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 ZMYM6 9204 hgsc.bcm.edu hg19 1 35453206 35453206 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ZMYM6 NM_007167 exon16 c.A3477G p.Q1159Q ATTCTCTTGTGTG . 266.0 91.0 325.0 0.0 . 110 . . . none . . PASS Atlas-SNP SZT2 23334 hgsc.bcm.edu hg19 1 43907699 43907699 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SZT2 NM_015284 exon55 c.T7600C p.C2534R GGCCCTTGTTCCC . 100.0 39.0 96.0 0.0 . 383 . . . none . . PASS Atlas-SNP AGBL4 84871 hgsc.bcm.edu hg19 1 49100226 49100226 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . AGBL4 NM_032785 exon9 c.C890T p.P297L ACCCATGGAGAGG . 103.0 5.0 34.0 0.0 . 54 . . . none . . PASS Atlas-SNP ALG14 199857 hgsc.bcm.edu hg19 1 95448663 95448663 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ALG14 NM_144988 exon4 c.C620A p.P207H GATTTGGGATACT . 97.0 36.0 62.0 0.0 . 13 . . . none . . PASS Atlas-SNP COL11A1 1301 hgsc.bcm.edu hg19 1 103461460 103461460 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 COL11A1_ENST00000370096,NS,carcinoma,0,2 COL11A1 NM_080629 exon28 c.C2336G p.A779G CCATCTGCTCCCT . 184.0 10.0 115.0 0.0 . 972 . . . none . . PASS Atlas-SNP LRIG2 9860 hgsc.bcm.edu hg19 1 113661942 113661942 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . LRIG2 NM_014813 exon17 c.A2768G p.Y923C ACACCTATATTGC . 118.0 8.0 103.0 0.0 . 67 . . . none . . PASS Atlas-SNP FLG2 388698 hgsc.bcm.edu hg19 1 152324407 152324407 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . FLG2 NM_001014342 exon3 c.G5855A p.G1952E CCAGATCCCCTTC . 69.0 31.0 31.0 0.0 . 431 . . . none . . PASS Atlas-SNP ADAM15 8751 hgsc.bcm.edu hg19 1 155028274 155028274 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ADAM15 NM_001261464 exon7 c.T651G p.D217E GCGGGATGTGGTA . 86.0 32.0 96.0 0.0 . 92 . . . none . . PASS Atlas-SNP EFNA1 1942 hgsc.bcm.edu hg19 1 155106478 155106478 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . EFNA1 NM_004428 exon5 c.C553A p.P185T GCTGCCCCACGCC . 47.0 14.0 64.0 0.0 . 10 . . . none . . PASS Atlas-SNP FDPS 2224 hgsc.bcm.edu hg19 1 155279709 155279709 + Silent SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . FDPS NM_001135821 exon2 c.C129T p.A43A CCTGGCCTGGCAC . 75.0 33.0 87.0 0.0 . 41 . . . none . . PASS Atlas-SNP OR10K2 391107 hgsc.bcm.edu hg19 1 158390085 158390085 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . OR10K2 NM_001004476 exon1 c.A572G p.H191R TGGTTATGGTGAG . 127.0 8.0 57.0 0.0 . 69 . . . none . . PASS Atlas-SNP SPTA1 6708 hgsc.bcm.edu hg19 1 158592846 158592846 + Missense_Mutation SNP C C T rs199993378 bycluster TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 SPTA1,colon,carcinoma,0,2 SPTA1 NM_003126 exon43 c.G6047A p.R2016H TCCCAGCGCTTCA . 124.0 40.0 74.0 0.0 . 720 . . . weak . . PASS Atlas-SNP MAPKAPK2 9261 hgsc.bcm.edu hg19 1 206905963 206905963 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . MAPKAPK2 NM_032960 exon10 c.A1103G p.E368G ACTACGAGCAGAT . 199.0 64.0 232.0 0.0 . 45 . . . none . . PASS Atlas-SNP DNAH14 127602 hgsc.bcm.edu hg19 1 225445671 225445671 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DNAH14 NM_001373 exon45 c.T6857C p.L2286S CTTCATTACTAAC . 64.0 31.0 64.0 0.0 . 300 . . . none . . PASS Atlas-SNP OR2T34 127068 hgsc.bcm.edu hg19 1 248737994 248737994 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . OR2T34 NM_001001821 exon1 c.T65C p.L22P GCAAAGAGTCCCG . 429.0 111.0 223.0 0.0 . 72 . . . none . . PASS Atlas-SNP OR2T34 127068 hgsc.bcm.edu hg19 1 248737995 248737995 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . OR2T34 NM_001001821 exon1 c.C64A p.L22I CAAAGAGTCCCGT . 429.0 110.0 219.0 0.0 . 72 . . . none . . PASS Atlas-SNP OR2T34 127068 hgsc.bcm.edu hg19 1 248738035 248738035 + Silent SNP A A C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . OR2T34 NM_001001821 exon1 c.T24G p.S8S ATTCTGAGAAGTC . 391.0 118.0 204.0 0.0 . 72 . . . none . . PASS Atlas-SNP GREB1 9687 hgsc.bcm.edu hg19 2 11758487 11758487 + Silent SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . GREB1 NM_014668 exon22 c.G3486A p.Q1162Q GCCCCAGCCCCGT . 113.0 38.0 224.0 0.0 . 308 . . . none . . PASS Atlas-SNP DNAJC5G 285126 hgsc.bcm.edu hg19 2 27500849 27500849 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DNAJC5G NM_173650 exon4 c.G341C p.R114T GCGTCAGATACTA . 149.0 53.0 120.0 0.0 . 19 . . . none . . PASS Atlas-SNP AQP12B 653437 hgsc.bcm.edu hg19 2 241622206 241622206 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . AQP12B NM_001102467 exon1 c.C49A p.L17I CACAGAGGGTGAA . 64.0 44.0 109.0 0.0 . 33 . . . none . . PASS Atlas-SNP BAP1 8314 hgsc.bcm.edu hg19 3 52437657 52437657 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . BAP1 NM_004656 exon13 c.G1504C p.A502P TGAAAGCACTGCC . 50.0 41.0 108.0 0.0 . 371 . . . none . . PASS Atlas-SNP CACNA1D 776 hgsc.bcm.edu hg19 3 53684852 53684852 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CACNA1D NM_001128840 exon4 c.T530G p.F177C AGACATTTTTGAA . 66.0 57.0 44.0 0.0 . 324 . . . none . . PASS Atlas-SNP CCDC39 339829 hgsc.bcm.edu hg19 3 180334122 180334122 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CCDC39 NM_181426 exon19 c.A2616G p.T872T GCCTTTTGTGCTA . 102.0 70.0 45.0 0.0 . 242 . . . none . . PASS Atlas-SNP ZNF141 7700 hgsc.bcm.edu hg19 4 366865 366865 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ZNF141 NM_003441 exon4 c.A639G p.I213M TTTAATATTTAAT . 77.0 33.0 59.0 0.0 . 48 . . . none . . PASS Atlas-SNP LOC650293 0 hgsc.bcm.edu hg19 4 8951827 8951827 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_001040071 exon1 c.C351G p.F117L CTTTTTCCTTAGC . 8.0 4.0 5.0 0.0 . . . . . none . . PASS Atlas-SNP KIAA1239 57495 hgsc.bcm.edu hg19 4 37445619 37445619 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . KIAA1239 NM_001144990 exon7 c.T2009C p.M670T CCAAAATGGGTCT . 143.0 54.0 81.0 0.0 . 79 . . . none . . PASS Atlas-SNP N4BP2 55728 hgsc.bcm.edu hg19 4 40121601 40121601 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . N4BP2 NM_018177 exon9 c.T1870C p.S624P ATTTTATCTTTAT . 257.0 92.0 182.0 0.0 . 166 . . . none . . PASS Atlas-SNP SHROOM3 57619 hgsc.bcm.edu hg19 4 77660481 77660481 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SHROOM3 NM_020859 exon5 c.T1155C p.P385P CCTGCCTCCAGCT . 91.0 33.0 113.0 0.0 . 134 . . . none . . PASS Atlas-SNP IL6ST 3572 hgsc.bcm.edu hg19 5 55247359 55247359 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . IL6ST NM_002184 exon14 c.A1773G p.R591R TGCCATTCGTACC . 51.0 17.0 36.0 0.0 . 75 . . . none . . PASS Atlas-SNP GFM2 84340 hgsc.bcm.edu hg19 5 74017604 74017604 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . GFM2 NM_032380 exon21 c.A2216G p.Y739C GTTGAATAACCCT . 65.0 32.0 36.0 0.0 . 38 . . . none . . PASS Atlas-SNP PCDHGB2 56103 hgsc.bcm.edu hg19 5 140741837 140741837 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PCDHGB2 NM_018923 exon1 c.C2135T p.S712F CAATCTCCCTGCG . 92.0 10.0 163.0 0.0 . 196 . . . none . . PASS Atlas-SNP PCDHGB6 56100 hgsc.bcm.edu hg19 5 140788766 140788766 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PCDHGB6 NM_032100 exon1 c.G997T p.V333L TGTAAAGTAATCA . 131.0 54.0 263.0 0.0 . 120 . . . none . . PASS Atlas-SNP ARHGAP26 23092 hgsc.bcm.edu hg19 5 142281604 142281604 + Missense_Mutation SNP C C A rs142837036 alternate_allele TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 ARHGAP26,colon,carcinoma,+1,1 ARHGAP26 NM_015071 exon7 c.C702A p.N234K ACAGAACGTGAGT . 119.0 40.0 47.0 0.0 . 57 . . . alt C|1.000;T|0.000 . PASS Atlas-SNP FAXDC2 10826 hgsc.bcm.edu hg19 5 154200926 154200926 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_032385 exon8 c.A739G p.I247V TGGTGATGGAGGA . 139.0 52.0 61.0 0.0 . . . . . none . . PASS Atlas-SNP DOCK2 1794 hgsc.bcm.edu hg19 5 169127100 169127100 + Silent SNP C C A rs141406325 bycluster;byfrequency;by1000genomes;alternate_allele TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DOCK2 NM_004946 exon13 c.C1215A p.T405T GACCACCGTGGTG . 74.0 25.0 20.0 0.0 . 389 . . . alt C|0.999;T|0.001 . PASS Atlas-SNP PGC 5225 hgsc.bcm.edu hg19 6 41712458 41712458 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PGC NM_002630 exon2 c.C148G p.P50A AAGCAGGATCATA . 79.0 33.0 62.0 0.0 . 56 . . . none . . PASS Atlas-SNP CUL7 9820 hgsc.bcm.edu hg19 6 43020188 43020188 + Missense_Mutation SNP G G C rs4711738 bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes;alternate_allele TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CUL7 NM_001168370 exon2 c.C495G p.D165E CTTCACGTCGGTT . 51.0 19.0 74.0 0.0 . 133 . . . alt G|0.755;A|0.245 . PASS Atlas-SNP PKHD1 5314 hgsc.bcm.edu hg19 6 51523921 51523921 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PKHD1 NM_138694 exon61 c.A11003T p.D3668V GGCGAATCACCAA . 69.0 25.0 21.0 0.0 . 927 . . . none . . PASS Atlas-SNP COL19A1 1310 hgsc.bcm.edu hg19 6 70850849 70850849 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . COL19A1 NM_001858 exon20 c.G1450C p.E484Q TAGGGAGAGCCTT . 91.0 28.0 32.0 0.0 . 232 . . . none . . PASS Atlas-SNP EEF1A1 1915 hgsc.bcm.edu hg19 6 74227637 74227637 + Missense_Mutation SNP T T C rs9718686 bycluster TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . EEF1A1 NM_001402 exon8 c.A1285G p.M429V GTCTCATATCACG . 339.0 134.0 335.0 0.0 . 56 . . . weak . . PASS Atlas-SNP LATS1 9113 hgsc.bcm.edu hg19 6 150004253 150004253 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . LATS1 NM_001270519 exon4 c.C1972G p.L658V GATGTAGACGCTG . 80.0 24.0 58.0 0.0 . 241 . . . none . . PASS Atlas-SNP KIAA1324L 222223 hgsc.bcm.edu hg19 7 86568242 86568242 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . KIAA1324L NM_001142749 exon7 c.G882T p.K294N GCCTGGCTTGCAA . 78.0 40.0 28.0 0.0 . 225 . . . none . . PASS Atlas-SNP PON1 5444 hgsc.bcm.edu hg19 7 94931604 94931604 + Missense_Mutation SNP A A T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PON1 NM_000446 exon8 c.T822A p.D274E CTCAGGATCCACA . 86.0 15.0 45.0 0.0 . 55 . . . none . . PASS Atlas-SNP TMEM139 135932 hgsc.bcm.edu hg19 7 142983809 142983809 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . TMEM139 NM_001242773 exon4 c.T538C p.L180L CAGAGCTTGGCGG . 128.0 39.0 102.0 0.0 . 18 . . . none . . PASS Atlas-SNP CLCN1 1180 hgsc.bcm.edu hg19 7 143047464 143047464 + Splice_Site SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CLCN1 NM_000083 exon21 c.2404-1G>T . CTGACAGATTGAG . 77.0 46.0 59.0 0.0 . 141 . . . none . . PASS Atlas-SNP MTUS1 57509 hgsc.bcm.edu hg19 8 17613134 17613134 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . MTUS1 NM_001001924 exon2 c.C183G p.D61E AGCAGGGTCAGTT . 105.0 13.0 100.0 0.0 . 144 . . . none . . PASS Atlas-SNP SNAI2 6591 hgsc.bcm.edu hg19 8 49831524 49831524 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SNAI2 NM_003068 exon3 c.C649A p.H217N TGCAGTGAGGGCA . 38.0 10.0 33.0 0.0 . 53 . . . none . . PASS Atlas-SNP CRH 1392 hgsc.bcm.edu hg19 8 67089639 67089639 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CRH NM_000756 exon2 c.T74C p.L25P CTCAGGAGCGCCC . 50.0 19.0 100.0 0.0 . 8 . . . none . . PASS Atlas-SNP ESRP1 54845 hgsc.bcm.edu hg19 8 95653652 95653652 + Nonsense_Mutation SNP A A T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ESRP1 NM_001122827 exon1 c.A106T p.K36X TTCTGGAAAGTCG . 57.0 28.0 88.0 0.0 . 148 . . . none . . PASS Atlas-SNP OXR1 55074 hgsc.bcm.edu hg19 8 107670240 107670240 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . OXR1 NM_181354 exon1 c.A26G p.E9G TCACCGAGAAGAG . 217.0 89.0 413.0 0.0 . 190 . . . none . . PASS Atlas-SNP EBAG9 9166 hgsc.bcm.edu hg19 8 110567083 110567083 + Missense_Mutation SNP G G T rs370306388 alternate_allele TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . EBAG9 NM_004215 exon4 c.G288T p.K96N TTTTAAGGACATG . 114.0 5.0 36.0 0.0 . 23 . . . alt . . PASS Atlas-SNP ZFAT 57623 hgsc.bcm.edu hg19 8 135521962 135521962 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ZFAT NM_020863 exon15 c.T3392C p.I1131T TGCAGGATGTTCA . 40.0 15.0 53.0 0.0 . 265 . . . none . . PASS Atlas-SNP PTK2 5747 hgsc.bcm.edu hg19 8 141685559 141685559 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PTK2 NM_005607 exon28 c.G2668A p.D890N CTTTACCTGGTTT . 86.0 32.0 85.0 0.0 . 311 . . . none . . PASS Atlas-SNP GPT 2875 hgsc.bcm.edu hg19 8 145732381 145732381 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . GPT NM_005309 exon11 c.T1489C p.X497R TACTCCTGAGCAC . 86.0 32.0 135.0 0.0 . 31 . . . none . . PASS Atlas-SNP SMARCA2 6595 hgsc.bcm.edu hg19 9 2115822 2115822 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SMARCA2 NM_139045 exon25 c.G3457C p.D1153H AAACAGGATCTGC . 236.0 84.0 130.0 0.0 . 313 . . . none . . PASS Atlas-SNP TLN1 7094 hgsc.bcm.edu hg19 9 35706215 35706215 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . TLN1 NM_006289 exon40 c.A5339G p.K1780R GCCTCCTTGGCAG . 32.0 7.0 29.0 0.0 . 185 . . . none . . PASS Atlas-SNP TJP2 9414 hgsc.bcm.edu hg19 9 71855017 71855017 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . TJP2 NM_001170416 exon17 c.T2613G p.F871L GTTATTTGATCAA . 74.0 14.0 50.0 0.0 . 120 . . . none . . PASS Atlas-SNP TMEM245 23731 hgsc.bcm.edu hg19 9 111849612 111849612 + Silent SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_032012 exon6 c.C1161T p.L387L CTTTTTGAGTATC . 64.0 23.0 35.0 0.0 . . . . . none . . PASS Atlas-SNP DENND1A 57706 hgsc.bcm.edu hg19 9 126143930 126143930 + Silent SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DENND1A NM_020946 exon22 c.G2811A p.K937K CCCCTGCTTGGTC . 91.0 24.0 176.0 0.0 . 112 . . . none . . PASS Atlas-SNP ABL1 25 hgsc.bcm.edu hg19 9 133748374 133748374 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ABL1 NM_007313 exon6 c.T1092C p.T364T GGCCACTCAGATC . 105.0 34.0 71.0 0.0 . 1632 . . . none . . PASS Atlas-SNP PPP1R26 9858 hgsc.bcm.edu hg19 9 138379517 138379517 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_014811 exon4 c.G3161C p.G1054A GGGGGGGCGTCGG . 49.0 18.0 101.0 0.0 . . . . . none . . PASS Atlas-SNP SEC16A 9919 hgsc.bcm.edu hg19 9 139369535 139369535 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SEC16A NM_014866 exon3 c.T2533C p.F845L CAGAAAAGTTAAT . 57.0 18.0 101.0 0.0 . 249 . . . none . . PASS Atlas-SNP ATP5C1 509 hgsc.bcm.edu hg19 10 7842038 7842038 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ATP5C1 NM_001001973 exon6 c.T621C p.N207N CCTTAATACCGTT . 67.0 18.0 67.0 0.0 . 32 . . . none . . PASS Atlas-SNP ARID5B 84159 hgsc.bcm.edu hg19 10 63851119 63851119 + Silent SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ARID5B NM_032199 exon10 c.C1897T p.L633L GACCAGCTGGGCA . 140.0 53.0 53.0 0.0 . 125 . . . none . . PASS Atlas-SNP PDZD8 118987 hgsc.bcm.edu hg19 10 119044910 119044910 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PDZD8 NM_173791 exon5 c.A1334G p.Y445C CTTTCATAGTACA . 82.0 34.0 62.0 0.0 . 85 . . . none . . PASS Atlas-SNP SFXN4 119559 hgsc.bcm.edu hg19 10 120919242 120919242 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SFXN4 NM_213649 exon6 c.A358T p.T120S TCACCGTGGGTGC . 89.0 50.0 61.0 0.0 . 24 . . . none . . PASS Atlas-SNP ACADSB 36 hgsc.bcm.edu hg19 10 124793964 124793964 + Silent SNP A A C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ACADSB NM_001609 exon2 c.A135C p.T45T TATAACAAATAAT . 26.0 10.0 29.0 0.0 . 45 . . . none . . PASS Atlas-SNP RRP8 23378 hgsc.bcm.edu hg19 11 6624661 6624661 + Silent SNP A A T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . RRP8 NM_015324 exon1 c.T72A p.P24P AGGCGGAGGTCGT . 76.0 27.0 154.0 0.0 . 40 . . . none . . PASS Atlas-SNP GLYAT 10249 hgsc.bcm.edu hg19 11 58482795 58482795 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . GLYAT NM_005838 exon3 c.G183T p.Q61H CTGCTCCTGAGGG . 29.0 8.0 5.0 0.0 . 53 . . . none . . PASS Atlas-SNP PLA2G16 11145 hgsc.bcm.edu hg19 11 63342507 63342507 + Silent SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PLA2G16 NM_001128203 exon5 c.C399T p.V133V GATGATGACATCT . 41.0 16.0 23.0 0.0 . 12 . . . none . . PASS Atlas-SNP RTN3 10313 hgsc.bcm.edu hg19 11 63487846 63487846 + Missense_Mutation SNP A A T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . RTN3 NM_001265589 exon3 c.A1872T p.E624D GACAGAATTCTCA . 75.0 31.0 58.0 0.0 . 104 . . . none . . PASS Atlas-SNP SAC3D1 29901 hgsc.bcm.edu hg19 11 64811959 64811959 + Silent SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SAC3D1 NM_013299 exon2 c.C837T p.V279V CATGGTCAACCTC . 53.0 26.0 79.0 0.0 . 13 . . . none . . PASS Atlas-SNP PPFIA1 8500 hgsc.bcm.edu hg19 11 70179622 70179622 + Missense_Mutation SNP A A C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PPFIA1 NM_177423 exon10 c.A1259C p.E420A AGATGGAAGCACA . 200.0 83.0 213.0 0.0 . 114 . . . none . . PASS Atlas-SNP KIAA1551 55196 hgsc.bcm.edu hg19 12 32134899 32134899 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_018169 exon4 c.T1010A p.F337Y GAAATTTCACTAA . 174.0 62.0 104.0 0.0 . . . . . none . . PASS Atlas-SNP GXYLT1 283464 hgsc.bcm.edu hg19 12 42481670 42481670 + Missense_Mutation SNP C C T rs200973030 bycluster TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 Q8IXV1_HUMAN,NS,carcinoma,-1,2 GXYLT1 NM_173601 exon8 c.G1241A p.C414Y TTTCCACAGTATG . 42.0 5.0 30.0 0.0 . 47 . . . weak . . PASS Atlas-SNP GXYLT1 283464 hgsc.bcm.edu hg19 12 42481671 42481671 + Missense_Mutation SNP A A G rs202200134 bycluster TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 Q8IXV1_HUMAN,NS,carcinoma,0,2 GXYLT1 NM_173601 exon8 c.T1240C p.C414R TTCCACAGTATGT . 42.0 5.0 31.0 0.0 . 47 . . . weak . . PASS Atlas-SNP KRT2 3849 hgsc.bcm.edu hg19 12 53040651 53040651 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 KRT2,NS,carcinoma,0,1 KRT2 NM_000423 exon7 c.G1342T p.A448S GCAGGGCCTCCTC . 38.0 13.0 30.0 1.0 . 94 . . . none . . PASS Atlas-SNP MTERFD3 80298 hgsc.bcm.edu hg19 12 107372223 107372223 + Silent SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . MTERFD3 NM_001033050 exon3 c.T270C p.D90D AGTCTCATCGGCA . 48.0 18.0 59.0 0.0 . 32 . . . none . . PASS Atlas-SNP CDADC1 81602 hgsc.bcm.edu hg19 13 49852539 49852539 + Silent SNP T T A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CDADC1 NM_030911 exon7 c.T1104A p.A368A CAATGCTTTTCCT . 79.0 31.0 53.0 0.0 . 40 . . . none . . PASS Atlas-SNP MYH6 4624 hgsc.bcm.edu hg19 14 23862152 23862152 + Missense_Mutation SNP C C T rs375169402 TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 MYH6,neck,malignant_melanoma,0,1 MYH6 NM_002471 exon24 c.G3220A p.D1074N GTTTATCATTTTC . 42.0 17.0 40.0 1.0 . 274 . . . weak . . PASS Atlas-SNP SIPA1L1 26037 hgsc.bcm.edu hg19 14 72200389 72200389 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SIPA1L1 NM_015556 exon19 c.T4931C p.F1644S GAGAGTTCTCAGC . 28.0 12.0 28.0 0.0 . 219 . . . none . . PASS Atlas-SNP COQ6 51004 hgsc.bcm.edu hg19 14 74422588 74422588 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . COQ6 NM_182476 exon4 c.T438C p.D146D GAATGATGTCATC . 29.0 12.0 38.0 0.0 . 27 . . . none . . PASS Atlas-SNP INO80 54617 hgsc.bcm.edu hg19 15 41313309 41313309 + Silent SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . INO80 NM_017553 exon26 c.A3063G p.P1021P ATCCAATGGCACT . 45.0 20.0 35.0 0.0 . 122 . . . none . . PASS Atlas-SNP GANC 2595 hgsc.bcm.edu hg19 15 42640335 42640335 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . GANC NM_198141 exon21 c.C2339A p.P780Q TGATACCAATAAA . 64.0 29.0 52.0 0.0 . 57 . . . none . . PASS Atlas-SNP SLC28A1 9154 hgsc.bcm.edu hg19 15 85438656 85438656 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SLC28A1 NM_201651 exon7 c.A509G p.Q170R TCCCTCAGATCAC . 123.0 55.0 104.0 0.0 . 118 . . . none . . PASS Atlas-SNP TMEM8A 58986 hgsc.bcm.edu hg19 16 426371 426371 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . TMEM8A NM_021259 exon6 c.C989T p.S330F CTCGGGGACAGCA . 57.0 27.0 110.0 0.0 . 49 . . . none . . PASS Atlas-SNP RHOT2 89941 hgsc.bcm.edu hg19 16 720472 720472 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . RHOT2 NM_138769 exon8 c.T455C p.L152P AGAACCTGAGGAA . 56.0 16.0 117.0 0.0 . 35 . . . none . . PASS Atlas-SNP DNAH3 55567 hgsc.bcm.edu hg19 16 21147803 21147803 + Missense_Mutation SNP C C T rs200178510 TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DNAH3 NM_017539 exon6 c.G728A p.R243H TCTTTGCGAATTC . 106.0 39.0 59.0 0.0 . 1142 . . . weak C|0.999;T|0.001 0.001 PASS Atlas-SNP E2F4 1874 hgsc.bcm.edu hg19 16 67226969 67226969 + Silent SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . E2F4 NM_001950 exon3 c.G303A p.K101K GCTCAAGGCAGAG . 40.0 17.0 64.0 0.0 . 25 . . . none . . PASS Atlas-SNP ZFHX3 463 hgsc.bcm.edu hg19 16 72845510 72845510 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ZFHX3 NM_006885 exon7 c.T3830C p.V1277A GGTGCCACGCTGT . 43.0 22.0 36.0 0.0 . 404 . . . none . . PASS Atlas-SNP DEF8 54849 hgsc.bcm.edu hg19 16 90021581 90021581 + Silent SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DEF8 NM_207514 exon4 c.C312A p.A104A AGAGGCCCTGCCT . 34.0 9.0 37.0 0.0 . 28 . . . none . . PASS Atlas-SNP SPAG7 9552 hgsc.bcm.edu hg19 17 4863151 4863151 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SPAG7 NM_004890 exon6 c.G478T p.A160S CGCTGGCAGGGCT . 54.0 12.0 31.0 0.0 . 22 . . . none . . PASS Atlas-SNP CLDN7 1366 hgsc.bcm.edu hg19 17 7164034 7164034 + Silent SNP A A G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CLDN7 NM_001307 exon3 c.T400C p.L134L CTACCAAGGCGGC . 123.0 29.0 124.0 0.0 . 11 . . . none . . PASS Atlas-SNP MPRIP 23164 hgsc.bcm.edu hg19 17 17049353 17049353 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 MPRIP,NS,carcinoma,0,1 MPRIP NM_015134 exon10 c.G1153A p.D385N CAGCCCGACCTGC . 114.0 35.0 80.0 0.0 . 87 . . . none . . PASS Atlas-SNP TSHZ1 10194 hgsc.bcm.edu hg19 18 72999615 72999615 + Silent SNP C C A novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . TSHZ1 NM_005786 exon2 c.C2118A p.S706S GCAGTCCATCATG . 63.0 24.0 91.0 0.0 . 104 . . . none . . PASS Atlas-SNP PODNL1 79883 hgsc.bcm.edu hg19 19 14063934 14063934 + Silent SNP G G T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PODNL1 NM_001146255 exon1 c.C15A p.T5T TACCTGGGTGGGC . 58.0 17.0 84.0 0.0 . 27 . . . none . . PASS Atlas-SNP LPHN1 22859 hgsc.bcm.edu hg19 19 14281546 14281546 + Silent SNP G G A rs149098258 TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . LPHN1 NM_001008701 exon4 c.C342T p.P114P AGGACAGGGGTCA . 91.0 43.0 104.0 0.0 . 107 . . . weak G|1.000;A|0.000 0.000 PASS Atlas-SNP ZBTB32 27033 hgsc.bcm.edu hg19 19 36205878 36205878 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ZBTB32 NM_014383 exon2 c.C350T p.A117V ACAGGGCTAAAAA . 99.0 42.0 92.0 0.0 . 33 . . . none . . PASS Atlas-SNP SIPA1L3 23094 hgsc.bcm.edu hg19 19 38684203 38684203 + Silent SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SIPA1L3 NM_015073 exon18 c.G4623C p.R1541R GCAGCGGACGCTG . 35.0 12.0 100.0 0.0 . 150 . . . none . . PASS Atlas-SNP ATP1A3 478 hgsc.bcm.edu hg19 19 42492528 42492528 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . ATP1A3 NM_001256214 exon3 c.C134G p.T45R TGCTCTGTCTGAG . 42.0 15.0 73.0 0.0 . 117 . . . none . . PASS Atlas-SNP RTN2 6253 hgsc.bcm.edu hg19 19 45991773 45991773 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . RTN2 NM_005619 exon9 c.G1453A p.V485M CAATCACTCCTGT . 85.0 7.0 83.0 0.0 . 45 . . . none . . PASS Atlas-SNP GRIN2D 2906 hgsc.bcm.edu hg19 19 48945411 48945411 + Missense_Mutation SNP G G C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . GRIN2D NM_000836 exon12 c.G2445C p.E815D AGATGAGATCGAG . 45.0 14.0 77.0 0.0 . 76 . . . none . . PASS Atlas-SNP RIPK4 54101 hgsc.bcm.edu hg19 21 43164161 43164161 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . RIPK4 NM_020639 exon7 c.A1076G p.E359G TTGGACTCAGAGG . 70.0 28.0 98.0 0.0 . 151 . . . none . . PASS Atlas-SNP SLITRK4 139065 hgsc.bcm.edu hg19 X 142718226 142718226 + Nonsense_Mutation SNP A A C novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SLITRK4 NM_001184750 exon2 c.T699G p.Y233X AATGTTATATGGC . 101.0 78.0 107.0 0.0 . 162 . . . none . . PASS Atlas-SNP MSH2 4436 hgsc.bcm.edu hg19 2 47637500 47637500 + Frame_Shift_Del DEL A A - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . MSH2 NM_000251 exon3 c.633delG p.G211fs . . 105.0 42.0 80.0 0.0 . 198 . 0.4 0 none . . PASS Atlas-Indel,Pindel CASC5 57082 hgsc.bcm.edu hg19 15 40915982 40915983 + Frame_Shift_Ins INS - - T novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . CASC5 NM_170589 exon11 c.3598_3599insT p.I1200fs . . 99.0 33.0 82.0 0.0 . 269 . 0.333333 0 none . . PASS Atlas-Indel,Pindel WDR81 124997 hgsc.bcm.edu hg19 17 1634093 1634093 + Frame_Shift_Del DEL C C - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . WDR81 NM_001163809 exon3 c.3819delA p.P1273fs . . 81.0 29.0 88.0 0.0 . 180 . 0.358025 0 none . . PASS Atlas-Indel,Pindel PDZK1 5174 hgsc.bcm.edu hg19 1 145756430 145756430 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . PDZK1 NM_002614 exon7 c.806delA p.K269fs . . 286.0 31.0 167.0 0.0 . 15 . 0.108392 0 none . . PASS Atlas-Indel,Pindel FBLN5 10516 hgsc.bcm.edu hg19 14 92336630 92336630 + Frame_Shift_Del DEL T T - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . FBLN5 NM_006329 exon11 c.1286delT p.I429fs . . 97.0 33.0 61.0 0.0 . 60 . 0.340206 0 none . . PASS Atlas-Indel,Pindel SWI5 375757 hgsc.bcm.edu hg19 9 131038966 131038966 + Frame_Shift_Del DEL C C - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_001040011 exon2 c.357delT p.F119fs . . 52.0 15.0 60.0 0.0 . . . 0.288462 0 none . . PASS Atlas-Indel,Pindel PRKAG2 51422 hgsc.bcm.edu hg19 7 151372596 151372597 + Frame_Shift_Ins INS - - G novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 .,4 PRKAG2 NM_016203 exon4 c.594_595insC p.P198fs . . 166.0 85.0 81.0 0.0 . 86 . 0.512048 0 none . . PASS Atlas-Indel,Pindel DYNC2LI1 51626 hgsc.bcm.edu hg19 2 44014392 44014392 + Splice_Site DEL A A - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . DYNC2LI1 NM_016008 exon4 c.231+2A>- . . . 83.0 27.0 53.0 0.0 . 46 . 0.325301 0 none . . PASS Atlas-Indel,Pindel EP400 57634 hgsc.bcm.edu hg19 12 132505838 132505838 + Frame_Shift_Del DEL C C - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . EP400 NM_015409 exon23 c.4661delT p.L1554fs . . 56.0 20.0 111.0 0.0 . 370 . 0.357143 0 none . . PASS Atlas-Indel,Pindel NUGGC 389643 hgsc.bcm.edu hg19 8 27931921 27931923 + In_Frame_Del DEL CTG CTG - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 CTG CTG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . NM_001010906 exon2 c.6_8del p.2_3del . . 59.0 12.0 32.0 0.0 . . . 0.20339 0 none . . PASS Atlas-Indel,Pindel LDB3 11155 hgsc.bcm.edu hg19 10 88441289 88441290 + Frame_Shift_Del DEL CC CC - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 CC CC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 LDB3_ENST00000429277,NS,carcinoma,0,3 LDB3 NM_001171611 exon4 c.417_418del p.139_140del . . 79.0 27.0 176.0 0.0 . 164 . 0.341772 0 none . . PASS Atlas-Indel,Pindel RERE 473 hgsc.bcm.edu hg19 1 8425963 8425975 + Frame_Shift_Del DEL CCTACGATGGGCT CCTACGATGGGCT - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 CCTACGATGGGCT CCTACGATGGGCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . RERE NM_012102 exon14 c.1345_1357del p.449_453del . . 54.0 14.0 70.0 0.0 . 129 . 0.259259 0 none . . PASS Atlas-Indel,Pindel SGK1 6446 hgsc.bcm.edu hg19 6 134494465 134494467 + In_Frame_Del DEL CTT CTT - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 CTT CTT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . SGK1 NM_001143676 exon7 c.648_650del p.216_217del . . 119.0 38.0 141.0 0.0 . 387 . 0.319328 0 none . . PASS Atlas-Indel,Pindel BAP1 8314 hgsc.bcm.edu hg19 3 52437652 52437652 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . BAP1 NM_004656 exon13 c.1510delA p.N504fs . . 50.0 39.0 112.0 0.0 . 371 . 0.78 0 none . . PASS Atlas-Indel,Pindel MIR30A 407029 hgsc.bcm.edu hg19 6 72113259 72113260 + RNA INS - - GCAAAC novel TCGA-2Z-A9JD-01A-11D-A42J-10 TCGA-2Z-A9JD-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d0c6a1f3-cb7d-4abc-b7be-b60b373335bb edf87796-76e3-4a71-8bb0-cb01677c6e77 . . . . . . . . 51.0 14.0 21.0 0.0 . . . 0.275 . none . . PASS Pindel