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 Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values ACHILLES_Lineage_Results_Top_Genes CGC_CancerGermlineMut CGC_CancerMolecularGenetics CGC_CancerSomaticMut CGC_CancerSyndrome CGC_Chr CGC_ChrBand CGC_GeneID CGC_Name CGC_OtherGermlineMut CGC_TissueType COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs Ensembl_so_accession Ensembl_so_term Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym annotation_transcript bcgsc broad build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP_NR dbNSFP_GERP_RS dbNSFP_GERP_RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_folddegenerate dbNSFP_genename dbNSFP_hg18_pos1coor dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon entrez_gene_id external_id_capture gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_type havana_transcript hgsc igv_bad ucsc t_alt_count t_ref_count n_alt_count n_ref_count validation_judgement_rna validation_power_rna validation_tumor_alt_count_rna validation_tumor_ref_count_rna validation_normal_alt_count_rna validation_normal_ref_count_rna min_val_count_rna validation_judgement_targeted validation_power_targeted validation_tumor_alt_count_targeted validation_tumor_ref_count_targeted validation_normal_alt_count_targeted validation_normal_ref_count_targeted min_val_count_targeted validation_judgement_localAssembly validation_power_localAssembly t_alt_count_localAssembly t_ref_count_localAssembly n_alt_count_localAssembly n_ref_count_localAssembly min_val_count_localAssembly validation_judgement_KRAS validation_power_KRAS t_alt_count_KRAS t_ref_count_KRAS n_alt_count_KRAS n_ref_count_KRAS min_val_count_KRAS pon_loglike pon_pass_loglike localAssembly_detected ExAC_AN ExAC_AC ExAC_LQ passExAC SCNA_NA SCNA_NB SCNA_q_hat SCNA_tau IS_SCNA purity ploidy dna_fraction_in_tumor CCF_hat CCF_CI95_low CCF_CI95_high CCF_mode CCF_mean CCF_median clonal CCF_CI_low CCF_CI_high CDKN2A 1029 broad.mit.edu 37 9 21971063 21971068 + In_Frame_Del DEL GGTGCA GGTGCA - rs34886500 TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 GGTGCA - GGTGCA GGTGCA Valid Somatic Phase_I WXS targeted Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr9:21971063_21971068delGGTGCA ENST00000304494.5 - 2 560_565 c.290_295delTGCACC c.(289-297)ctgcaccgg>cgg p.LH97del CDKN2A_ENST00000530628.2_In_Frame_Del_p.AP112del|CDKN2A_ENST00000498124.1_In_Frame_Del_p.LH97del|CDKN2A_ENST00000579755.1_In_Frame_Del_p.AP112del|CDKN2A_ENST00000494262.1_In_Frame_Del_p.LH46del|CDKN2A_ENST00000497750.1_In_Frame_Del_p.LH46del|CDKN2A_ENST00000578845.2_In_Frame_Del_p.LH46del|CDKN2A_ENST00000446177.1_In_Frame_Del_p.LH97del|CDKN2A_ENST00000361570.3_In_Frame_Del_p.AP153del|CDKN2A_ENST00000498628.2_In_Frame_Del_p.LH46del|CDKN2A_ENST00000579122.1_In_Frame_Del_p.LH97del|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_In_Frame_Del_p.LH46del NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.L97R(5)|p.L97P(4)|p.H98P(3)|p.H98R(2)|p.H83fs*2(2)|p.R99W(2)|p.H98Y(1)|p.A153A(1)|p.H98H(1)|p.0(1)|p.L97fs*21(1)|p.T93_D105del(1)|p.R137fs*48(1)|p.A68fs*3(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) GCCCCGGCCCGGTGCAGCACCACCAG 0.748000 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1385 Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(17)|Deletion - Frameshift(5)|Substitution - coding silent(2)|Deletion - In frame(1) GRCh37 CM045408|CM056555|CM980329 CDKN2A M rs34886500 SO:0001651 inframe_deletion ENST00000304494.5 1 1 hg19 CCDS6510.1 TCGA-FB-A545-01A-11D-A26I-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 67 166 0 26 0 9.976177e-01 0 26 0 26 2 1 1 65 140 0 143 2 1 1.000000 72 169 0 23 2 0 0 0 0 0 0 -6.194341 1 1 0 0 1 0 2 2 1.520844 1 0.530000 3.130000 0.530000 0.990000 0.870000 1.000000 1.000000 0.986910 0.990000 1 0.970000 1.000000 PCDH15 65217 broad.mit.edu 37 10 55616938 55616938 + Missense_Mutation SNP G G T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr10:55616938G>T ENST00000320301.6 - 28 4197 c.3803C>A c.(3802-3804)aCa>aAa p.T1268K PCDH15_ENST00000395433.1_Missense_Mutation_p.T1246K|PCDH15_ENST00000373965.2_Missense_Mutation_p.T1275K|PCDH15_ENST00000395430.1_Missense_Mutation_p.T1268K|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.T879K|PCDH15_ENST00000395438.1_Missense_Mutation_p.T1268K|PCDH15_ENST00000361849.3_Missense_Mutation_p.T1268K|PCDH15_ENST00000437009.1_Missense_Mutation_p.T1197K|PCDH15_ENST00000395445.1_Missense_Mutation_p.T1275K|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395432.2_Missense_Mutation_p.T1231K|PCDH15_ENST00000414778.1_Missense_Mutation_p.T1273K NM_033056.3 NP_149045.3 Q96QU1 PCD15_HUMAN protocadherin-related 15 237 Melanoma(3;0.117)|Lung SC(717;0.238) CAATTACTCTGTAAGATCTTC 0.313000 HNSCC(58;0.16) 0 SO:0001583 missense ENST00000320301.6 1 1 hg19 CCDS7248.1 . . . . . . . . . . G 21.9 4.210653 0.79240 . . ENSG00000150275 ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009 T;T;T;T;T;T;T;T;T;T;T 0.57273 0.5;0.55;0.49;0.48;0.46;0.44;0.42;0.46;0.44;0.42;0.41 5.17 4.26 0.50523 . . . . . T 0.42108 0.1188 N 0.14661 0.345 0.33977 D 0.647511 D;D;D;P;D;D;D;P;P;P;P;P;D 0.54397 0.966;0.959;0.959;0.932;0.958;0.959;0.966;0.59;0.926;0.926;0.814;0.729;0.959 P;P;B;B;P;P;P;B;B;B;B;B;B 0.53035 0.716;0.544;0.424;0.326;0.69;0.544;0.716;0.315;0.424;0.424;0.315;0.315;0.424 T 0.51505 -0.8697 9 0.42905 T 0.14 . 5.2011 0.15264 0.2905:0.0:0.7095:0.0 . 1246;1268;1268;1273;1197;1231;1268;1268;1275;1275;1268;1273;1268 A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1 .;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN K 1275;1273;1268;1268;879;1275;1231;1268;1246;1268;1268;1273;1197 ENSP00000363076:T1275K;ENSP00000410304:T1273K;ENSP00000378826:T1268K;ENSP00000386693:T879K;ENSP00000378832:T1275K;ENSP00000378820:T1231K;ENSP00000354950:T1268K;ENSP00000378821:T1246K;ENSP00000322604:T1268K;ENSP00000378818:T1268K;ENSP00000412628:T1197K ENSP00000322604:T1268K T - 2 0 PCDH15 55286944 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.204000 0.77872 2.418000 0.82041 0.655000 0.94253 ACA TCGA-FB-A545-01A-11D-A26I-08 PCDH15-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000048121.2 1 0 1 95 92 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1.000000 95 92 0 29 2 0 0 0 0 30 2 -19.999940 1 1 0 0 1 0 2 2 1.605404 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 QSER1 79832 broad.mit.edu 37 11 32955744 32955744 + Silent SNP A A G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr11:32955744A>G ENST00000399302.2 + 4 2888 c.2553A>G c.(2551-2553)gtA>gtG p.V851V QSER1_ENST00000527788.1_Silent_p.V612V NM_001076786.1 NP_001070254.1 Q2KHR3 QSER1_HUMAN glutamine and serine rich 1 48 Breast(20;0.158) TATCAAATGTAGATGATATCT 0.383000 0 SO:0001819 synonymous_variant ENST00000399302.2 1 1 hg19 CCDS41631.1 TCGA-FB-A545-01A-11D-A26I-08 QSER1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388448.1 1 0 1 426 443 0 57 1 7.993490e-01 2 3 0 57 2 0 0 0 0 0 2 1 1.000000 425 436 0 57 2 0 0 0 0 57 2 -20.000000 1 1 0 0 1 2 4 6 3.214197 1 0.530000 3.130000 0.771845 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CD44 960 broad.mit.edu 37 11 35218359 35218359 + Missense_Mutation SNP T T G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr11:35218359T>G ENST00000428726.2 + 6 857 c.734T>G c.(733-735)tTt>tGt p.F245C CD44_ENST00000433354.2_Missense_Mutation_p.F245C|CD44_ENST00000526669.2_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000449691.2_Missense_Mutation_p.F245C|CD44_ENST00000434472.2_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.F245C|CD44_ENST00000263398.6_Intron|CD44_ENST00000415148.2_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000278386.6_Intron NM_000610.3 NP_000601.3 P16070 CD44_HUMAN CD44 molecule (Indian blood group) 23 all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112) all_hematologic(20;0.107) STAD - Stomach adenocarcinoma(6;0.00731) Hyaluronan(DB08818) TGGGATTGGTTTTCATGGTTG 0.378000 0 SO:0001583 missense ENST00000428726.2 1 1 hg19 CCDS7897.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 12.77|12.77 2.039051|2.039051 0.35989|0.35989 .|. .|. ENSG00000026508|ENSG00000026508 ENST00000433354;ENST00000449691;ENST00000437706;ENST00000428726|ENST00000525685 T;T;T;T|T 0.18502|0.20463 2.34;2.21;2.33;2.41|2.07 5.04|5.04 5.04|5.04 0.67666|0.67666 .|. 0.497457|0.497457 0.17058|0.17058 N|N 0.188655|0.188655 T|T 0.22475|0.22475 0.0542|0.0542 L|L 0.29908|0.29908 0.895|0.895 0.80722|0.80722 D|D 1|1 D|. 0.63046|. 0.992|. P|. 0.52710|. 0.707|. T|T 0.02950|0.02950 -1.1090|-1.1090 10|8 0.35671|0.34782 T|T 0.21|0.22 -0.253|-0.253 11.1936|11.1936 0.48700|0.48700 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. 245|. P16070|. CD44_HUMAN|. C|V 245|113 ENSP00000414567:F245C;ENSP00000391008:F245C;ENSP00000403990:F245C;ENSP00000398632:F245C|ENSP00000436623:F113V ENSP00000398632:F245C|ENSP00000436623:F113V F|F +|+ 2|1 0|0 CD44|CD44 35174935|35174935 1.000000|1.000000 0.71417|0.71417 0.944000|0.944000 0.38274|0.38274 0.132000|0.132000 0.20833|0.20833 3.427000|3.427000 0.52785|0.52785 1.873000|1.873000 0.54277|0.54277 0.533000|0.533000 0.62120|0.62120 TTT|TTT TCGA-FB-A545-01A-11D-A26I-08 CD44-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000388927.1 1 0 1 84 227 0 23 1 1 51 31 0 23 2 0 0 0 0 0 2 1 1.000000 83 223 0 23 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 2 4 6 3.214197 1 0.530000 3.130000 0.771845 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TMEM132D 121256 broad.mit.edu 37 12 130184677 130184677 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr12:130184677C>T ENST00000422113.2 - 2 972 c.646G>A c.(646-648)Gtg>Atg p.V216M RP11-174M13.2_ENST00000544036.1_lincRNA NM_133448.2 NP_597705.2 Q14C87 T132D_HUMAN transmembrane protein 132D 152 all_neural(191;0.101)|Medulloblastoma(191;0.163) all_epithelial(31;0.0934)|Breast(359;0.133) GGCTGGTCCACGGACTTCCTC 0.692000 0 SO:0001583 missense ENST00000422113.2 1 1 hg19 CCDS9266.1 . . . . . . . . . . C 3.487 -0.104728 0.06967 . . ENSG00000151952 ENST00000422113 T 0.12039 2.72 5.35 -1.38 0.09027 . 1.295410 0.05175 N 0.500234 T 0.04815 0.0130 N 0.01482 -0.84 0.09310 N 1 B 0.21225 0.053 B 0.09377 0.004 T 0.39461 -0.9613 9 . . . -2.439 9.4725 0.38851 0.0:0.1393:0.6062:0.2545 . 216 Q14C87 T132D_HUMAN M 216 ENSP00000408581:V216M . V - 1 0 TMEM132D 128750630 0.000000 0.05858 0.000000 0.03702 0.035000 0.12851 -0.785000 0.04628 0.059000 0.16252 0.650000 0.86243 GTG TCGA-FB-A545-01A-11D-A26I-08 TMEM132D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399592.1 1 0 1 132 187 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 132 185 0 54 2 0 0 0 0 55 2 -20.000000 1 1 121410 3 33 1 1 3 4 2.098671 1 0.530000 3.130000 0.643399 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SOX5 6660 broad.mit.edu 37 12 24048945 24048945 + Nonsense_Mutation SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr12:24048945G>A ENST00000451604.2 - 2 153 c.52C>T c.(52-54)Cga>Tga p.R18* SOX5_ENST00000546136.1_Nonsense_Mutation_p.R5*|SOX5_ENST00000381381.2_Nonsense_Mutation_p.R5*|SOX5_ENST00000545921.1_Nonsense_Mutation_p.R8*|SOX5_ENST00000541536.1_Nonsense_Mutation_p.R5*|SOX5_ENST00000537393.1_Nonsense_Mutation_p.R18*|SOX5_ENST00000309359.1_Nonsense_Mutation_p.R5*|SOX5_ENST00000541847.1_Nonsense_Mutation_p.R8*|SOX5_ENST00000441133.2_Nonsense_Mutation_p.R18* P35711 SOX5_HUMAN SRY (sex determining region Y)-box 5 57 GAGGCTGGTCGCTTGGAAGAC 0.493000 0 SO:0001587 stop_gained ENST00000451604.2 0 1 hg19 CCDS8699.1 . . . . . . . . . . G 40 8.211190 0.98706 . . ENSG00000134532 ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083 . . . 5.88 5.88 0.94601 . 0.000000 0.64402 D 0.000001 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 20.2366 0.98359 0.0:0.0:1.0:0.0 . . . . X 5;5;5;18;5;18;5;8;8;18;5 . ENSP00000308927:R5X R - 1 2 SOX5 23940212 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.069000 0.93967 2.792000 0.96026 0.557000 0.71058 CGA TCGA-FB-A545-01A-11D-A26I-08 SOX5-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000402006.2 1 0 0 385 452 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 1.000000 381 450 0 93 2 0 0 0 0 93 2 -20.000000 1 1 0 0 1 2 6 8 2.179788 1 0.530000 3.130000 0.671168 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-FB-A545-01A-11D-A26I-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 38 67 0 13 1 8.861739e-01 7 2 0 13 2 1 1 103 193 0 271 2 1 1.000000 37 66 0 13 2 1 1 3587 4415 0 13 2 -20.000000 1 1 0 0 1 2 6 8 2.179788 1 0.530000 3.130000 0.671168 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KCNA6 3742 broad.mit.edu 37 12 4920057 4920057 + Missense_Mutation SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr12:4920057G>A ENST00000280684.3 + 1 1716 c.850G>A c.(850-852)Gcc>Acc p.A284T RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Missense_Mutation_p.A284T P17658 KCNA6_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 6 49 Dalfampridine(DB06637) GCGCTTCTCCGCCTGCCCTAG 0.542000 HNSCC(72;0.22) 0 SO:0001583 missense ENST00000280684.3 1 1 hg19 CCDS8534.1 . . . . . . . . . . G 21.1 4.102426 0.76983 . . ENSG00000151079 ENST00000433855;ENST00000280684 D;D 0.99023 -5.34;-5.34 5.28 5.28 0.74379 Ion transport (1); 0.108992 0.64402 D 0.000010 D 0.96756 0.8941 N 0.21142 0.635 0.53688 D 0.999972 P 0.47910 0.902 B 0.43155 0.41 D 0.96581 0.9430 10 0.56958 D 0.05 . 13.4363 0.61086 0.0772:0.0:0.9228:0.0 . 284 P17658 KCNA6_HUMAN T 284 ENSP00000408321:A284T;ENSP00000280684:A284T ENSP00000280684:A284T A + 1 0 KCNA6 4790318 1.000000 0.71417 0.992000 0.48379 0.991000 0.79684 7.736000 0.84948 2.746000 0.94184 0.655000 0.94253 GCC TCGA-FB-A545-01A-11D-A26I-08 KCNA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398909.1 1 0 1 258 381 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 1.000000 257 381 0 91 2 0 0 0 0 92 2 -20.000000 1 1 0 0 1 2 5 7 2.133899 1 0.530000 3.130000 0.663685 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ADAMTS7 11173 broad.mit.edu 37 15 79090455 79090455 + Splice_Site SNP T T C TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr15:79090455T>C ENST00000388820.4 - 3 667 c.457A>G c.(457-459)Aaa>Gaa p.K153E ADAMTS7_ENST00000566303.1_5'UTR NM_014272.3 NP_055087.2 Q9UKP4 ATS7_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 7 54 AACACACCTTTCTGGGGAAGA 0.652000 0 SO:0001630 splice_region_variant ENST00000388820.4 1 0 hg19 CCDS32303.1 . . . . . . . . . . T 15.07 2.722889 0.48728 . . ENSG00000136378 ENST00000388820;ENST00000456326 T 0.05786 3.39 4.5 3.36 0.38483 Peptidase M12B, propeptide (1); 0.255369 0.38492 N 0.001670 T 0.08802 0.0218 M 0.68317 2.08 0.36372 D 0.861369 B;B;P 0.35527 0.24;0.24;0.507 B;B;B 0.37731 0.253;0.232;0.257 T 0.23511 -1.0186 10 0.17369 T 0.5 . 10.1068 0.42539 0.0:0.0:0.1867:0.8133 . 153;153;153 E7EP58;A8MQ00;Q9UKP4 .;.;ATS7_HUMAN E 153 ENSP00000373472:K153E ENSP00000373472:K153E K - 1 0 ADAMTS7 76877510 1.000000 0.71417 0.999000 0.59377 0.620000 0.37586 3.905000 0.56333 0.671000 0.31185 0.260000 0.18958 AAA TCGA-FB-A545-01A-11D-A26I-08 ADAMTS7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000421331.1 1 0 1 169 149 0 58 0 5.466691e-01 0 3 0 58 2 0 0 0 0 0 2 1 1.000000 166 149 0 57 2 0 0 0 0 58 2 -20.000000 1 1 0 0 1 0 2 2 1.600549 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 NTRK3 4916 broad.mit.edu 37 15 88483870 88483870 + Missense_Mutation SNP A A G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr15:88483870A>G ENST00000360948.2 - 14 1861 c.1700T>C c.(1699-1701)aTg>aCg p.M567T NTRK3_ENST00000558676.1_Missense_Mutation_p.M559T|NTRK3_ENST00000394480.2_Missense_Mutation_p.M567T|NTRK3_ENST00000542733.2_Missense_Mutation_p.M469T|NTRK3_ENST00000557856.1_Missense_Mutation_p.M559T|NTRK3_ENST00000357724.2_Missense_Mutation_p.M559T|NTRK3_ENST00000355254.2_Missense_Mutation_p.M567T NM_001012338.2 NP_001012338.1 Q16288 NTRK3_HUMAN neurotrophic tyrosine kinase, receptor, type 3 ETV6/NTRK3(238) 119 BRCA - Breast invasive adenocarcinoma(143;0.211) AGCCACAAGCATCTTGTCCTT 0.592000 T ETV6 congenital fibrosarcoma, Secretory breast TSP Lung(13;0.10) Dom yes 15 15q25 4916 neurotrophic tyrosine kinase, receptor, type 3 E, M 0 SO:0001583 missense ENST00000360948.2 1 1 hg19 CCDS32322.1 . . . . . . . . . . A 15.52 2.858456 0.51376 . . ENSG00000140538 ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000343782 D;D;D;D;D 0.88201 -2.35;-2.35;-2.35;-2.35;-2.35 5.29 5.29 0.74685 Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.74458 0.3719 N 0.01473 -0.845 0.80722 D 1 B;B;B;B;B 0.33919 0.253;0.432;0.236;0.213;0.115 B;B;B;B;B 0.41466 0.208;0.358;0.241;0.14;0.115 T 0.75584 -0.3267 10 0.02654 T 1 . 14.3918 0.66983 1.0:0.0:0.0:0.0 . 469;559;559;567;567 B7Z7U4;E9PG56;B7Z4C5;Q16288-3;Q16288 .;.;.;.;NTRK3_HUMAN T 567;567;559;567;469;63 ENSP00000377990:M567T;ENSP00000354207:M567T;ENSP00000350356:M559T;ENSP00000347397:M567T;ENSP00000437773:M469T ENSP00000342792:M63T M - 2 0 NTRK3 86284874 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.020000 0.93667 2.004000 0.58718 0.533000 0.62120 ATG TCGA-FB-A545-01A-11D-A26I-08 NTRK3-204 KNOWN basic|CCDS protein_coding protein_coding 1 0 1 208 240 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1.000000 206 235 0 75 2 0 0 0 0 75 2 -20.000000 1 1 0 0 1 0 2 2 1.600549 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ATXN2L 11273 broad.mit.edu 37 16 28841310 28841310 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr16:28841310C>T ENST00000336783.4 + 8 1132 c.965C>T c.(964-966)aCt>aTt p.T322I ATXN2L_ENST00000325215.6_Missense_Mutation_p.T322I|ATXN2L_ENST00000395547.2_Missense_Mutation_p.T322I|ATXN2L_ENST00000382686.4_Missense_Mutation_p.T322I|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000564304.1_Missense_Mutation_p.T322I|ATXN2L_ENST00000570200.1_Missense_Mutation_p.T322I|ATXN2L_ENST00000340394.8_Missense_Mutation_p.T322I NM_007245.3 NP_009176.2 Q8WWM7 ATX2L_HUMAN ataxin 2-like 36 GATGGGCGCACTGAAGAGGAG 0.612000 0 SO:0001583 missense ENST00000336783.4 1 1 hg19 CCDS10641.1 . . . . . . . . . . . 23.5 4.424961 0.83667 . . ENSG00000168488 ENST00000340394;ENST00000395547;ENST00000336783;ENST00000359153;ENST00000382686;ENST00000325215 T;T;T;T;T 0.47869 0.83;0.83;0.83;0.84;0.83 5.7 5.7 0.88788 LsmAD domain (1); 0.000000 0.85682 D 0.000000 T 0.63271 0.2497 L 0.43152 1.355 0.52099 D 0.999944 D;D;D;D;D;D;D;D 0.76494 0.999;0.999;0.999;0.999;0.999;0.999;0.999;0.999 D;D;D;D;D;D;D;D 0.72338 0.961;0.961;0.977;0.977;0.961;0.961;0.977;0.961 T 0.64292 -0.6442 10 0.87932 D 0 -12.0156 18.5887 0.91200 0.0:1.0:0.0:0.0 . 322;322;322;322;322;322;322;322 Q8WWM7-6;Q8WWM7-5;Q63ZY4;Q8WWM7;Q8WWM7-2;Q8WWM7-4;A8K1R6;Q8WWM7-3 .;.;.;ATX2L_HUMAN;.;.;.;. I 322 ENSP00000341459:T322I;ENSP00000378917:T322I;ENSP00000338718:T322I;ENSP00000372133:T322I;ENSP00000315650:T322I ENSP00000315650:T322I T + 2 0 ATXN2L 28748811 0.877000 0.30153 0.994000 0.49952 0.990000 0.78478 1.577000 0.36515 2.702000 0.92279 0.491000 0.48974 ACT TCGA-FB-A545-01A-11D-A26I-08 ATXN2L-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000214139.1 0 0 0 128 213 1 33 1 1 37 63 1 33 11 0 0 0 0 0 2 1 1.000000 128 211 1 33 28 0 0 0 1 33 2 -20.000000 1 1 0 0 1 2 2 4 2.242656 1 0.530000 3.130000 0.678325 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TP53 7157 broad.mit.edu 37 17 7577121 7577121 + Missense_Mutation SNP G G A rs121913343 TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr17:7577121G>A ENST00000269305.4 - 8 1006 c.817C>T c.(817-819)Cgt>Tgt p.R273C TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCACAAACACGCACCTCAAAG 0.542000 R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID) 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 533 Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2) GRCh37 CM010471|CM010473|CM951233 TP53 M rs121913343 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 17.48 3.400216 0.62177 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.92 3.95 0.45737 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99851 0.9931 M 0.90759 3.145 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.998;0.998;0.999;0.996 D 0.96877 0.9643 10 0.87932 D 0 -11.9995 11.2235 0.48869 0.0895:0.0:0.9105:0.0 . 273;273;273;273 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. C 273;273;273;273;273;262;141 ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C ENSP00000269305:R273C R - 1 0 TP53 7517846 1.000000 0.71417 0.066000 0.19879 0.723000 0.41478 4.540000 0.60664 1.299000 0.44798 0.462000 0.41574 CGT TCGA-FB-A545-01A-11D-A26I-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 87 73 0 21 1 1 17 20 0 21 2 1 1 380 262 0 731 2 1 1.000000 86 73 0 21 2 0 0 0 0 21 2 -20.000000 1 1 121412 1 37 1 0 2 2 1.413790 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 USH2A 7399 broad.mit.edu 37 1 215960150 215960150 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr1:215960150C>T ENST00000307340.3 - 52 10635 c.10249G>A c.(10249-10251)Gac>Aac p.D3417N USH2A_ENST00000366943.2_Missense_Mutation_p.D3417N NM_206933.2 NP_996816 O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 527 AAGTTGAAGTCACACCTGCCA 0.493000 HNSCC(13;0.011) 0 SO:0001583 missense ENST00000307340.3 1 1 hg19 CCDS31025.1 . . . . . . . . . . C 16.80 3.223870 0.58668 . . ENSG00000042781 ENST00000307340;ENST00000366943 T;T 0.16897 2.33;2.31 4.88 3.96 0.45880 Fibronectin, type III (3); 0.000000 0.47455 D 0.000226 T 0.20007 0.0481 M 0.69823 2.125 0.43637 D 0.996032 B 0.19200 0.034 B 0.16722 0.016 T 0.03453 -1.1035 10 0.39692 T 0.17 . 10.8728 0.46894 0.0:0.9128:0.0:0.0872 . 3417 O75445 USH2A_HUMAN N 3417 ENSP00000305941:D3417N;ENSP00000355910:D3417N ENSP00000305941:D3417N D - 1 0 USH2A 214026773 1.000000 0.71417 0.997000 0.53966 0.930000 0.56654 1.227000 0.32576 2.225000 0.72522 0.655000 0.94253 GAC TCGA-FB-A545-01A-11D-A26I-08 USH2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128138.1 1 0 1 64 213 0 33 0 0 0 0 33 2 0 0 0 0 0 2 1 1.000000 61 203 0 33 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 1 3 4 2.024946 1 0.530000 3.130000 0.637569 0.990000 0.910000 1.000000 1.000000 0.994242 0.990000 1 0.990000 1.000000 SPATA17 128153 broad.mit.edu 37 1 217947827 217947827 + Missense_Mutation SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr1:217947827G>A ENST00000366933.4 + 7 726 c.671G>A c.(670-672)cGt>cAt p.R224H NM_138796.2 NP_620151.1 Q96L03 SPT17_HUMAN spermatogenesis associated 17 21 ACAAGCGCCCGTTCTTTTCCT 0.403000 0 SO:0001583 missense ENST00000366933.4 1 1 hg19 CCDS1519.1 . . . . . . . . . . G 9.603 1.129341 0.21041 2.27E-4 0.0 ENSG00000162814 ENST00000366933 T 0.46451 0.87 5.45 1.39 0.22231 . 0.436237 0.24820 N 0.035323 T 0.20618 0.0496 N 0.25890 0.77 0.09310 N 1 B 0.12630 0.006 B 0.04013 0.001 T 0.10177 -1.0641 10 0.15499 T 0.54 -12.9268 1.6448 0.02759 0.3165:0.1634:0.4025:0.1176 . 224 Q96L03 SPT17_HUMAN H 224 ENSP00000355900:R224H ENSP00000355900:R224H R + 2 0 SPATA17 216014450 0.000000 0.05858 0.053000 0.19242 0.387000 0.30353 -0.047000 0.11963 0.339000 0.23719 0.563000 0.77884 CGT TCGA-FB-A545-01A-11D-A26I-08 SPATA17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092433.2 1 0 1 146 202 0 39 0 1.770940e-01 1 1 0 39 2 0 0 0 0 0 2 1 1.000000 145 200 0 39 2 0 0 0 0 39 2 -20.000000 1 1 121412 2 35 1 1 3 4 2.024946 1 0.530000 3.130000 0.637569 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 BAI2 576 broad.mit.edu 37 1 32196436 32196436 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr1:32196436C>T ENST00000373658.3 - 29 4686 c.4345G>A c.(4345-4347)Gtg>Atg p.V1449M BAI2_ENST00000257070.4_Missense_Mutation_p.V1416M|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000440175.2_Missense_Mutation_p.V1058M|BAI2_ENST00000398542.1_Missense_Mutation_p.V1349M|BAI2_ENST00000398556.3_Missense_Mutation_p.V1364M|BAI2_ENST00000398547.1_Missense_Mutation_p.V1382M|BAI2_ENST00000527361.1_Missense_Mutation_p.V1416M|BAI2_ENST00000398538.1_Missense_Mutation_p.V1437M|BAI2_ENST00000373655.2_Missense_Mutation_p.V1449M NM_001703.2 NP_001694.2 O60241 BAI2_HUMAN brain-specific angiogenesis inhibitor 2 55 Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174) GAGCCGGGCACGGTGCGAGGC 0.647000 0 SO:0001583 missense ENST00000373658.3 1 1 hg19 CCDS346.2 . . . . . . . . . . C 20.9 4.061905 0.76187 . . ENSG00000121753 ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538 T;T;T;T;T;T;T;T;T 0.05382 3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45 5.74 5.74 0.90152 . 0.000000 0.38897 N 0.001528 T 0.19248 0.0462 L 0.43152 1.355 0.39977 D 0.974866 D;D;P;D;D;D;D 0.89917 0.997;0.996;0.454;1.0;0.997;0.993;1.0 D;P;B;D;D;P;D 0.65233 0.933;0.85;0.072;0.925;0.933;0.713;0.925 T 0.00057 -1.2171 10 0.54805 T 0.06 . 19.9066 0.97010 0.0:1.0:0.0:0.0 . 1416;1437;1058;1364;1449;1449;1437 O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2 .;.;.;.;.;BAI2_HUMAN;. M 1364;1382;1449;1449;1349;1416;1416;1058;1437 ENSP00000381564:V1364M;ENSP00000381555:V1382M;ENSP00000362762:V1449M;ENSP00000362759:V1449M;ENSP00000381550:V1349M;ENSP00000257070:V1416M;ENSP00000435397:V1416M;ENSP00000391071:V1058M;ENSP00000381548:V1437M ENSP00000257070:V1416M V - 1 0 BAI2 31969023 0.999000 0.42202 0.997000 0.53966 0.975000 0.68041 4.281000 0.58965 2.884000 0.98904 0.655000 0.94253 GTG TCGA-FB-A545-01A-11D-A26I-08 BAI2-015 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000381838.1 1 0 1 94 402 0 91 0 3.220598e-01 0 6 0 91 2 0 0 0 0 0 2 1 1.000000 93 400 0 91 2 0 0 0 0 91 2 -20.000000 1 1 0 0 1 1 2 3 1.993825 1 0.530000 3.130000 0.628458 0.900000 0.740000 1.000000 1.000000 0.902904 0.900000 1 0.810000 0.990000 C1orf174 339448 broad.mit.edu 37 1 3809528 3809528 + Missense_Mutation SNP C C G rs35157037 byFrequency TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr1:3809528C>G ENST00000361605.3 - 2 146 c.48G>C c.(46-48)ttG>ttC p.L16F C1orf174_ENST00000486765.1_5'UTR NM_207356.2 NP_997239.2 Q8IYL3 CA174_HUMAN chromosome 1 open reading frame 174 11 all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227) all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127) TTCGTGCTTTCAAGCGCGCTG 0.552000 0 SO:0001583 missense ENST00000361605.3 1 0 hg19 CCDS53.1 . . . . . . . . . . C 10.49 1.364705 0.24684 . . ENSG00000198912 ENST00000361605 T 0.27256 1.68 4.32 -3.09 0.05331 . 0.201603 0.32884 N 0.005522 T 0.33235 0.0856 L 0.58101 1.795 0.09310 N 0.999999 D 0.89917 1.0 D 0.81914 0.995 T 0.17137 -1.0379 10 0.52906 T 0.07 -21.7736 1.8365 0.03141 0.1312:0.3716:0.1314:0.3657 . 16 Q8IYL3 CA174_HUMAN F 16 ENSP00000355306:L16F ENSP00000355306:L16F L - 3 2 C1orf174 3799388 0.067000 0.21026 0.017000 0.16124 0.017000 0.09413 -0.052000 0.11865 -0.454000 0.07066 0.462000 0.41574 TTG TCGA-FB-A545-01A-11D-A26I-08 C1orf174-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000010539.1 1 0 1 39 151 0 34 1 8.866638e-01 7 10 0 34 2 0 0 0 0 0 2 1 1.000000 39 150 0 34 2 0 0 0 0 34 2 -2.019185 0 1 0 0 1 1 2 3 1.962060 1 0.530000 3.130000 0.628458 0.970000 0.720000 1.000000 1.000000 0.939783 0.970000 1 0.840000 1.000000 C1orf87 127795 broad.mit.edu 37 1 60491098 60491098 + Missense_Mutation SNP C C G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr1:60491098C>G ENST00000371201.3 - 8 1209 c.1102G>C c.(1102-1104)Gat>Cat p.D368H C1orf87_ENST00000450089.2_Missense_Mutation_p.D139H NM_152377.2 NP_689590.1 Q8N0U7 CA087_HUMAN chromosome 1 open reading frame 87 33 TAACCCAAATCTTGATGGTTA 0.363000 NSCLC(75;811 1386 4923 13371 51772) 0 SO:0001583 missense ENST00000371201.3 1 1 hg19 CCDS614.1 . . . . . . . . . . C 15.78 2.935246 0.52866 . . ENSG00000162598 ENST00000371201;ENST00000450089 T 0.61158 0.13 5.09 2.2 0.27929 EF-hand-like domain (1); 0.584662 0.16488 N 0.212227 T 0.47820 0.1466 L 0.56769 1.78 0.80722 D 1 B 0.31931 0.347 B 0.29176 0.099 T 0.44065 -0.9352 10 0.72032 D 0.01 -3.802 5.065 0.14578 0.0:0.6433:0.1715:0.1851 . 368 Q8N0U7 CA087_HUMAN H 368;139 ENSP00000360244:D368H ENSP00000360244:D368H D - 1 0 C1orf87 60263686 0.912000 0.30974 0.991000 0.47740 0.886000 0.51366 1.044000 0.30329 0.322000 0.23283 0.555000 0.69702 GAT TCGA-FB-A545-01A-11D-A26I-08 C1orf87-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000024943.1 1 0 1 96 196 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 1.000000 95 195 0 38 2 0 0 0 0 39 2 -20.000000 1 1 0 0 1 1 2 3 1.993825 1 0.530000 3.130000 0.628458 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 COL24A1 255631 broad.mit.edu 37 1 86497562 86497562 + Splice_Site SNP C C G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr1:86497562C>G ENST00000370571.2 - 14 2414 c.2048G>C c.(2047-2049)aGa>aCa p.R683T COL24A1_ENST00000436319.1_Splice_Site_p.R683T NM_152890.5 NP_690850.2 Q17RW2 COOA1_HUMAN collagen, type XXIV, alpha 1 101 GATACTCACTCTAAGCCCAGG 0.338000 0 SO:0001630 splice_region_variant ENST00000370571.2 1 0 hg19 CCDS41353.1 . . . . . . . . . . C 12.12 1.843508 0.32606 . . ENSG00000171502 ENST00000370571;ENST00000436319 D;D 0.94330 -3.4;-3.4 5.87 3.98 0.46160 . 0.392618 0.18587 N 0.136858 D 0.84737 0.5538 L 0.49256 1.55 0.46631 D 0.999131 B 0.10296 0.003 B 0.10450 0.005 T 0.79497 -0.1779 10 0.10902 T 0.67 . 16.8292 0.85939 0.0:0.758:0.242:0.0 . 683 Q17RW2 COOA1_HUMAN T 683 ENSP00000359603:R683T;ENSP00000392531:R683T ENSP00000359603:R683T R - 2 0 COL24A1 86270150 1.000000 0.71417 0.998000 0.56505 0.998000 0.95712 2.828000 0.48120 0.912000 0.36772 0.655000 0.94253 AGA TCGA-FB-A545-01A-11D-A26I-08 COL24A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029335.4 1 0 1 203 289 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 200 284 0 48 2 0 0 0 0 48 2 -20.000000 1 1 0 0 1 1 2 3 1.993825 1 0.530000 3.130000 0.628458 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TOX2 84969 broad.mit.edu 37 20 42635419 42635419 + Missense_Mutation SNP G G T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr20:42635419G>T ENST00000358131.5 + 3 633 c.425G>T c.(424-426)gGc>gTc p.G142V TOX2_ENST00000372999.1_Missense_Mutation_p.G91V|RN7SL443P_ENST00000464331.2_RNA|TOX2_ENST00000341197.4_Missense_Mutation_p.G133V|TOX2_ENST00000423191.2_Missense_Mutation_p.G91V NM_001098798.1 NP_001092268.1 Q96NM4 TOX2_HUMAN TOX high mobility group box family member 2 26 Myeloproliferative disorder(115;0.00452) COAD - Colon adenocarcinoma(18;0.00189) CTGCTGTCGGGCCAGCTGCCC 0.587000 0 SO:0001583 missense ENST00000358131.5 1 1 hg19 CCDS42875.1 . . . . . . . . . . G 13.96 2.391733 0.42410 . . ENSG00000124191 ENST00000341197;ENST00000442881;ENST00000423191;ENST00000372999;ENST00000358131 T;T;T;T;T 0.21361 2.01;2.01;2.01;2.01;2.01 5.61 5.61 0.85477 . 0.440984 0.25575 N 0.029739 T 0.19805 0.0476 L 0.29908 0.895 0.80722 D 1 P;B;B;B 0.39480 0.675;0.151;0.058;0.115 B;B;B;B 0.41988 0.372;0.045;0.022;0.033 T 0.01476 -1.1345 10 0.40728 T 0.16 . 13.8806 0.63680 0.0:0.1528:0.8472:0.0 . 133;91;142;91 G3XAC7;A8K1J1;Q96NM4;E1P5X0 .;.;TOX2_HUMAN;. V 133;91;91;91;142 ENSP00000344724:G133V;ENSP00000396584:G91V;ENSP00000390278:G91V;ENSP00000362090:G91V;ENSP00000350849:G142V ENSP00000344724:G133V G + 2 0 TOX2 42068833 0.999000 0.42202 0.981000 0.43875 0.998000 0.95712 4.475000 0.60210 2.631000 0.89168 0.655000 0.94253 GGC TCGA-FB-A545-01A-11D-A26I-08 TOX2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000079329.2 1 0 1 55 131 0 30 0 8.983452e-02 0 2 0 30 2 0 0 0 0 0 2 1 1.000000 54 129 0 29 2 0 0 0 0 30 2 -20.000000 1 1 0 0 1 2 2 4 2.276915 1 0.530000 3.130000 0.682925 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 ZNF74 7625 broad.mit.edu 37 22 20760941 20760941 + Missense_Mutation SNP A A G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr22:20760941A>G ENST00000400451.2 + 5 2132 c.1618A>G c.(1618-1620)Aac>Gac p.N540D ZNF74_ENST00000405993.1_Missense_Mutation_p.N508D|ZNF74_ENST00000356671.5_Missense_Mutation_p.N540D|ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000403682.3_3'UTR NM_003426.3 NP_003417.2 Q16587 ZNF74_HUMAN zinc finger protein 74 19 Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219) Lung SC(17;0.0262)|all_lung(157;0.248) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173) CTTCAGCCAGAACCACTGTCT 0.547000 0 SO:0001583 missense ENST00000400451.2 1 1 hg19 CCDS42982.1 . . . . . . . . . . A 17.26 3.343858 0.61073 . . ENSG00000185252 ENST00000400451;ENST00000356671;ENST00000405993 T;T;T 0.28255 1.62;1.62;1.62 4.15 4.15 0.48705 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.43747 D 0.000526 T 0.25306 0.0615 N 0.17564 0.495 0.21579 N 0.999635 D 0.58268 0.982 P 0.52554 0.702 T 0.05037 -1.0910 10 0.36615 T 0.2 -40.4338 7.9518 0.30019 0.7914:0.2086:0.0:0.0 . 540 Q16587 ZNF74_HUMAN D 540;540;508 ENSP00000383301:N540D;ENSP00000349098:N540D;ENSP00000385855:N508D ENSP00000349098:N540D N + 1 0 ZNF74 19090941 0.000000 0.05858 1.000000 0.80357 0.980000 0.70556 0.322000 0.19576 2.097000 0.63578 0.533000 0.62120 AAC TCGA-FB-A545-01A-11D-A26I-08 ZNF74-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319648.2 1 0 1 203 410 0 75 0 6.445573e-01 0 6 0 75 2 0 0 0 0 0 2 1 1.000000 201 405 0 74 2 0 0 0 0 75 2 -20.000000 1 1 0 0 1 2 2 4 2.312570 1 0.530000 3.130000 0.687396 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TRIOBP 11078 broad.mit.edu 37 22 38119251 38119251 + Missense_Mutation SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr22:38119251G>A ENST00000406386.3 + 7 943 c.688G>A c.(688-690)Ggg>Agg p.G230R NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 12 Melanoma(58;0.0574) GGGAGAAAGCGGGTTGTCCCT 0.647000 0 SO:0001583 missense ENST00000406386.3 1 1 hg19 CCDS43015.1 . . . . . . . . . . G 8.003 0.755843 0.15846 . . ENSG00000100106 ENST00000406386;ENST00000417174 T 0.29917 1.55 4.74 1.45 0.22620 . . . . . T 0.16085 0.0387 N 0.14661 0.345 0.09310 N 1 B 0.13145 0.007 B 0.09377 0.004 T 0.21109 -1.0255 9 0.66056 D 0.02 . 4.2708 0.10785 0.2696:0.0:0.5734:0.157 . 230 Q9H2D6 TARA_HUMAN R 230 ENSP00000384312:G230R ENSP00000384312:G230R G + 1 0 TRIOBP 36449197 0.006000 0.16342 0.021000 0.16686 0.137000 0.21094 0.354000 0.20146 0.456000 0.26937 -0.381000 0.06696 GGG TCGA-FB-A545-01A-11D-A26I-08 TRIOBP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000319439.2 1 0 1 76 173 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 1.000000 75 171 0 34 2 0 0 0 0 34 2 -7.784357 1 1 0 0 1 2 2 4 2.318011 1 0.530000 3.130000 0.688494 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TTN 7273 broad.mit.edu 37 2 179655562 179655562 + Missense_Mutation SNP T T C TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr2:179655562T>C ENST00000591111.1 - 11 1897 c.1673A>G c.(1672-1674)gAa>gGa p.E558G TTN_ENST00000360870.5_Missense_Mutation_p.E558G|TTN_ENST00000342992.6_Missense_Mutation_p.E558G|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.E558G|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TATCTCAGTTTCCTGTCTTAT 0.393000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . T 12.33 1.904601 0.33628 . . ENSG00000155657 ENST00000342992;ENST00000360870 T;T 0.79247 -1.25;-1.25 5.07 3.89 0.44902 Titin Z (1);Ribonuclease H-like (1); . . . . T 0.67316 0.2880 N 0.24115 0.695 0.80722 D 1 B;B 0.34329 0.099;0.449 B;B 0.37091 0.112;0.241 T 0.68450 -0.5405 9 0.87932 D 0 . 12.0991 0.53772 0.0:0.0:0.1438:0.8562 . 558;558 Q8WZ42;Q8WZ42-6 TITIN_HUMAN;. G 558 ENSP00000343764:E558G;ENSP00000354117:E558G ENSP00000343764:E558G E - 2 0 TTN 179363807 0.995000 0.38212 1.000000 0.80357 0.927000 0.56198 2.570000 0.45981 0.921000 0.36994 0.533000 0.62120 GAA TCGA-FB-A545-01A-11D-A26I-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 214 343 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 1.000000 213 337 0 50 2 0 0 0 0 50 2 -20.000000 1 1 0 0 1 2 2 4 2.275913 1 0.530000 3.130000 0.682925 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TMEM198 130612 broad.mit.edu 37 2 220414568 220414568 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr2:220414568C>T ENST00000344458.2 + 6 1660 c.1075C>T c.(1075-1077)Cgg>Tgg p.R359W RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA|TMEM198_ENST00000373883.3_Missense_Mutation_p.R359W Q66K66 TM198_HUMAN transmembrane protein 198 16 Renal(207;0.0376) CCCCCCAGTGCGGGTATAGCC 0.622000 0 SO:0001583 missense ENST00000344458.2 1 1 hg19 CCDS33385.1 . . . . . . . . . . C 19.08 3.757344 0.69648 . . ENSG00000188760 ENST00000344458;ENST00000373883 . . . 5.1 5.1 0.69264 . 0.070539 0.56097 D 0.000030 T 0.34978 0.0916 N 0.14661 0.345 0.53005 D 0.999966 B 0.33022 0.394 B 0.25291 0.059 T 0.37267 -0.9713 9 0.87932 D 0 -11.0301 14.7067 0.69198 0.1454:0.8546:0.0:0.0 . 359 Q66K66 TM198_HUMAN W 359 . ENSP00000343507:R359W R + 1 2 TMEM198 220122812 1.000000 0.71417 1.000000 0.80357 0.744000 0.42396 2.741000 0.47426 2.824000 0.97209 0.655000 0.94253 CGG TCGA-FB-A545-01A-11D-A26I-08 TMEM198-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131063.1 1 0 1 190 426 0 80 0 4.899558e-01 1 4 0 80 2 0 0 0 0 0 2 1 1.000000 190 419 0 79 2 0 0 0 0 80 2 -20.000000 1 1 121412 2 36 1 2 2 4 2.275913 1 0.530000 3.130000 0.682925 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 UNC50 25972 broad.mit.edu 37 2 99226308 99226308 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr2:99226308C>T ENST00000357765.2 + 2 238 c.86C>T c.(85-87)gCg>gTg p.A29V COA5_ENST00000483527.1_5'Flank|COA5_ENST00000328709.3_5'Flank|UNC50_ENST00000409347.1_Missense_Mutation_p.A46V|UNC50_ENST00000409975.1_Missense_Mutation_p.A46V|COA5_ENST00000409997.1_5'Flank NM_014044.5 NP_054763.2 Q53HI1 UNC50_HUMAN unc-50 homolog (C. elegans) 10 ACAGCCGGAGCGAAACGCTAC 0.493000 0 SO:0001583 missense ENST00000357765.2 1 1 hg19 CCDS2035.1 . . . . . . . . . . C 27.2 4.810691 0.90707 . . ENSG00000115446 ENST00000357765;ENST00000409975;ENST00000409347 . . . 5.06 5.06 0.68205 . 0.153865 0.56097 D 0.000026 T 0.70727 0.3257 L 0.58810 1.83 0.80722 D 1 D 0.67145 0.996 P 0.55345 0.774 T 0.69551 -0.5115 9 0.35671 T 0.21 -29.8512 17.7675 0.88482 0.0:1.0:0.0:0.0 . 29 Q53HI1 UNC50_HUMAN V 29;46;46 . ENSP00000350409:A29V A + 2 0 UNC50 98592740 1.000000 0.71417 0.999000 0.59377 0.989000 0.77384 5.595000 0.67563 2.505000 0.84491 0.591000 0.81541 GCG TCGA-FB-A545-01A-11D-A26I-08 UNC50-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252987.1 1 0 1 500 1002 0 142 1 1 20 45 0 142 2 0 0 0 0 0 2 1 1.000000 498 998 0 142 2 0 0 0 0 142 2 -20.000000 1 1 0 0 1 2 2 4 2.367309 1 0.530000 3.130000 0.692810 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 IFT122 55764 broad.mit.edu 37 3 129195581 129195581 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr3:129195581C>T ENST00000348417.2 + 11 1161 c.1084C>T c.(1084-1086)Cgc>Tgc p.R362C IFT122_ENST00000440957.2_Missense_Mutation_p.R153C|IFT122_ENST00000349441.2_Missense_Mutation_p.R251C|IFT122_ENST00000431818.2_Missense_Mutation_p.R212C|IFT122_ENST00000347300.2_Missense_Mutation_p.R303C|IFT122_ENST00000507564.1_Missense_Mutation_p.R354C|IFT122_ENST00000504021.1_Missense_Mutation_p.R256C|IFT122_ENST00000296266.3_Missense_Mutation_p.R413C NM_052989.1 NP_443715.1 Q9HBG6 IF122_HUMAN intraflagellar transport 122 52 TTACAAGGACCGCTATGCCTA 0.537000 0 SO:0001583 missense ENST00000348417.2 1 1 hg19 CCDS3061.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 29.9|29.9 5.043912|5.043912 0.93685|0.93685 .|. .|. ENSG00000163913|ENSG00000163913 ENST00000512157;ENST00000515783|ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957 .|T;T;T;D;T;T;T;D .|0.90261 .|0.5;-0.16;-0.04;-2.64;0.65;0.63;0.47;-2.64 5.65|5.65 5.65|5.65 0.86999|0.86999 .|. .|0.000000 .|0.85682 .|D .|0.000000 D|D 0.96012|0.96012 0.8701|0.8701 M|M 0.86178|0.86178 2.8|2.8 0.80722|0.80722 D|D 1|1 .|D;D;D;D;D;D;D;D .|0.89917 .|1.0;1.0;0.997;0.986;0.986;0.992;1.0;1.0 .|D;D;P;P;P;P;D;D .|0.85130 .|0.997;0.988;0.755;0.568;0.568;0.805;0.993;0.997 D|D 0.95987|0.95987 0.8982|0.8982 5|10 .|0.66056 .|D .|0.02 -24.8899|-24.8899 19.7278|19.7278 0.96172|0.96172 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|153;354;256;202;251;303;362;413 .|E9PDG2;E7EQF4;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1 .|.;.;.;.;.;.;IF122_HUMAN;. L|C 240;188|303;413;354;303;212;256;251;362;202;153 .|ENSP00000323973:R303C;ENSP00000296266:R413C;ENSP00000425536:R354C;ENSP00000410946:R212C;ENSP00000422179:R256C;ENSP00000324165:R251C;ENSP00000324005:R362C;ENSP00000401569:R153C .|ENSP00000296266:R413C P|R +|+ 2|1 0|0 IFT122|IFT122 130678271|130678271 1.000000|1.000000 0.71417|0.71417 0.994000|0.994000 0.49952|0.49952 0.950000|0.950000 0.60333|0.60333 7.440000|7.440000 0.80464|0.80464 2.656000|2.656000 0.90262|0.90262 0.591000|0.591000 0.81541|0.81541 CCG|CGC TCGA-FB-A545-01A-11D-A26I-08 IFT122-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000355852.1 1 0 1 181 252 0 65 1 6.928083e-01 2 3 0 65 2 0 0 0 0 0 2 1 1.000000 180 251 0 65 2 0 0 0 0 65 2 -3.318794 1 1 121412 6 42 1 1 2 3 1.984701 1 0.530000 3.130000 0.628458 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SATB1 6304 broad.mit.edu 37 3 18462359 18462359 + Missense_Mutation SNP T T G TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr3:18462359T>G ENST00000338745.6 - 2 1835 c.101A>C c.(100-102)gAg>gCg p.E34A SATB1_ENST00000454909.2_Missense_Mutation_p.E34A|SATB1_ENST00000417717.2_Missense_Mutation_p.E34A|SATB1_ENST00000493952.2_Missense_Mutation_p.E34A|TBC1D5_ENST00000414318.2_Intron NM_002971.4 NP_002962.1 Q01826 SATB1_HUMAN SATB homeobox 1 32 CCCGTTCTGCTCCAGGCGGGC 0.507000 0 SO:0001583 missense ENST00000338745.6 1 1 hg19 CCDS2631.1 . . . . . . . . . . T 27.1 4.796438 0.90453 . . ENSG00000182568 ENST00000338745;ENST00000454909;ENST00000417717;ENST00000440737;ENST00000452260;ENST00000415069;ENST00000457005;ENST00000414509;ENST00000444341 T;T;T;T;T;T;T;T;T 0.58940 0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3 5.83 5.83 0.93111 . 0.000000 0.85682 D 0.000000 T 0.70962 0.3284 L 0.50333 1.59 0.80722 D 1 D;D 0.71674 0.998;0.997 D;D 0.69142 0.962;0.955 T 0.73616 -0.3926 10 0.87932 D 0 -13.3153 16.2147 0.82198 0.0:0.0:0.0:1.0 . 34;34 Q01826-2;Q01826 .;SATB1_HUMAN A 34 ENSP00000341024:E34A;ENSP00000399708:E34A;ENSP00000399518:E34A;ENSP00000402982:E34A;ENSP00000406727:E34A;ENSP00000390529:E34A;ENSP00000398072:E34A;ENSP00000408871:E34A;ENSP00000391344:E34A ENSP00000341024:E34A E - 2 0 SATB1 18437363 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 7.698000 0.84413 2.231000 0.72958 0.460000 0.39030 GAG TCGA-FB-A545-01A-11D-A26I-08 SATB1-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252138.4 1 0 1 377 517 0 93 1 9.644280e-01 5 5 0 93 2 0 0 0 0 0 2 1 1.000000 374 516 0 92 2 0 0 0 0 93 2 -20.000000 1 1 0 0 1 1 2 3 1.963190 1 0.530000 3.130000 0.627679 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 DLEC1 9940 broad.mit.edu 37 3 38087134 38087134 + Missense_Mutation SNP T T C TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr3:38087134T>C ENST00000308059.6 + 2 533 c.512T>C c.(511-513)aTg>aCg p.M171T DLEC1_ENST00000452631.2_Missense_Mutation_p.M171T|DLEC1_ENST00000346219.3_Missense_Mutation_p.M171T deleted in lung and esophageal cancer 1 51 GAGCGGGTCATGAGCCAGGCT 0.532000 0 SO:0001583 missense ENST00000308059.6 1 1 hg19 CCDS2672.2 . . . . . . . . . . T 3.529 -0.096060 0.07010 . . ENSG00000008226 ENST00000308059;ENST00000346219;ENST00000452631 T;T;T 0.04454 3.64;3.62;3.86 4.8 1.09 0.20402 . 0.831243 0.11038 N 0.606427 T 0.03520 0.0101 L 0.27053 0.805 0.09310 N 1 B;B;B 0.09022 0.0;0.002;0.0 B;B;B 0.09377 0.004;0.004;0.004 T 0.47824 -0.9087 10 0.21540 T 0.41 -1.8806 6.245 0.20811 0.0:0.3221:0.0:0.6779 . 171;171;171 F8W6T4;Q9Y238-3;Q9Y238 .;.;DLEC1_HUMAN T 171 ENSP00000308597:M171T;ENSP00000315914:M171T;ENSP00000410427:M171T ENSP00000308597:M171T M + 2 0 DLEC1 38062138 0.000000 0.05858 0.000000 0.03702 0.046000 0.14306 -0.141000 0.10327 0.040000 0.15660 0.533000 0.62120 ATG TCGA-FB-A545-01A-11D-A26I-08 DLEC1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000253745.3 1 0 1 167 232 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1.000000 165 232 0 64 2 0 0 0 0 65 2 -20.000000 1 1 0 0 1 1 2 3 1.963190 1 0.530000 3.130000 0.627679 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MST1R 4486 broad.mit.edu 37 3 49936017 49936017 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr3:49936017C>T ENST00000296474.3 - 4 1680 c.1653G>A c.(1651-1653)atG>atA p.M551I MST1R_ENST00000344206.4_Missense_Mutation_p.M551I|CTD-2330K9.2_ENST00000435478.1_RNA NM_002447.2 NP_002438 Q04912 RON_HUMAN macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 37 GCTGGCCGCACATGTTCCCAC 0.602000 0 SO:0001583 missense ENST00000296474.3 1 1 hg19 CCDS2807.1 . . . . . . . . . . C 6.278 0.419493 0.11928 . . ENSG00000164078 ENST00000296474;ENST00000344206 T;T 0.40476 1.03;3.05 5.78 2.89 0.33648 . 0.728645 0.13917 N 0.353825 T 0.26122 0.0637 N 0.26042 0.785 0.23572 N 0.997382 B;B;B;B 0.19817 0.039;0.012;0.004;0.003 B;B;B;B 0.14023 0.009;0.01;0.007;0.001 T 0.13335 -1.0513 10 0.54805 T 0.06 -3.2634 3.9856 0.09514 0.1046:0.5013:0.2391:0.155 . 445;551;551;551 Q04912-4;Q04912-6;Q04912-5;Q04912 .;.;.;RON_HUMAN I 551 ENSP00000296474:M551I;ENSP00000341325:M551I ENSP00000296474:M551I M - 3 0 MST1R 49911021 0.000000 0.05858 0.890000 0.34922 0.746000 0.42486 -0.224000 0.09164 1.452000 0.47756 0.491000 0.48974 ATG TCGA-FB-A545-01A-11D-A26I-08 MST1R-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000345403.1 1 0 1 209 336 0 78 1 1 38 38 0 78 2 0 0 0 0 0 2 1 1.000000 206 329 0 78 2 0 0 0 0 78 2 -20.000000 1 1 0 0 1 1 2 3 1.919557 1 0.530000 3.130000 0.625319 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ATP8A1 10396 broad.mit.edu 37 4 42580334 42580334 + Silent SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr4:42580334G>A ENST00000381668.5 - 12 1302 c.1071C>T c.(1069-1071)atC>atT p.I357I ATP8A1_ENST00000264449.10_Silent_p.I357I NM_006095.2 NP_006086.1 Q9Y2Q0 AT8A1_HUMAN ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 51 Phosphatidylserine(DB00144) CCAATAAGCTGATAGGAATGA 0.348000 0 SO:0001819 synonymous_variant ENST00000381668.5 1 1 hg19 CCDS3466.1 TCGA-FB-A545-01A-11D-A26I-08 ATP8A1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000216861.2 1 0 1 220 326 0 52 0 0 0 1 0 52 2 0 0 0 0 0 2 1 1.000000 219 323 0 52 2 0 0 0 0 52 2 -20.000000 1 1 0 0 1 1 2 3 2.029622 1 0.530000 3.130000 0.628458 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 GAK 2580 broad.mit.edu 37 4 864531 864531 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr4:864531C>T ENST00000314167.4 - 19 2326 c.2216G>A c.(2215-2217)cGg>cAg p.R739Q GAK_ENST00000511163.1_Missense_Mutation_p.R660Q|GAK_ENST00000509566.1_5'UTR NM_005255.2 NP_005246.2 O14976 GAK_HUMAN cyclin G associated kinase 39 CTGCTCCTCCCGGCTGGAAAA 0.562000 0 SO:0001583 missense ENST00000314167.4 1 1 hg19 CCDS3340.1 . . . . . . . . . . C 20.7 4.037804 0.75617 0.0 1.16E-4 ENSG00000178950 ENST00000314167;ENST00000511163 T;T 0.77358 -0.65;-1.09 5.62 5.62 0.85841 . 0.125201 0.56097 D 0.000034 T 0.75700 0.3885 L 0.57536 1.79 0.80722 D 1 P;P;P;P 0.51791 0.791;0.948;0.791;0.898 B;P;B;B 0.44897 0.126;0.463;0.126;0.27 T 0.72567 -0.4254 10 0.12103 T 0.63 -23.5808 17.155 0.86788 0.0:1.0:0.0:0.0 . 660;660;739;635 Q5U4P5;E9PGR2;O14976;Q59HA5 .;.;GAK_HUMAN;. Q 739;660 ENSP00000314499:R739Q;ENSP00000421361:R660Q ENSP00000314499:R739Q R - 2 0 GAK 854531 1.000000 0.71417 0.965000 0.40720 0.997000 0.91878 7.656000 0.83736 2.643000 0.89663 0.655000 0.94253 CGG TCGA-FB-A545-01A-11D-A26I-08 GAK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239188.1 0 0 0 17 473 0 61 1 7.666833e-01 2 77 0 61 2 0 0 0 0 0 2 1 0.999965 16 471 0 61 2 0 0 0 0 61 2 -2.374798 0 1 121412 3 36 1 1 2 3 2.001705 1 0.530000 3.130000 0.628458 0.160000 0.090000 0.260000 0.160000 0.174426 0.160000 0 0.120000 0.210000 ZNF354A 6940 broad.mit.edu 37 5 178139093 178139093 + Missense_Mutation SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr5:178139093G>A ENST00000335815.2 - 5 1983 c.1786C>T c.(1786-1788)Cat>Tat p.H596Y NM_005649.2 NP_005640.2 O60765 Z354A_HUMAN zinc finger protein 354A 19 all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536) all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) ATTTTATAATGATTAGTAAGG 0.373000 0 SO:0001583 missense ENST00000335815.2 1 1 hg19 CCDS4438.1 . . . . . . . . . . G 9.811 1.183252 0.21870 . . ENSG00000169131 ENST00000335815 D 0.96168 -3.93 4.47 4.47 0.54385 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . D 0.97996 0.9340 M 0.93420 3.415 0.42876 D 0.994154 D 0.76494 0.999 D 0.63703 0.917 D 0.99133 1.0853 9 0.87932 D 0 -12.4023 14.9914 0.71390 0.0:0.0:1.0:0.0 . 596 O60765 Z354A_HUMAN Y 596 ENSP00000337122:H596Y ENSP00000337122:H596Y H - 1 0 ZNF354A 178071699 . . 0.998000 0.56505 0.200000 0.23975 . . 2.477000 0.83638 0.655000 0.94253 CAT TCGA-FB-A545-01A-11D-A26I-08 ZNF354A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253481.1 1 0 1 138 119 0 35 1 9.965874e-01 6 5 0 35 2 0 0 0 0 0 2 1 1.000000 137 118 0 35 2 0 0 0 0 35 2 -20.000000 1 1 0 0 1 0 2 2 1.583779 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CYB5R4 51167 broad.mit.edu 37 6 84649843 84649843 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr6:84649843C>T ENST00000369681.5 + 13 1317 c.1177C>T c.(1177-1179)Ctc>Ttc p.L393F CYB5R4_ENST00000479164.1_3'UTR NM_016230.3 NP_057314.2 Q7L1T6 NB5R4_HUMAN cytochrome b5 reductase 4 23 all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128) ATTAGAAGATCTCTTTTTGTT 0.348000 Esophageal Squamous(86;1289 1332 25971 40349 52675) 0 SO:0001583 missense ENST00000369681.5 1 1 hg19 CCDS5000.2 . . . . . . . . . . C 20.0 3.930026 0.73327 . . ENSG00000065615 ENST00000369681 D 0.95412 -3.7 5.93 5.93 0.95920 . 0.057149 0.64402 D 0.000001 D 0.95146 0.8427 M 0.78344 2.41 0.80722 D 1 P 0.48294 0.908 P 0.46885 0.53 D 0.95436 0.8521 10 0.72032 D 0.01 . 15.4232 0.75031 0.0:0.8614:0.1385:0.0 . 393 Q7L1T6 NB5R4_HUMAN F 393 ENSP00000358695:L393F ENSP00000358695:L393F L + 1 0 CYB5R4 84706562 1.000000 0.71417 1.000000 0.80357 0.934000 0.57294 2.088000 0.41663 2.805000 0.96524 0.655000 0.94253 CTC TCGA-FB-A545-01A-11D-A26I-08 CYB5R4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041362.4 1 0 1 207 179 0 48 1 9.936827e-01 6 4 0 48 2 0 0 0 0 0 2 1 1.000000 207 176 0 47 2 0 0 0 0 48 2 -20.000000 1 1 0 0 1 0 2 2 1.573032 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KLHL38 340359 broad.mit.edu 37 8 124664070 124664070 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr8:124664070C>T ENST00000325995.7 - 1 1120 c.1097G>A c.(1096-1098)gGg>gAg p.G366E CTD-2552K11.2_ENST00000524355.1_RNA NM_001081675.2 NP_001075144.2 Q2WGJ6 KLH38_HUMAN kelch-like family member 38 38 CATGGGCTCCCCCAGCCTCCA 0.572000 0 SO:0001583 missense ENST00000325995.7 1 1 hg19 CCDS43766.1 . . . . . . . . . . C 15.75 2.924416 0.52653 . . ENSG00000175946 ENST00000325995 T 0.67345 -0.26 5.18 4.3 0.51218 Kelch-type beta propeller (1); 0.153290 0.56097 D 0.000021 T 0.67411 0.2890 M 0.83012 2.62 0.33365 D 0.572771 B 0.17268 0.021 B 0.17098 0.017 T 0.72988 -0.4124 10 0.51188 T 0.08 . 10.1655 0.42877 0.1802:0.6871:0.1327:0.0 . 366 Q2WGJ6 KLH38_HUMAN E 366 ENSP00000321475:G366E ENSP00000321475:G366E G - 2 0 KLHL38 124733251 0.997000 0.39634 1.000000 0.80357 0.976000 0.68499 3.244000 0.51399 1.278000 0.44430 0.561000 0.74099 GGG TCGA-FB-A545-01A-11D-A26I-08 KLHL38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381288.1 1 0 1 199 436 0 79 0 0 0 1 0 79 2 0 0 0 0 0 2 1 1.000000 200 436 0 77 2 0 0 0 0 79 2 -13.868340 1 1 0 0 1 2 2 4 2.347604 1 0.530000 3.130000 0.692810 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KCNT1 57582 broad.mit.edu 37 9 138641963 138641963 + Missense_Mutation SNP G G A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr9:138641963G>A ENST00000263604.3 + 3 217 c.217G>A c.(217-219)Gtc>Atc p.V73I KCNT1_ENST00000486577.2_Missense_Mutation_p.V53I|KCNT1_ENST00000488444.2_Missense_Mutation_p.V73I|KCNT1_ENST00000298480.5_Missense_Mutation_p.V92I|KCNT1_ENST00000371757.2_Missense_Mutation_p.V92I|KCNT1_ENST00000491806.2_Missense_Mutation_p.V59I|KCNT1_ENST00000487664.1_Missense_Mutation_p.V44I|KCNT1_ENST00000490355.2_Missense_Mutation_p.V73I Q5JUK3 KCNT1_HUMAN potassium channel, subfamily T, member 1 50 Myeloproliferative disorder(178;0.0821) GGAGTTCTACGTCAACGAGAA 0.607000 0 SO:0001583 missense ENST00000263604.3 0 1 hg19 . . . . . . . . . . g 22.2 4.255822 0.80135 . . ENSG00000107147 ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604 T;T;T;T;T 0.50548 1.75;1.66;1.66;0.74;1.72 4.18 4.18 0.49190 . 0.000000 0.64402 D 0.000002 T 0.59622 0.2207 M 0.72353 2.195 0.80722 D 1 D;D 0.58268 0.97;0.982 P;P 0.53006 0.522;0.715 T 0.66630 -0.5875 10 0.59425 D 0.04 -9.5267 15.8483 0.78907 0.0:0.0:1.0:0.0 . 92;44 B9EGP2;G5E9V0 .;. I 44;92;92;39;53;59;73;73;73 ENSP00000417851:V44I;ENSP00000298480:V92I;ENSP00000360822:V92I;ENSP00000420764:V39I;ENSP00000263604:V73I ENSP00000263604:V73I V + 1 0 KCNT1 137781784 1.000000 0.71417 0.951000 0.38953 0.904000 0.53231 9.449000 0.97603 2.053000 0.61076 0.561000 0.74099 GTC TCGA-FB-A545-01A-11D-A26I-08 KCNT1-201 KNOWN basic|appris_candidate protein_coding protein_coding 0 0 0 5 223 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.937506 5 222 0 23 2 0 0 0 0 23 2 -6.385526 1 0 121400 1 30 1 1 2 3 2.018806 1 0.530000 3.130000 0.624526 0.110000 0.030000 1.000000 0.110000 0.156207 0.110000 0 0.060000 0.180000 AQP7 364 broad.mit.edu 37 9 33386077 33386077 + Missense_Mutation SNP C C T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chr9:33386077C>T ENST00000537089.1 - 5 565 c.247G>A c.(247-249)Gag>Aag p.E83K AQP7_ENST00000541274.1_Intron|AQP7_ENST00000377425.4_Missense_Mutation_p.E118K|AQP7_ENST00000539936.1_Missense_Mutation_p.E175K O14520 AQP7_HUMAN aquaporin 7 17 LUSC - Lung squamous cell carcinoma(29;0.00788) CCACTGACCTCATTCAGGAAG 0.592000 0 SO:0001583 missense ENST00000537089.1 0 1 hg19 . . . . . . . . . . N 24.0 4.485614 0.84854 . . ENSG00000165269 ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503 T;T;T;T;T;T;T;T;T 0.29917 1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55 3.98 3.98 0.46160 Aquaporin-like (2); 0.106561 0.64402 D 0.000003 T 0.67618 0.2912 H 0.98238 4.18 0.44789 D 0.997793 P;D;P;D 0.63046 0.9;0.992;0.948;0.982 P;D;P;P 0.70227 0.643;0.968;0.771;0.752 T 0.78526 -0.2170 10 0.87932 D 0 -26.5908 11.903 0.52694 0.0:1.0:0.0:0.0 . 174;175;118;175 Q5T5M0;B7Z4U2;Q6P5T0;O14520 .;.;.;AQP7_HUMAN K 83;174;43;175;118;83;174;175;111 ENSP00000441619:E83K;ENSP00000368821:E174K;ENSP00000412868:E43K;ENSP00000297988:E175K;ENSP00000396111:E118K;ENSP00000410138:E83K;ENSP00000368820:E174K;ENSP00000439534:E175K;ENSP00000368817:E111K ENSP00000297988:E175K E - 1 0 AQP7 33376077 0.998000 0.40836 0.999000 0.59377 0.984000 0.73092 1.723000 0.38053 2.507000 0.84556 0.645000 0.84053 GAG TCGA-FB-A545-01A-11D-A26I-08 AQP7-202 KNOWN basic protein_coding protein_coding 0 0 0 12 379 0 51 0 0 0 1 0 51 2 0 0 0 0 0 2 1 0.998849 8 364 0 50 2 0 0 0 0 51 2 -2.565206 1 1 0 0 1 0 2 2 1.520844 1 0.530000 3.130000 0.530000 0.110000 0.050000 0.190000 0.120000 0.124526 0.110000 0 0.080000 0.160000 COL4A5 1287 broad.mit.edu 37 X 107925082 107925082 + Missense_Mutation SNP G G T TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chrX:107925082G>T ENST00000361603.2 + 45 4406 c.4162G>T c.(4162-4164)Ggt>Tgt p.G1388C COL4A5_ENST00000328300.6_Missense_Mutation_p.G1394C NM_000495.4 NP_000486.1 P29400 CO4A5_HUMAN collagen, type IV, alpha 5 99 TGGGCTAAAGGGTCTACCAGG 0.458000 Alport syndrome with Diffuse Leiomyomatosis 0 SO:0001583 missense Familial Cancer Database ENST00000361603.2 1 1 hg19 CCDS14543.1 . . . . . . . . . . G 18.11 3.549782 0.65311 . . ENSG00000188153 ENST00000328300;ENST00000361603;ENST00000508186 D;D 0.97089 -4.24;-4.24 5.0 5.0 0.66597 . 0.000000 0.85682 D 0.000000 D 0.99089 0.9687 H 0.97587 4.035 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.99236 1.0883 10 0.87932 D 0 . 17.7015 0.88296 0.0:0.0:1.0:0.0 . 1391;1388 E7EVY4;P29400 .;CO4A5_HUMAN C 1394;1388;1394 ENSP00000331902:G1394C;ENSP00000354505:G1388C ENSP00000331902:G1394C G + 1 0 COL4A5 107811738 1.000000 0.71417 1.000000 0.80357 0.444000 0.32077 8.937000 0.92936 2.196000 0.70406 0.506000 0.49869 GGT TCGA-FB-A545-01A-11D-A26I-08 COL4A5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000057880.2 1 0 1 115 174 0 41 0 3.505188e-01 1 2 0 41 2 0 0 0 0 0 2 1 1.000000 115 174 0 41 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 0 1 1 0.530000 3.130000 0.530000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SPANXD 64648 broad.mit.edu 37 X 140785784 140785784 + Silent SNP T T A TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chrX:140785784T>A ENST00000370515.3 - 2 465 c.132A>T c.(130-132)acA>acT p.T44T NM_032417.2|NM_145665.1 NP_115793.1|NP_663698.1 Q9BXN6 SPNXD_HUMAN SPANX family, member D 9 Acute lymphoblastic leukemia(192;7.65e-05) AGGACTCAGATGTTTTTAGTT 0.478000 0 SO:0001819 synonymous_variant ENST00000370515.3 1 1 hg19 CCDS14675.1 TCGA-FB-A545-01A-11D-A26I-08 SPANXD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058598.1 0 0 0 27 1117 0 181 0 0 0 0 181 2 0 0 0 0 0 2 1 1.000000 27 1076 0 182 2 0 0 0 0 181 2 -3.195774 1 1 0 0 1 0 1 1 0.530000 3.130000 0.530000 0.080000 0.050000 0.130000 0.090000 0.092115 0.080000 0 0.060000 0.110000 MECP2 4204 broad.mit.edu 37 X 153296531 153296531 + Missense_Mutation SNP G G A rs61750225 byFrequency TCGA-FB-A545-01A-11D-A26I-08 TCGA-FB-A545-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b6a5fc11-2047-4c23-b325-4cd21131fdf6 01505e81-dfca-433f-80ac-458881d3d217 g.chrX:153296531G>A ENST00000303391.6 - 4 997 c.748C>T c.(748-750)Cgc>Tgc p.R250C MECP2_ENST00000453960.2_Missense_Mutation_p.R262C|MECP2_ENST00000407218.1_3'UTR|MECP2_ENST00000460227.1_5'Flank NM_004992.3 NP_004983.1 P51608 MECP2_HUMAN methyl CpG binding protein 2 23 all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CTGCCGGGGCGTTTGATCACC 0.642000 0 GRCh37 CM023415 MECP2 M rs141382970 SO:0001583 missense ENST00000303391.6 1 1 hg19 CCDS14741.1 . . . . . . . . . . G 17.11 3.305397 0.60305 0.0 1.49E-4 ENSG00000169057 ENST00000303391;ENST00000545451;ENST00000453960;ENST00000369964 D;D 0.93019 -3.13;-3.15 5.48 5.48 0.80851 . 0.000000 0.85682 D 0.000000 D 0.94089 0.8105 L 0.32530 0.975 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.996;0.99 D 0.94482 0.7694 10 0.87932 D 0 -14.0476 12.1758 0.54184 0.0:0.0:0.8291:0.1709 . 262;250 P51608-2;P51608 .;MECP2_HUMAN C 250;250;262;250 ENSP00000301948:R250C;ENSP00000395535:R262C ENSP00000301948:R250C R - 1 0 MECP2 152949725 1.000000 0.71417 0.988000 0.46212 0.974000 0.67602 4.846000 0.62860 2.285000 0.76669 0.600000 0.82982 CGC TCGA-FB-A545-01A-11D-A26I-08 MECP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000061144.1 1 0 0 34 691 0 160 0 4.242639e-01 0 30 0 160 2 0 0 0 0 0 2 1 1.000000 33 677 0 159 2 0 0 0 0 160 2 -5.633248 1 1 121410 3 40 1 0 1 1 0.530000 3.130000 0.530000 0.170000 0.120000 0.240000 0.180000 0.181434 0.170000 0 0.140000 0.210000