlas-SNP IPO4 79711 hgsc.bcm.edu hg19 14 24651547 24651547 + Silent SNP C C A rs374946858 alternate_allele TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . IPO4 NM_024658 exon25 c.G2535T p.A845A CCCAGCCGCGGCT . 135.0 35.0 229.0 0.0 . 74 . . . alt . . PASS Atlas-SNP CREBBP 1387 hgsc.bcm.edu hg19 16 3778974 3778974 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CREBBP NM_004380 exon31 c.C6074A p.P2025H GGAAGGGGCGCCT . 32.0 8.0 67.0 0.0 . 546 . . . none . . PASS Atlas-SNP MARVELD3 91862 hgsc.bcm.edu hg19 16 71668183 71668183 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed MARVELD3_ENST00000268485,lower_third,carcinoma,0,1 MARVELD3 NM_052858 exon3 c.G683C p.G228A ACACGGGCATCAC . 59.0 16.0 87.0 0.0 . 63 . . . none . . PASS Atlas-SNP ANKRD11 29123 hgsc.bcm.edu hg19 16 89341269 89341269 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ANKRD11 NM_001256183 exon11 c.A7666G p.T2556A GCATCGTGCAGGC . 65.0 12.0 94.0 0.0 . 195 . . . none . . PASS Atlas-SNP SMYD4 114826 hgsc.bcm.edu hg19 17 1687738 1687738 + Silent SNP G G C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SMYD4 NM_052928 exon8 c.C1902G p.R634R GCCACAGCGCAGC . 62.0 14.0 88.0 0.0 . 50 . . . none . . PASS Atlas-SNP PAFAH1B1 5048 hgsc.bcm.edu hg19 17 2577395 2577395 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . PAFAH1B1 NM_000430 exon8 c.G713A p.R238H GGGTACGTATGGT . 267.0 20.0 373.0 0.0 . 26 . . . none . . PASS Atlas-SNP GLP2R 9340 hgsc.bcm.edu hg19 17 9792980 9792980 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . GLP2R NM_004246 exon13 c.G1620A p.M540I CACCATGGCCAAC . 73.0 31.0 96.0 0.0 . 90 . . . none . . PASS Atlas-SNP MYO18A 399687 hgsc.bcm.edu hg19 17 27437065 27437065 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . MYO18A NM_078471 exon19 c.C3142G p.L1048V CAGGCAGGAAGCA . 66.0 19.0 85.0 0.0 . 217 . . . none . . PASS Atlas-SNP RNF213 57674 hgsc.bcm.edu hg19 17 78321044 78321044 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . RNF213 NM_001256071 exon29 c.C8909T p.S2970L AGGCTTCAAATAG . 84.0 17.0 86.0 0.0 . 766 . . . none . . PASS Atlas-SNP ZCCHC2 54877 hgsc.bcm.edu hg19 18 60241523 60241523 + Missense_Mutation SNP G G A rs377112503 TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ZCCHC2 NM_017742 exon13 c.G2209A p.V737I GTTGTCGTTCCTG . 117.0 25.0 121.0 0.0 . 64 . . . weak . . PASS Atlas-SNP CD226 10666 hgsc.bcm.edu hg19 18 67614032 67614032 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CD226 NM_006566 exon3 c.C320T p.S107F GAGCAGGAATAGT . 167.0 39.0 192.0 0.0 . 51 . . . none . . PASS Atlas-SNP SALL3 27164 hgsc.bcm.edu hg19 18 76753052 76753052 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SALL3 NM_171999 exon2 c.C1061T p.A354V TGGGTGCGGCGCC . 54.0 11.0 84.0 0.0 . 162 . . . none . . PASS Atlas-SNP ZNF823 55552 hgsc.bcm.edu hg19 19 11833714 11833714 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ZNF823 NM_001080493 exon4 c.G635T p.R212I TGTGTTCTTTCGT . 95.0 25.0 80.0 0.0 . 104 . . . none . . PASS Atlas-SNP ZNF546 339327 hgsc.bcm.edu hg19 19 40521590 40521590 + Missense_Mutation SNP T T C rs371824172 alternate_allele TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ZNF546 NM_178544 exon7 c.T2413C p.Y805H AAACCCTATCAAT . 172.0 43.0 180.0 0.0 . 93 . . . alt . . PASS Atlas-SNP ZNF534 147658 hgsc.bcm.edu hg19 19 52941686 52941686 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed ZNF534_ENST00000332323,NS,carcinoma,0,1 ZNF534 NM_001143939 exon4 c.C1012T p.P338S GAGAAACCTTATG . 79.0 28.0 72.0 0.0 . 105 . . . none . . PASS Atlas-SNP CEP250 11190 hgsc.bcm.edu hg19 20 34091233 34091233 + Missense_Mutation SNP A A T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CEP250 NM_007186 exon30 c.A5036T p.K1679M AGACCAAGATCCT . 111.0 20.0 171.0 0.0 . 141 . . . none . . PASS Atlas-SNP DIDO1 11083 hgsc.bcm.edu hg19 20 61528138 61528138 + Missense_Mutation SNP A A T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . DIDO1 NM_080797 exon7 c.T1799A p.L600H GCGGAGAGCCATG . 82.0 15.0 120.0 0.0 . 321 . . . none . . PASS Atlas-SNP HELZ2 85441 hgsc.bcm.edu hg19 20 62191860 62191860 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . . NM_001037335 exon17 c.A7472T p.K2491M TTGGCCTTGGAGT . 28.0 7.0 49.0 0.0 . . . . . none . . PASS Atlas-SNP HELZ2 85441 hgsc.bcm.edu hg19 20 62202151 62202151 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . . NM_001037335 exon3 c.C349T p.R117W TGCGCCGGACCCA . 101.0 20.0 162.0 0.0 . . . . . none . . PASS Atlas-SNP YWHAH 7533 hgsc.bcm.edu hg19 22 32352566 32352566 + Silent SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . YWHAH NM_003405 exon2 c.C528T p.A176A CCTGGCCCTCAAC . 61.0 18.0 90.0 0.0 . 14 . . . none . . PASS Atlas-SNP DDX17 10521 hgsc.bcm.edu hg19 22 38897263 38897263 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . DDX17 NM_006386 exon2 c.G310T p.G104C GAAGGCCACCACC . 108.0 28.0 85.0 0.0 . 73 . . . none . . PASS Atlas-SNP LDOC1L 84247 hgsc.bcm.edu hg19 22 44892956 44892956 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . LDOC1L NM_032287 exon2 c.C481G p.P161A GCAAGGGGCTGTC . 63.0 17.0 114.0 0.0 . 24 . . . none . . PASS Atlas-SNP TAF7L 54457 hgsc.bcm.edu hg19 X 100533091 100533091 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . TAF7L NM_024885 exon8 c.G781A p.V261M TTTCCACGTCTGG . 26.0 6.0 32.0 0.0 . 64 . . . none . . PASS Atlas-SNP GLRA4 441509 hgsc.bcm.edu hg19 X 102979831 102979831 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . GLRA4 NM_001024452 exon2 c.T197C p.F66S CCTTTAAAATTGG . 46.0 23.0 53.0 0.0 . 86 . . . none . . PASS Atlas-SNP BCORL1 63035 hgsc.bcm.edu hg19 X 129189870 129189870 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . BCORL1 NM_021946 exon12 c.T4895G p.L1632R AGAGGCTGAAGCT . 52.0 28.0 70.0 0.0 . 213 . . . none . . PASS Atlas-SNP ND5 0 hgsc.bcm.edu hg19 MT 13721 13721 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . . ENST00000361567 exon1 c.T1385C p.L462P GAAGCCTATTCGC . 33.0 5.0 13.0 0.0 . . . . . none . . PASS Atlas-SNP CPSF6 11052 hgsc.bcm.edu hg19 12 69656194 69656194 + Frame_Shift_Del DEL A A - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CPSF6 NM_007007 exon9 c.1510delG p.E504fs . . 103.0 35.0 145.0 0.0 . 96 . 0.339806 0 none . . PASS Atlas-Indel,Pindel EIF2AK3 9451 hgsc.bcm.edu hg19 2 88926504 88926505 + Frame_Shift_Ins INS - - T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . EIF2AK3 NM_004836 exon1 c.289_290insA p.E97fs . . 219.0 50.0 476.0 0.0 . 160 . 0.22831 0 none . . PASS Atlas-Indel,Pindel EME1 146956 hgsc.bcm.edu hg19 17 48452912 48452918 + Frame_Shift_Del DEL TCTAGCT TCTAGCT - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 TCTAGCT TCTAGCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . EME1 NM_152463 exon2 c.342_348del p.114_116del . . 112.0 19.0 162.0 0.0 . 39 . 0.169643 0 none . . PASS Atlas-Indel,Pindel DOCK2 1794 hgsc.bcm.edu hg19 5 169463521 169463521 + Frame_Shift_Del DEL T T - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . DOCK2 NM_004946 exon36 c.3626delA p.N1209fs . . 70.0 31.0 93.0 0.0 . 389 . 0.442857 0 none . . PASS Atlas-INDEL C15orf39 56905 hgsc.bcm.edu hg19 15 75499492 75499494 + In_Frame_Del DEL CAT CAT - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 CAT CAT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed C15orf39,colon,carcinoma,0,1 C15orf39 NM_015492 exon2 c.1102_1104del p.368_368del . . 104.0 34.0 149.0 0.0 . 64 . 0.326923 0 none . . PASS Atlas-Indel,Pindel KLHL15 80311 hgsc.bcm.edu hg19 X 24006241 24006241 + Frame_Shift_Del DEL T T - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . KLHL15 NM_030624 exon4 c.1613delC p.T538fs . . 137.0 65.0 117.0 0.0 . 50 . 0.474453 0 none . . PASS Atlas-Indel,Pindel BAP1 8314 hgsc.bcm.edu hg19 3 52441229 52441230 + Frame_Shift_Del DEL AG AG - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 AG AG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . BAP1 NM_004656 exon7 c.541_542del p.181_181del . . 67.0 23.0 172.0 0.0 . 371 . 0.343284 0 none . . PASS Atlas-Indel,Pindel SEMA6A 57556 hgsc.bcm.edu hg19 5 115803312 115803312 + Frame_Shift_Del DEL C C - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . SEMA6A NM_020796 exon18 c.1862delC p.A621fs . . 90.0 12.0 84.0 0.0 . 93 . 0.133333 0 none . . PASS Atlas-INDEL CMYA5 202333 hgsc.bcm.edu hg19 5 79041105 79041106 + Frame_Shift_Ins INS - - T novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . CMYA5 NM_153610 exon4 c.10795_10796insT p.V3599fs . . 348.0 28.0 444.0 0.0 . 643 . 0.0804598 0 none . . PASS Atlas-Indel,Pindel ATG14 22863 hgsc.bcm.edu hg19 14 55836392 55836395 + Frame_Shift_Del DEL GAGA GAGA - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 GAGA GAGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . ATG14 NM_014924 exon10 c.1422_1425del p.474_475del . . 75.0 29.0 182.0 0.0 . 36 . 0.386667 0 none . . PASS Atlas-Indel,Pindel VKORC1L1 154807 hgsc.bcm.edu hg19 7 65413712 65413713 + Frame_Shift_Del DEL AA AA - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 AA AA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . VKORC1L1 NM_173517 exon2 c.248_249del p.83_83del . . 763.0 78.0 894.0 0.0 . 14 . 0.102228 0 none . . PASS Atlas-INDEL DOCK2 1794 hgsc.bcm.edu hg19 5 169463522 169463523 + Frame_Shift_Del DEL TT TT - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 TT TT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . DOCK2 NM_004946 exon36 c.3627_3628del p.1209_1210del . . 72.0 26.0 96.0 0.0 . 389 . 0.361 . none . . PASS Pindel MUC4 4585 hgsc.bcm.edu hg19 3 195510678 195510773 + In_Frame_Del DEL GGTGGTGTCACCTGTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCTGTGGATGCTGCGGAAGTGTCGGTGACAGGAAGAGA GGTGGTGTCACCTGTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCTGTGGATGCTGCGGAAGTGTCGGTGACAGGAAGAGA - novel TCGA-2Z-A9JK-01A-11D-A42J-10 TCGA-2Z-A9JK-10A-01D-A42M-10 GGTGGTGTCACCTGTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCTGTGGATGCTGCGGAAGTGTCGGTGACAGGAAGAGA GGTGGTGTCACCTGTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCTGTGGATGCTGCGGAAGTGTCGGTGACAGGAAGAGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d3603eaf-6e76-43f5-b87f-ab5d8e0f825f 8d7349a0-4f31-4374-9461-c37dd99f05ed . MUC4 NM_018406 exon2 c.7679_7774del p.2560_2592del . . 225.0 12.0 364.0 0.0 . 1505 . 0.053 . none . . PASS Pindel