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 KIAA2013 90231 hgsc.bcm.edu hg19 1 11983151 11983151 + Silent SNP G G A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . KIAA2013 NM_138346 exon2 c.C1429T p.L477L TGTGCAGCACGTC . 133.0 48.0 180.0 0.0 . 25 . . . none . . PASS Atlas-SNP SPEN 23013 hgsc.bcm.edu hg19 1 16257405 16257405 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SPEN NM_015001 exon11 c.C4670T p.S1557F TCATTTCTGGTAG . 152.0 72.0 184.0 0.0 . 374 . . . none . . PASS Atlas-SNP PADI1 29943 hgsc.bcm.edu hg19 1 17555524 17555524 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . PADI1 NM_013358 exon8 c.C907G p.P303A CAGCCTCCTGAGG . 21.0 9.0 25.0 0.0 . 77 . . . none . . PASS Atlas-SNP OR10K1 391109 hgsc.bcm.edu hg19 1 158436100 158436100 + Missense_Mutation SNP T T G rs202043017 by1000genomes;alternate_allele TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . OR10K1 NM_001004473 exon1 c.T749G p.V250G TAACTGTTCACTA . 60.0 28.0 96.0 0.0 . 80 . . . alt T|1.000;C|0.000 . PASS Atlas-SNP TEX35 84066 hgsc.bcm.edu hg19 1 178483864 178483864 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . TEX35 NM_001170722 exon3 c.A144C p.E48D ACAAGAAGGGCGG . 107.0 55.0 135.0 0.0 . 15 . . . none . . PASS Atlas-SNP HMCN1 83872 hgsc.bcm.edu hg19 1 186099715 186099715 + Silent SNP G G A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . HMCN1 NM_031935 exon85 c.G13116A p.E4372E TTGTGAGGTGAAA . 112.0 53.0 147.0 0.0 . 797 . . . none . . PASS Atlas-SNP PLXNA2 5362 hgsc.bcm.edu hg19 1 208215625 208215625 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . PLXNA2 NM_025179 exon22 c.C4104G p.F1368L GCGGATGAAGGTC . 66.0 26.0 101.0 0.0 . 178 . . . none . . PASS Atlas-SNP FOSL2 2355 hgsc.bcm.edu hg19 2 28634997 28634997 + Silent SNP G G C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . FOSL2 NM_005253 exon4 c.G663C p.V221V AGTGGTGAAACAG . 80.0 28.0 87.0 0.0 . 39 . . . none . . PASS Atlas-SNP BIRC6 57448 hgsc.bcm.edu hg19 2 32824826 32824826 + Silent SNP G G T rs144649481 byfrequency;alternate_allele TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e BIRC6_ENST00000421745,colon,carcinoma,0,2 BIRC6 NM_016252 exon70 c.G13851T p.A4617A TCCAGCGGACACC . 68.0 3.0 71.0 0.0 . 838 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP LHCGR 3973 hgsc.bcm.edu hg19 2 48982764 48982764 + Missense_Mutation SNP A A T rs4539842 bycluster TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . LHCGR NM_000233 exon1 c.T47A p.L16Q TGCAGCAGCAGCA . 23.0 5.0 54.0 0.0 . 154 . . . weak . . PASS Atlas-SNP NRXN1 9378 hgsc.bcm.edu hg19 2 50850545 50850545 + Silent SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NRXN1 NM_001135659 exon7 c.A1140G p.G380G CCCTGATCCCAAA . 67.0 25.0 91.0 0.0 . 1118 . . . none . . PASS Atlas-SNP ALMS1 7840 hgsc.bcm.edu hg19 2 73676852 73676852 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ALMS1 NM_015120 exon8 c.C3195G p.D1065E ATCAGACAGTCAT . 150.0 48.0 176.0 0.0 . 384 . . . none . . PASS Atlas-SNP ALMS1 7840 hgsc.bcm.edu hg19 2 73680924 73680924 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ALMS1 NM_015120 exon8 c.G7267T p.G2423C GGAAATGGTTCCT . 78.0 30.0 136.0 0.0 . 384 . . . none . . PASS Atlas-SNP ALMS1 7840 hgsc.bcm.edu hg19 2 73680925 73680925 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ALMS1 NM_015120 exon8 c.G7268T p.G2423V GAAATGGTTCCTG . 78.0 30.0 136.0 0.0 . 384 . . . none . . PASS Atlas-SNP POLR1A 25885 hgsc.bcm.edu hg19 2 86302371 86302371 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . POLR1A NM_015425 exon12 c.A1393C p.K465Q TCAGTTTTGTGGC . 63.0 23.0 74.0 0.0 . 137 . . . none . . PASS Atlas-SNP XIRP2 129446 hgsc.bcm.edu hg19 2 168106667 168106667 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e XIRP2,colon,carcinoma,0,1 XIRP2 NM_152381 exon9 c.A8765G p.Q2922R TTACACAGAACAA . 254.0 110.0 355.0 0.0 . 914 . . . none . . PASS Atlas-SNP SLC40A1 30061 hgsc.bcm.edu hg19 2 190439896 190439896 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SLC40A1 NM_014585 exon3 c.A262G p.R88G TAAGTCTAGCATT . 113.0 41.0 142.0 0.0 . 51 . . . none . . PASS Atlas-SNP BMPR2 659 hgsc.bcm.edu hg19 2 203420241 203420241 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . BMPR2 NM_001204 exon12 c.C1853T p.T618I ACACCACAGGACT . 95.0 29.0 93.0 0.0 . 142 . . . none . . PASS Atlas-SNP CPS1 1373 hgsc.bcm.edu hg19 2 211523412 211523412 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CPS1 NM_001122633 exon32 c.G3774C p.L1258F TGTCTTGGTAAGA . 42.0 10.0 53.0 0.0 . 485 . . . none . . PASS Atlas-SNP NYAP2 57624 hgsc.bcm.edu hg19 2 226491661 226491661 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . . NM_020864 exon5 c.C1647A p.S549R CCGAAGCCACAGC . 221.0 96.0 335.0 0.0 . . . . . none . . PASS Atlas-SNP PID1 55022 hgsc.bcm.edu hg19 2 229890502 229890502 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . PID1 NM_017933 exon4 c.T593A p.V198E CACTCCACGGCGT . 82.0 30.0 108.0 0.0 . 43 . . . none . . PASS Atlas-SNP FAM107A 11170 hgsc.bcm.edu hg19 3 58555533 58555533 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . FAM107A NM_001076778 exon2 c.C55G p.P19A ATTCTGGCCGGGC . 42.0 12.0 48.0 0.0 . 33 . . . none . . PASS Atlas-SNP MAGEF1 64110 hgsc.bcm.edu hg19 3 184429221 184429221 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . MAGEF1 NM_022149 exon1 c.G389A p.G130D TCAAAACCAAAGA . 80.0 24.0 76.0 0.0 . 27 . . . none . . PASS Atlas-SNP SLC2A9 56606 hgsc.bcm.edu hg19 4 10020642 10020642 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SLC2A9 NM_020041 exon2 c.T206C p.F69S TAGAGGAAGGAGG . 188.0 60.0 266.0 0.0 . 158 . . . none . . PASS Atlas-SNP SDAD1 55153 hgsc.bcm.edu hg19 4 76896925 76896925 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SDAD1 NM_018115 exon6 c.A550C p.M184L CAATCATTACATC . 93.0 42.0 140.0 0.0 . 47 . . . none . . PASS Atlas-SNP IL2 3558 hgsc.bcm.edu hg19 4 123377451 123377451 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . IL2 NM_000586 exon1 c.A145T p.N49Y TTACATTAATTCC . 99.0 38.0 178.0 0.0 . 23 . . . none . . PASS Atlas-SNP ITPR3 3710 hgsc.bcm.edu hg19 6 33632875 33632875 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e ITPR3_ENST00000374316,colon,carcinoma,0,2 ITPR3 NM_002224 exon13 c.G1294A p.V432M GCCATCGTGTCAG . 46.0 34.0 52.0 0.0 . 409 . . . none . . PASS Atlas-SNP FOXP4 116113 hgsc.bcm.edu hg19 6 41555205 41555205 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . FOXP4 NM_001012426 exon7 c.C827G p.T276S ACCATACCCTGCC . 137.0 114.0 171.0 0.0 . 83 . . . none . . PASS Atlas-SNP PCLO 27445 hgsc.bcm.edu hg19 7 82508768 82508768 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . PCLO NM_014510 exon10 c.A13539C p.L4513F AATTCCTAATCCA . 210.0 51.0 165.0 0.0 . 1506 . . . none . . PASS Atlas-SNP AP4M1 9179 hgsc.bcm.edu hg19 7 99703890 99703890 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . AP4M1 NM_004722 exon13 c.T1001C p.L334P TGCACCTCCCCCT . 77.0 4.0 52.0 0.0 . 39 . . . none . . PASS Atlas-SNP POT1 25913 hgsc.bcm.edu hg19 7 124493170 124493170 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e POT1_ENST00000357628,NS,NS,0,2 POT1 NM_015450 exon10 c.A725G p.Y242C AGGCTATAGATTC . 131.0 83.0 133.0 0.0 . 186 . . . none . . PASS Atlas-SNP PTPRD 5789 hgsc.bcm.edu hg19 9 8460470 8460470 + Silent SNP A A G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . PTPRD NM_002839 exon33 c.T3816C p.G1272G GACAGGACCTACA . 90.0 28.0 99.0 0.0 . 1348 . . . none . . PASS Atlas-SNP BAAT 570 hgsc.bcm.edu hg19 9 104130573 104130573 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . BAAT NM_001127610 exon3 c.G498C p.L166F ACCAAACAAATCA . 157.0 64.0 213.0 0.0 . 52 . . . none . . PASS Atlas-SNP UVRAG 7405 hgsc.bcm.edu hg19 11 75826995 75826995 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . UVRAG NM_003369 exon14 c.C1333A p.P445T GGGACTCCAGACT . 69.0 22.0 94.0 0.0 . 69 . . . none . . PASS Atlas-SNP CALCOCO1 57658 hgsc.bcm.edu hg19 12 54115291 54115291 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CALCOCO1 NM_020898 exon6 c.A718G p.I240V CACTGATGGTCTG . 63.0 25.0 79.0 0.0 . 50 . . . none . . PASS Atlas-SNP CDK4 1019 hgsc.bcm.edu hg19 12 58145350 58145350 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CDK4 NM_000075 exon2 c.A151G p.I51V TGCTGATGGGAAG . 96.0 34.0 120.0 0.0 . 36 . . . none . . PASS Atlas-SNP FLT1 2321 hgsc.bcm.edu hg19 13 28880844 28880844 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . FLT1 NM_002019 exon29 c.C3786G p.D1262E TTTGCTGTCAGTC . 59.0 29.0 67.0 0.0 . 393 . . . none . . PASS Atlas-SNP SETDB2 83852 hgsc.bcm.edu hg19 13 50041999 50041999 + Splice_Site SNP G G A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SETDB2 NM_031915 exon6 c.245-1G>A . TGTGTAGATCCTA . 35.0 17.0 32.0 0.0 . 48 . . . none . . PASS Atlas-SNP SYNE2 23224 hgsc.bcm.edu hg19 14 64669618 64669618 + Silent SNP C C T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SYNE2 NM_182914 exon100 c.C18138T p.S6046S GCTTTCCAAGCCT . 65.0 31.0 87.0 0.0 . 577 . . . none . . PASS Atlas-SNP SNW1 22938 hgsc.bcm.edu hg19 14 78203382 78203382 + Silent SNP A A G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SNW1 NM_012245 exon6 c.T570C p.S190S AGCTCCAGAGTTG . 22.0 13.0 24.0 0.0 . 44 . . . none . . PASS Atlas-SNP ZWILCH 55055 hgsc.bcm.edu hg19 15 66838985 66838985 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ZWILCH NM_017975 exon18 c.A1744G p.M582V ACTAACATGGTTA . 50.0 21.0 76.0 0.0 . 46 . . . none . . PASS Atlas-SNP CYP1A2 1544 hgsc.bcm.edu hg19 15 75042609 75042609 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CYP1A2 NM_000761 exon2 c.A530C p.Q177P GGTTGCAGGAGCT . 58.0 22.0 53.0 0.0 . 70 . . . none . . PASS Atlas-SNP IL16 3603 hgsc.bcm.edu hg19 15 81598444 81598444 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . IL16 NM_001172128 exon17 c.C3616G p.L1206V CCCGACCTCAACT . 32.0 10.0 43.0 0.0 . 254 . . . none . . PASS Atlas-SNP NLRP1 22861 hgsc.bcm.edu hg19 17 5445303 5445303 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NLRP1 NM_033007 exon6 c.C2573A p.A858D CCAAAGGCAAGGT . 51.0 17.0 50.0 0.0 . 358 . . . none . . PASS Atlas-SNP SENP3 26168 hgsc.bcm.edu hg19 17 7474735 7474735 + Silent SNP G G A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SENP3 NM_015670 exon12 c.G1659A p.Q553Q CACCCAGCAGGAC . 52.0 9.0 69.0 0.0 . 18 . . . none . . PASS Atlas-SNP MAPT 4137 hgsc.bcm.edu hg19 17 44073780 44073780 + Nonsense_Mutation SNP C C A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . MAPT NM_001123066 exon11 c.C1577A p.S526X CAAAATCAGGGGA . 59.0 32.0 56.0 0.0 . 135 . . . none . . PASS Atlas-SNP BZRAP1 9256 hgsc.bcm.edu hg19 17 56405116 56405116 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . BZRAP1 NM_024418 exon1 c.A166G p.R56G CAGACCTCAGTTC . 59.0 16.0 50.0 0.0 . 287 . . . none . . PASS Atlas-SNP CLUL1 27098 hgsc.bcm.edu hg19 18 619309 619309 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CLUL1 NM_199167 exon3 c.A203G p.K68R AAGAGAAGGAACA . 146.0 59.0 215.0 0.0 . 57 . . . none . . PASS Atlas-SNP CLIP3 25999 hgsc.bcm.edu hg19 19 36510103 36510103 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CLIP3 NM_001199570 exon7 c.G1024A p.V342I ACCGAACGCCCCC . 26.0 11.0 35.0 0.0 . 53 . . . none . . PASS Atlas-SNP PRR12 57479 hgsc.bcm.edu hg19 19 50105116 50105116 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . PRR12 NM_020719 exon6 c.G4714C p.G1572R GGAGAGGGCATCT . 69.0 27.0 122.0 0.0 . 157 . . . none . . PASS Atlas-SNP ZNF616 90317 hgsc.bcm.edu hg19 19 52618903 52618903 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ZNF616 NM_178523 exon4 c.A1514G p.H505R CGTGAATGTTGAC . 55.0 21.0 57.0 0.0 . 109 . . . none . . PASS Atlas-SNP NPEPL1 79716 hgsc.bcm.edu hg19 20 57268881 57268881 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NPEPL1 NM_024663 exon2 c.C239G p.P80R CCCTGCCCTGCAG . 97.0 25.0 166.0 0.0 . 36 . . . none . . PASS Atlas-SNP ND5 0 hgsc.bcm.edu hg19 MT 13286 13286 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . . ENST00000361567 exon1 c.T950C p.I317T TTACAATCGGCAT . 11.0 6.0 22.0 0.0 . . . . . none . . PASS Atlas-SNP ZNF256 10172 hgsc.bcm.edu hg19 19 58452978 58452978 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ZNF256 NM_005773 exon3 c.1199delT p.L400fs . . 61.0 27.0 66.0 0.0 . 117 . 0.442623 0 none . . PASS Atlas-Indel,Pindel OBSCN 84033 hgsc.bcm.edu hg19 1 228404296 228404297 + Frame_Shift_Ins INS - - A novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . OBSCN NM_001098623 exon7 c.2270_2271insA p.S757fs . . 127.0 52.0 151.0 0.0 . 2142 . 0.409449 0 none . . PASS Atlas-Indel,Pindel ALMS1 7840 hgsc.bcm.edu hg19 2 73680903 73680911 + In_Frame_Del DEL AGTGATGCC AGTGATGCC - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 AGTGATGCC AGTGATGCC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . ALMS1 NM_015120 exon8 c.7245_7253del p.2415_2418del . . 77.0 23.0 122.0 0.0 . 384 . 0.298701 0 none . . PASS Atlas-Indel,Pindel SENP3 26168 hgsc.bcm.edu hg19 17 7474732 7474733 + In_Frame_Ins INS - - CAA novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SENP3 NM_015670 exon12 c.1656_1657insCAA p.T552delinsTQ . . 52.0 18.0 70.0 0.0 . 18 . 0.346154 0 none . . PASS Atlas-INDEL NAA50 80218 hgsc.bcm.edu hg19 3 113441795 113441795 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NAA50 NM_025146 exon4 c.291delA p.L97fs . . 522.0 145.0 536.0 0.0 . 10 . 0.277778 0 none . . PASS Atlas-Indel,Pindel SYNE2 23224 hgsc.bcm.edu hg19 14 64519388 64519388 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SYNE2 NM_015180 exon48 c.8756delA p.N2919fs . . 120.0 52.0 146.0 0.0 . 577 . 0.433333 0 none . . PASS Atlas-Indel,Pindel NPEPL1 79716 hgsc.bcm.edu hg19 20 57268883 57268883 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NPEPL1 NM_024663 exon2 c.240delC p.P80fs . . 96.0 26.0 166.0 0.0 . 36 . 0.270833 0 none . . PASS Atlas-INDEL DHX30 22907 hgsc.bcm.edu hg19 3 47891247 47891253 + Frame_Shift_Del DEL GTGCACA GTGCACA - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 GTGCACA GTGCACA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . DHX30 NM_138615 exon21 c.3318_3324del p.1106_1108del . . 62.0 27.0 80.0 0.0 . 101 . 0.435484 0 none . . PASS Atlas-Indel,Pindel NPEPL1 79716 hgsc.bcm.edu hg19 20 57268875 57268875 + Frame_Shift_Del DEL C C - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NPEPL1 NM_024663 exon2 c.232delG p.A78fs . . 107.0 23.0 174.0 0.0 . 36 . 0.214953 0 none . . PASS Atlas-INDEL NBEA 26960 hgsc.bcm.edu hg19 13 35644191 35644191 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NBEA NM_015678 exon9 c.1385delC p.P462fs . . 96.0 40.0 133.0 0.0 . 340 . 0.416667 0 none . . PASS Atlas-Indel,Pindel POLR3H 171568 hgsc.bcm.edu hg19 22 41926870 41926871 + Frame_Shift_Del DEL CC CC - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 CC CC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . POLR3H NM_001018050 exon5 c.382_383del p.128_128del . . 69.0 34.0 84.0 0.0 . 30 . 0.492754 0 none . . PASS Atlas-Indel,Pindel CACNA1H 8912 hgsc.bcm.edu hg19 16 1270632 1270632 + Frame_Shift_Del DEL C C - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . CACNA1H NM_021098 exon35 c.6699delG p.E2233fs . . 74.0 21.0 52.0 0.0 . 317 . 0.283784 0 none . . PASS Atlas-Indel,Pindel LCE4A 199834 hgsc.bcm.edu hg19 1 152681648 152681648 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . LCE4A NM_178356 exon1 c.96delA p.S32fs . . 168.0 81.0 250.0 0.0 . 37 . 0.482143 0 none . . PASS Atlas-Indel,Pindel SENP3 26168 hgsc.bcm.edu hg19 17 7474735 7474736 + Frame_Shift_Ins INS - - GA novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . SENP3 NM_015670 exon12 c.1659_1660insGA p.Q553fs . . 52.0 18.0 69.0 0.0 . 18 . 0.346154 0 none . . PASS Atlas-Indel,Pindel NPEPL1 79716 hgsc.bcm.edu hg19 20 57268877 57268883 + Frame_Shift_Del DEL CTGCCCT CTGCCCT - novel TCGA-UZ-A9PU-01A-11D-A42J-10 TCGA-UZ-A9PU-10A-01D-A42M-10 CTGCCCT CTGCCCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3dc9ae4b-b140-4e01-9339-de952605d9eb b843c2a5-db31-4152-b8d4-7ad08f849f7e . NPEPL1 NM_024663 exon2 c.234_240del p.78_80del . . 106.0 19.0 171.0 0.0 . 36 . 0.179 . none . . PASS Pindel