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 TFAP2C 7022 broad.mit.edu 37 20 55212855 55212856 + Frame_Shift_Del DEL CA CA - TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr20:55212855_55212856delCA ENST00000201031.2 + 7 1382_1383 c.1139_1140delCA c.(1138-1140)ccafs p.P380fs TFAP2C_ENST00000544508.1_Frame_Shift_Del_p.P211fs NM_003222.3 NP_003213.1 Q92754 AP2C_HUMAN transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) 13 Colorectal(105;0.229) AGGCTCGCCCCAGTCTTGGAGA 0.550000 0 SO:0001589 frameshift_variant ENST00000201031.2 1 1 hg19 CCDS13454.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 TFAP2C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079823.2 1 0 0 116 486 0 81 0 9.850540e-02 0 3 0 81 2 0 0 0 0 0 0 1 1 113 471 0 79 2 -2.687192 1 1 0 0 1 3 4 7 2.450645 1 0.520000 3.450000 0.715808 0.990000 9.900000e-01 1.000000 1.000000 0.999876 0.990000 1 0.990000 1.000000 KIF1A 547 broad.mit.edu 37 2 241700765 241700776 + In_Frame_Del DEL CCAGCTCACACT CCAGCTCACACT - TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:241700765_241700776delCCAGCTCACACT ENST00000320389.7 - 23 2266_2277 c.2108_2119delAGTGTGAGCTGG c.(2107-2121)gagtgtgagctggcg>gcg p.ECEL703del KIF1A_ENST00000498729.2_In_Frame_Del_p.ECEL712del NM_004321.6 NP_004312.2 Q12756 KIF1A_HUMAN kinesin family member 1A 66 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) GCCCAGAGCGCCAGCTCACACTCCCGCTCTGT 0.632000 0 SO:0001651 inframe_deletion ENST00000320389.7 0 1 hg19 CCDS46561.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 KIF1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324536.3 1 0 0 29 184 0 23 0 2.002584e-02 0 2 0 23 2 0 0 0 0 0 0 1 1 37 185 0 22 2 -20.000000 1 1 0 0 1 2 3 5 2.294524 1 0.520000 3.450000 0.694151 0.870000 5.800000e-01 1.000000 1.000000 0.861717 0.870000 1 0.710000 1.000000 CCDC104 0 broad.mit.edu 37 2 55772051 55772052 + Frame_Shift_Del DEL AG AG - TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 AG - AG AG Valid Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:55772051_55772052delAG ENST00000349456.4 + 10 1084_1085 c.936_937delAG c.(934-939)acagagfs p.E313fs CCDC104_ENST00000407816.3_Frame_Shift_Del_p.E284fs|CCDC104_ENST00000339012.3_Frame_Shift_Del_p.E338fs Q96G28 CFA36_HUMAN 14 LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132) AGGAAATGACAGAGAAACCAGA 0.332000 0 SO:0001589 frameshift_variant ENST00000349456.4 0 1 hg19 CCDS1854.2 TCGA-HZ-A9TJ-01A-11D-A40W-08 CCDC104-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319610.2 1 0 0 11 168 0 22 1 9.999847e-01 30 324 0 22 2 0 0 0 0 0 0 1 9.984974e-01 11 168 0 22 2 -3.146440 1 0 0 0 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.440000 2.100000e-01 1.000000 0.390000 0.552407 0.440000 0 0.300000 1.000000 WTAP 9589 broad.mit.edu 37 6 160163179 160163180 + Splice_Site INS - - T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 - T - - Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr6:160163179_160163180insT ENST00000358372.4 + 4 1902 c.e4+1 SOD2_ENST00000546087.1_Intron|WTAP_ENST00000337387.4_Splice_Site NM_001270531.1|NM_004906.4 NP_001257460.1|NP_004897.2 Q15007 FL2D_HUMAN Wilms tumor 1 associated protein 18 Breast(66;0.000776)|Ovarian(120;0.0303) GATCTTAACTGTAAGTTTGAGT 0.282000 0 SO:0001630 splice_region_variant ENST00000358372.4 0 1 hg19 CCDS5266.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 WTAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042905.1 1 0 0 34 277 0 71 0 1 0 246 0 71 2 0 0 0 0 0 0 1 1 34 275 0 70 2 -20.000000 1 1 0 0 1 2 2 4 2.056728 0 0.520000 3.450000 0.661017 0.620000 4.300000e-01 1.000000 0.590000 0.667416 0.620000 0 0.510000 0.850000 CUBN 8029 broad.mit.edu 37 10 16877170 16877170 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr10:16877170G>A ENST00000377833.4 - 64 10270 c.10205C>T c.(10204-10206)gCa>gTa p.A3402V NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) GTTGCCAAATGCCTTGTGATA 0.438000 0 SO:0001583 missense ENST00000377833.4 1 1 hg19 CCDS7113.1 . . . . . . . . . . G 6.678 0.493742 0.12702 . . ENSG00000107611 ENST00000377833;ENST00000545090 T 0.19105 2.17 4.84 2.92 0.33932 CUB (5); 0.738516 0.11552 N 0.552718 T 0.24236 0.0587 L 0.47716 1.5 0.24037 N 0.996099 P 0.40360 0.714 B 0.43990 0.438 T 0.10291 -1.0636 10 0.30854 T 0.27 . 11.3802 0.49752 0.0:0.1371:0.7202:0.1427 . 3402 O60494 CUBN_HUMAN V 3402;243 ENSP00000367064:A3402V ENSP00000367064:A3402V A - 2 0 CUBN 16917176 0.660000 0.27420 0.004000 0.12327 0.008000 0.06430 2.533000 0.45667 0.593000 0.29745 -0.314000 0.08810 GCA TCGA-HZ-A9TJ-01A-11D-A40W-08 CUBN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047009.1 0 0 1 44 324 0 76 0 0 0 1 0 76 2 0 0 0 0 0 2 1 1 43 322 0 73 2 -3.318805 1 1 121412 2 31 1 2 2 4 2.106617 1 0.520000 3.450000 0.669513 0.680000 5.000000e-01 1.000000 0.670000 0.711963 0.680000 0 0.580000 0.830000 KRTAP5-3 387266 broad.mit.edu 37 11 1629414 1629414 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:1629414C>T ENST00000399685.1 - 1 279 c.202G>A c.(202-204)Ggc>Agc p.G68S NM_001012708.2 NP_001012726.1 Q6L8H2 KRA53_HUMAN keratin associated protein 5-3 8 all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) CCACAAGAGCCACAGACCCCC 0.667000 0 SO:0001583 missense ENST00000399685.1 1 1 hg19 CCDS41591.1 . . . . . . . . . . C 0.016 -1.519678 0.00967 . . ENSG00000196224 ENST00000399685 T 0.01548 4.78 3.39 3.39 0.38822 . . . . . T 0.03564 0.0102 M 0.66439 2.03 0.20975 N 0.999817 P 0.46142 0.873 P 0.46452 0.517 T 0.17653 -1.0362 9 0.06757 T 0.87 . 12.6532 0.56774 0.0:1.0:0.0:0.0 . 68 Q6L8H2 KRA53_HUMAN S 68 ENSP00000382592:G68S ENSP00000382592:G68S G - 1 0 KRTAP5-3 1585990 0.942000 0.31987 0.997000 0.53966 0.006000 0.05464 0.591000 0.23969 1.616000 0.50265 0.289000 0.19496 GGC TCGA-HZ-A9TJ-01A-11D-A40W-08 KRTAP5-3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000127924.1 1 0 0 31 452 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1 30 425 0 96 2 -7.318248 1 1 0 0 1 1 2 3 1.531864 1 0.520000 3.450000 0.583839 0.300000 1.900000e-01 1.000000 0.280000 0.458100 0.300000 0 0.240000 1.000000 NELL1 4745 broad.mit.edu 37 11 21556023 21556023 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:21556023C>T ENST00000357134.5 + 16 1901 c.1749C>T c.(1747-1749)gaC>gaT p.D583D NELL1_ENST00000298925.5_Silent_p.D611D|NELL1_ENST00000532434.1_Intron|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Silent_p.D526D NM_006157.3|NM_201551.1 NP_006148.2|NP_963845.1 Q92832 NELL1_HUMAN NEL-like 1 (chicken) 70 GTTTCCATGACGATGGGACCT 0.527000 0 SO:0001819 synonymous_variant ENST00000357134.5 1 1 hg19 CCDS7855.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 NELL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387588.1 1 0 0 63 263 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1 63 258 0 63 2 -20.000000 1 0 121410 1 31 1 1 2 3 1.837416 1 0.520000 3.450000 0.619048 0.930000 7.300000e-01 1.000000 1.000000 0.923167 0.930000 1 0.830000 1.000000 OSBPL5 114879 broad.mit.edu 37 11 3129166 3129166 + Nonsense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:3129166C>T ENST00000263650.7 - 8 860 c.701G>A c.(700-702)tGg>tAg p.W234* OSBPL5_ENST00000525498.1_Nonsense_Mutation_p.W145*|OSBPL5_ENST00000348039.5_Nonsense_Mutation_p.W166*|OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000389989.3_Nonsense_Mutation_p.W166* NM_020896.3 NP_065947.1 Q9H0X9 OSBL5_HUMAN oxysterol binding protein-like 5 25 all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681) GGCGTCCAGCCAGCAGCGACC 0.697000 0 SO:0001587 stop_gained ENST00000263650.7 0 1 hg19 CCDS31344.1 . . . . . . . . . . C 20.4 3.989428 0.74589 . . ENSG00000021762 ENST00000263650;ENST00000389989;ENST00000525498;ENST00000348039 . . . 4.2 4.2 0.49525 . 0.000000 0.64402 D 0.000003 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -11.0922 16.7016 0.85350 0.0:1.0:0.0:0.0 . . . . X 234;166;145;166 . ENSP00000263650:W234X W - 2 0 OSBPL5 3085742 1.000000 0.71417 1.000000 0.80357 0.254000 0.26022 7.116000 0.77119 2.156000 0.67533 0.455000 0.32223 TGG TCGA-HZ-A9TJ-01A-11D-A40W-08 OSBPL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032332.2 1 0 1 43 60 0 11 0 9.984169e-01 0 18 0 11 2 0 0 0 0 0 2 1 1 43 58 0 11 2 -20.000000 1 1 0 0 1 1 2 3 1.845570 1 0.520000 3.450000 0.619048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PRR5L 79899 broad.mit.edu 37 11 36472814 36472814 + Missense_Mutation SNP T T A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:36472814T>A ENST00000378867.3 + 9 996 c.641T>A c.(640-642)gTg>gAg p.V214E PRR5L_ENST00000530639.1_Missense_Mutation_p.V214E|PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000527487.1_Intron|PRR5L_ENST00000311599.5_Missense_Mutation_p.V141E NM_024841.4 NP_079117.3 Q6MZQ0 PRR5L_HUMAN proline rich 5 like 19 GAGGAGCTGGTGAAGCAAGTG 0.527000 0 SO:0001583 missense ENST00000378867.3 1 1 hg19 CCDS31463.1 . . . . . . . . . . T 21.4 4.144704 0.77888 . . ENSG00000135362 ENST00000530639;ENST00000311599;ENST00000378867 T;T;T 0.35973 1.41;1.28;1.41 5.16 4.02 0.46733 . 0.070757 0.56097 D 0.000027 T 0.51652 0.1687 M 0.72894 2.215 0.53688 D 0.999979 D;D 0.71674 0.99;0.998 P;P 0.58266 0.836;0.759 T 0.54166 -0.8334 10 0.87932 D 0 -8.0315 10.571 0.45200 0.0:0.0773:0.0:0.9227 . 86;214 Q6MZQ0-3;Q6MZQ0 .;PRR5L_HUMAN E 214;141;214 ENSP00000435050:V214E;ENSP00000310103:V141E;ENSP00000368144:V214E ENSP00000310103:V141E V + 2 0 PRR5L 36429390 1.000000 0.71417 1.000000 0.80357 0.959000 0.62525 4.302000 0.59092 0.810000 0.34279 0.260000 0.18958 GTG TCGA-HZ-A9TJ-01A-11D-A40W-08 PRR5L-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389209.1 0 0 1 69 298 1 65 0 9.460282e-02 0 3 1 65 2 0 0 0 0 0 2 1 1 67 291 1 63 19 -20.000000 1 1 0 0 1 1 2 3 1.837416 1 0.520000 3.450000 0.619048 0.900000 7.200000e-01 1.000000 1.000000 0.905818 0.900000 1 0.810000 1.000000 RAG1 5896 broad.mit.edu 37 11 36595176 36595176 + Nonsense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:36595176C>T ENST00000299440.5 + 2 434 c.322C>T c.(322-324)Cga>Tga p.R108* NM_000448.2 NP_000439 P15918 RAG1_HUMAN recombination activating gene 1 65 all_lung(20;0.226) all_hematologic(20;0.107) AGCCAACCTTCGACATCTCTG 0.463000 Familial Hemophagocytic Lymphohistiocytosis Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363) 0 SO:0001587 stop_gained Familial Cancer Database FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR ENST00000299440.5 0 1 hg19 CCDS7902.1 . . . . . . . . . . C 17.01 3.280336 0.59758 0.0 1.16E-4 ENSG00000166349 ENST00000534663;ENST00000299440 . . . 6.14 3.2 0.36748 . 0.352416 0.29522 N 0.011917 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.25106 T 0.35 . 10.0601 0.42270 0.3752:0.5616:0.0:0.0632 . . . . X 108 . ENSP00000299440:R108X R + 1 2 RAG1 36551752 . . 0.743000 0.31040 0.340000 0.28889 . . 0.439000 0.26476 -0.156000 0.13503 CGA TCGA-HZ-A9TJ-01A-11D-A40W-08 RAG1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389535.1 1 0 1 147 224 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1 142 219 0 67 2 -19.963560 1 1 121412 3 40 1 1 2 3 1.837416 1 0.520000 3.450000 0.619048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FOLH1 2346 broad.mit.edu 37 11 49221961 49221961 + Missense_Mutation SNP G G C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:49221961G>C ENST00000256999.2 - 3 517 c.257C>G c.(256-258)aCa>aGa p.T86R FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000340334.7_Missense_Mutation_p.T71R|FOLH1_ENST00000533034.1_Missense_Mutation_p.T71R|FOLH1_ENST00000356696.3_Missense_Mutation_p.T86R NM_004476.1 NP_004467.1 Q04609 FOLH1_HUMAN folate hydrolase (prostate-specific membrane antigen) 1 60 Capromab(DB00089) GTTTTGTTCTGTTCCTGCTAA 0.348000 0 SO:0001583 missense ENST00000256999.2 0 1 hg19 CCDS7946.1 . . . . . . . . . . G 21.5 4.161035 0.78226 . . ENSG00000086205 ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724;ENST00000529117 T;T;T;T;T 0.49720 0.77;0.77;0.77;0.77;0.77 4.78 4.78 0.61160 . 0.000000 0.56097 D 0.000031 T 0.73606 0.3608 M 0.90019 3.08 0.80722 D 1 D;D;P;D;D 0.89917 1.0;1.0;0.943;0.997;0.997 D;D;P;D;D 0.97110 1.0;1.0;0.791;0.964;0.962 T 0.78499 -0.2180 10 0.52906 T 0.07 . 15.3468 0.74343 0.0:0.0:1.0:0.0 . 71;71;71;86;86 Q04609-9;Q04609-7;A4UU13;Q04609-8;Q04609 .;.;.;.;FOLH1_HUMAN R 86;86;71;71;86;29 ENSP00000256999:T86R;ENSP00000349129:T86R;ENSP00000344131:T71R;ENSP00000431463:T71R;ENSP00000431577:T29R ENSP00000256999:T86R T - 2 0 FOLH1 49178537 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 6.854000 0.75440 2.496000 0.84212 0.508000 0.49915 ACA TCGA-HZ-A9TJ-01A-11D-A40W-08 FOLH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390896.1 1 0 0 8 157 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 9.879661e-01 7 151 0 26 2 -10.941140 1 1 0 0 1 1 2 3 1.837416 1 0.520000 3.450000 0.619048 0.240000 1.100000e-01 0.430000 0.240000 0.260197 0.240000 0 0.170000 0.340000 OR4C13 283092 broad.mit.edu 37 11 49974001 49974001 + Silent SNP G G A rs148894043 byFrequency TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:49974001G>A ENST00000555099.1 + 1 59 c.27G>A c.(25-27)gaG>gaA p.E9E NM_001001955.2 NP_001001955.2 Q8NGP0 OR4CD_HUMAN olfactory receptor, family 4, subfamily C, member 13 43 ATGTGACAGAGTTTATTCTAT 0.299000 0 SO:0001819 synonymous_variant ENST00000555099.1 1 1 hg19 CCDS31495.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 OR4C13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391103.1 1 0 1 92 358 0 91 0 0 0 0 91 2 0 0 0 0 0 2 1 1 92 353 0 89 2 -3.180657 1 1 0 0 1 1 2 3 1.837416 1 0.520000 3.450000 0.619048 0.980000 8.100000e-01 1.000000 1.000000 0.960823 0.980000 1 0.890000 1.000000 OR4D9 390199 broad.mit.edu 37 11 59282719 59282719 + Missense_Mutation SNP G G T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr11:59282719G>T ENST00000329328.3 + 1 334 c.334G>T c.(334-336)Gtt>Ttt p.V112F NM_001004711.1 NP_001004711.1 Q8NGE8 OR4D9_HUMAN olfactory receptor, family 4, subfamily D, member 9 26 GGGAGCAGACGTTTTTTCTCT 0.488000 0 SO:0001583 missense ENST00000329328.3 1 0 hg19 CCDS31564.1 . . . . . . . . . . G 10.18 1.279950 0.23392 . . ENSG00000172742 ENST00000329328 T 0.00406 7.55 4.06 0.928 0.19443 GPCR, rhodopsin-like superfamily (1); 0.211163 0.23577 U 0.046697 T 0.00300 0.0009 N 0.12746 0.255 0.09310 N 1 P 0.51351 0.944 P 0.55260 0.772 T 0.55749 -0.8092 10 0.87932 D 0 -7.0011 2.6652 0.05046 0.3837:0.0:0.4112:0.205 . 112 Q8NGE8 OR4D9_HUMAN F 112 ENSP00000328563:V112F ENSP00000328563:V112F V + 1 0 OR4D9 59039295 0.000000 0.05858 0.019000 0.16419 0.070000 0.16714 -1.393000 0.02521 0.250000 0.21479 0.557000 0.71058 GTT TCGA-HZ-A9TJ-01A-11D-A40W-08 OR4D9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394237.1 0 0 1 49 269 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 1 49 264 0 76 2 -3.230748 1 1 0 0 1 1 2 3 1.837416 1 0.520000 3.450000 0.619048 0.740000 5.600000e-01 0.940000 0.750000 0.755365 0.740000 0 0.650000 0.850000 TDG 6996 broad.mit.edu 37 12 104377099 104377099 + Missense_Mutation SNP G G T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:104377099G>T ENST00000392872.3 + 7 958 c.724G>T c.(724-726)Gtt>Ttt p.V242F TDG_ENST00000544861.1_Missense_Mutation_p.V99F|TDG_ENST00000542036.1_Missense_Mutation_p.V38F|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000266775.9_Missense_Mutation_p.V238F NM_003211.4 NP_003202.3 Q13569 TDG_HUMAN thymine-DNA glycosylase 24 TAGTAAAGAAGTTTTTGGAGT 0.284000 Base excision repair (BER), DNA glycosylases 0 SO:0001583 missense ENST00000392872.3 1 1 hg19 CCDS9095.1 . . . . . . . . . . G 18.06 3.539433 0.65085 . . ENSG00000139372 ENST00000392872;ENST00000266775;ENST00000544861;ENST00000537100;ENST00000542036 T;T;T;T;T 0.56275 0.47;0.47;0.47;0.92;0.92 5.4 5.4 0.78164 Uracil-DNA glycosylase-like (3); 0.258187 0.39083 N 0.001468 T 0.55737 0.1939 N 0.25380 0.74 0.40131 D 0.976715 D;P;B 0.71674 0.998;0.934;0.233 P;P;B 0.60789 0.879;0.545;0.151 T 0.59804 -0.7385 10 0.62326 D 0.03 -28.8349 12.5149 0.56026 0.0764:0.0:0.9236:0.0 . 38;242;242 B4DI29;B2R848;Q13569 .;.;TDG_HUMAN F 242;238;99;235;38 ENSP00000376611:V242F;ENSP00000266775:V238F;ENSP00000445899:V99F;ENSP00000439825:V235F;ENSP00000439054:V38F ENSP00000266775:V238F V + 1 0 TDG 102901229 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.522000 0.45572 2.518000 0.84900 0.563000 0.77884 GTT TCGA-HZ-A9TJ-01A-11D-A40W-08 TDG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399673.2 0 0 0 16 456 0 101 0 2.398531e-01 0 26 0 101 2 0 0 0 0 0 2 1 9.999294e-01 15 452 0 100 2 -3.663674 1 1 0 0 1 0 3 3 1.818911 1 0.520000 3.450000 0.619048 0.160000 9.000000e-02 0.260000 0.160000 0.173574 0.160000 0 0.120000 0.210000 GPR133 283383 broad.mit.edu 37 12 131593364 131593364 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:131593364G>A ENST00000261654.5 + 18 2542 c.1983G>A c.(1981-1983)gtG>gtA p.V661V GPR133_ENST00000535015.1_Silent_p.V693V|GPR133_ENST00000376682.4_Silent_p.V347V|GPR133_ENST00000543617.1_Silent_p.V180V NM_198827.3 NP_942122.2 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 67 all_neural(191;0.0982)|Medulloblastoma(191;0.163) ACAGCATGGTGATCAAGGTCT 0.612000 0 SO:0001819 synonymous_variant ENST00000261654.5 1 1 hg19 CCDS9272.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 GPR133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399356.1 1 0 1 267 175 0 82 0 9.813348e-01 0 7 0 82 2 0 0 0 0 0 2 1 1 263 171 0 80 2 -20.000000 1 1 0 0 1 0 3 3 1.818911 1 0.520000 3.450000 0.619048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PDE3A 5139 broad.mit.edu 37 12 20787935 20787935 + Missense_Mutation SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:20787935C>A ENST00000359062.3 + 8 1986 c.1946C>A c.(1945-1947)cCt>cAt p.P649H PDE3A_ENST00000544307.1_3'UTR NM_000921.4|NM_001244683.1 NP_000912.3|NP_001231612.1 Q14432 PDE3A_HUMAN phosphodiesterase 3A, cGMP-inhibited 58 Esophageal squamous(101;0.125) Breast(259;0.134) Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811) CTGAGAGAGCCTCTGAGGAAA 0.443000 0 SO:0001583 missense ENST00000359062.3 1 1 hg19 CCDS31754.1 . . . . . . . . . . C 4.426 0.078860 0.08533 . . ENSG00000172572 ENST00000359062 T 0.61859 0.07 5.64 3.77 0.43336 . 7739.210000 0.00166 N 0.000000 T 0.51227 0.1662 N 0.22421 0.69 0.09310 N 1 P 0.34837 0.472 B 0.33295 0.161 T 0.53114 -0.8484 10 0.52906 T 0.07 . 14.0504 0.64732 0.454:0.546:0.0:0.0 . 649 Q14432 PDE3A_HUMAN H 649 ENSP00000351957:P649H ENSP00000351957:P649H P + 2 0 PDE3A 20679202 0.242000 0.23868 0.016000 0.15963 0.040000 0.13550 0.863000 0.27913 0.699000 0.31761 -0.175000 0.13238 CCT TCGA-HZ-A9TJ-01A-11D-A40W-08 PDE3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401756.2 1 0 0 29 280 0 34 0 4.997669e-02 0 4 0 34 2 0 0 0 0 0 2 1 1 29 278 0 33 2 -3.075756 1 1 0 0 1 2 3 5 2.618221 1 0.520000 3.450000 0.730337 0.640000 4.400000e-01 0.880000 0.650000 0.659389 0.640000 0 0.530000 0.770000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 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-HZ-A9TJ-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 64 189 0 69 1 9.968643e-01 12 17 0 69 2 1 1 181 568 0 379 2 1 1 64 188 0 66 2 -20.000000 1 1 0 0 1 2 3 5 2.618221 1 0.520000 3.450000 0.730337 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PKP2 5318 broad.mit.edu 37 12 33031332 33031332 + Missense_Mutation SNP T T C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:33031332T>C ENST00000070846.6 - 3 506 c.482A>G c.(481-483)tAc>tGc p.Y161C PKP2_ENST00000340811.4_Missense_Mutation_p.Y161C NM_004572.3 NP_004563.2 Q99959 PKP2_HUMAN plakophilin 2 50 Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239) GCTGTGCGTGTAGTGAGCCCT 0.592000 0 SO:0001583 missense ENST00000070846.6 1 1 hg19 CCDS8731.1 . . . . . . . . . . T 14.39 2.522175 0.44866 . . ENSG00000057294 ENST00000340811;ENST00000070846;ENST00000537278 D;D 0.86030 -2.05;-2.06 4.98 4.98 0.66077 . 0.558681 0.16641 N 0.205627 D 0.89403 0.6705 L 0.59436 1.845 0.09310 N 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.73380 0.98;0.956;0.972 T 0.81169 -0.1055 10 0.59425 D 0.04 -5.6232 9.1145 0.36748 0.1628:0.0:0.0:0.8372 . 161;161;161 Q99959-2;A0AV37;Q99959 .;.;PKP2_HUMAN C 161 ENSP00000342800:Y161C;ENSP00000070846:Y161C ENSP00000070846:Y161C Y - 2 0 PKP2 32922599 0.061000 0.20836 0.007000 0.13788 0.021000 0.10359 2.011000 0.40922 1.865000 0.54081 0.529000 0.55759 TAC TCGA-HZ-A9TJ-01A-11D-A40W-08 PKP2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000404449.1 0 0 0 34 798 0 110 0 6.065670e-01 0 49 0 110 2 0 0 0 0 0 2 1 9.401543e-01 34 785 1 114 23 -20.000000 1 1 121410 1 34 1 2 3 5 2.618221 1 0.520000 3.450000 0.730337 0.270000 1.800000e-01 0.390000 0.300000 0.287138 0.270000 0 0.230000 0.340000 TMEM117 84216 broad.mit.edu 37 12 44782272 44782272 + Missense_Mutation SNP G G T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:44782272G>T ENST00000266534.3 + 8 1489 c.1362G>T c.(1360-1362)caG>caT p.Q454H TMEM117_ENST00000536799.1_Missense_Mutation_p.Q350H|TMEM117_ENST00000546978.1_3'UTR|TMEM117_ENST00000551577.1_3'UTR NM_032256.1 NP_115632.1 Q9H0C3 TM117_HUMAN transmembrane protein 117 23 Lung SC(27;0.192) AAAACACCCAGGCTTCAGTAG 0.443000 0 SO:0001583 missense ENST00000266534.3 1 1 hg19 CCDS8745.1 . . . . . . . . . . G 12.94 2.087281 0.36855 . . ENSG00000139173 ENST00000266534;ENST00000536799;ENST00000417623 T 0.46819 0.86 5.73 2.5 0.30297 . 0.052666 0.85682 D 0.000000 T 0.38081 0.1027 L 0.41236 1.265 0.39169 D 0.962561 B;B 0.11235 0.004;0.002 B;B 0.12156 0.007;0.002 T 0.33007 -0.9885 10 0.48119 T 0.1 -10.3341 12.0236 0.53358 0.2193:0.0:0.7807:0.0 . 350;454 F5H3Q2;Q9H0C3 .;TM117_HUMAN H 454;350;202 ENSP00000266534:Q454H ENSP00000266534:Q454H Q + 3 2 TMEM117 43068539 1.000000 0.71417 0.994000 0.49952 0.887000 0.51463 1.298000 0.33412 0.774000 0.33427 -0.142000 0.14014 CAG TCGA-HZ-A9TJ-01A-11D-A40W-08 TMEM117-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403969.1 1 0 0 14 386 0 68 0 8.522116e-02 0 13 0 68 2 0 0 0 0 0 2 1 9.997521e-01 14 383 0 66 2 -3.294724 1 1 0 0 1 0 3 3 1.818911 1 0.520000 3.450000 0.619048 0.170000 9.000000e-02 0.270000 0.180000 0.180543 0.170000 0 0.120000 0.230000 FMNL3 91010 broad.mit.edu 37 12 50044493 50044493 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:50044493G>A ENST00000293590.5 - 17 2199 c.1966C>T c.(1966-1968)Cgc>Tgc p.R656C FMNL3_ENST00000352151.5_Missense_Mutation_p.R605C|FMNL3_ENST00000335154.5_Missense_Mutation_p.R656C|FMNL3_ENST00000550488.1_Missense_Mutation_p.R656C Q8IVF7 FMNL3_HUMAN formin-like 3 39 TCAGCCGAGCGGCCAGCCTTG 0.582000 0 SO:0001583 missense ENST00000293590.5 1 1 hg19 . . . . . . . . . . G 21.0 4.085302 0.76642 . . ENSG00000161791 ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590 T;T;T;T 0.16897 2.31;2.31;2.31;2.31 5.12 5.12 0.69794 Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3); 0.050640 0.64402 D 0.000001 T 0.24774 0.0601 L 0.27053 0.805 0.53688 D 0.999977 D;D;D 0.76494 0.998;0.996;0.999 D;P;P 0.64042 0.921;0.736;0.848 T 0.00383 -1.1774 10 0.51188 T 0.08 . 11.2905 0.49247 0.0:0.0:0.72:0.28 . 605;656;656 Q8IVF7-2;Q8IVF7-3;Q8IVF7 .;.;FMNL3_HUMAN C 656;656;605;656 ENSP00000335655:R656C;ENSP00000447479:R656C;ENSP00000344311:R605C;ENSP00000293590:R656C ENSP00000293590:R656C R - 1 0 FMNL3 48330760 0.983000 0.35010 1.000000 0.80357 0.980000 0.70556 1.336000 0.33850 2.834000 0.97654 0.650000 0.86243 CGC TCGA-HZ-A9TJ-01A-11D-A40W-08 FMNL3-201 KNOWN basic protein_coding protein_coding 1 0 1 50 191 0 39 0 9.627637e-01 0 23 0 39 2 0 0 0 0 0 2 1 1 48 185 0 37 2 -3.759405 1 1 121006 1 39 1 0 3 3 1.818911 1 0.520000 3.450000 0.619048 0.990000 7.700000e-01 1.000000 1.000000 0.956598 0.990000 1 0.880000 1.000000 KCNA1 3736 broad.mit.edu 37 12 5021899 5021899 + Missense_Mutation SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr12:5021899C>A ENST00000382545.3 + 2 2462 c.1355C>A c.(1354-1356)tCt>tAt p.S452Y KCNA1_ENST00000543874.2_Intron NM_000217.2 NP_000208.2 Q09470 KCNA1_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia) 63 Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236) ATGAGCAAGTCTGAGTACATG 0.483000 0 SO:0001583 missense ENST00000382545.3 1 1 hg19 CCDS8535.1 . . . . . . . . . . C 19.25 3.790696 0.70452 . . ENSG00000111262 ENST00000382545;ENST00000228858 D 0.96716 -4.1 5.35 5.35 0.76521 . 0.000000 0.85682 D 0.000000 D 0.98157 0.9391 M 0.87269 2.87 0.80722 D 1 D 0.63880 0.993 D 0.63033 0.91 D 0.98623 1.0668 10 0.87932 D 0 . 18.5892 0.91202 0.0:1.0:0.0:0.0 . 452 Q09470 KCNA1_HUMAN Y 452 ENSP00000371985:S452Y ENSP00000228858:S452Y S + 2 0 KCNA1 4892160 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.651000 0.83577 2.941000 0.99782 0.655000 0.94253 TCT TCGA-HZ-A9TJ-01A-11D-A40W-08 KCNA1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000103343.2 0 0 1 160 1033 0 163 0 0 0 0 163 2 0 0 0 0 0 2 1 1 158 1027 0 161 2 -20.000000 1 1 0 0 1 2 3 5 2.618221 1 0.520000 3.450000 0.730337 0.910000 7.800000e-01 1.000000 1.000000 0.916958 0.910000 1 0.840000 0.990000 TM9SF2 9375 broad.mit.edu 37 13 100153955 100153955 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr13:100153955G>A ENST00000376387.4 + 1 285 c.95G>A c.(94-96)cGg>cAg p.R32Q LINC00449_ENST00000366259.2_RNA NM_004800.1 NP_004791.1 Q99805 TM9S2_HUMAN transmembrane 9 superfamily member 2 17 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218) GGCCCGCGCCGGAGCGGCGCT 0.667000 0 SO:0001583 missense ENST00000376387.4 0 1 hg19 CCDS9493.1 . . . . . . . . . . G 13.24 2.177171 0.38413 . . ENSG00000125304 ENST00000376387 T 0.41400 1.0 4.66 -3.93 0.04143 . 0.587551 0.19001 N 0.125345 T 0.21550 0.0519 N 0.14661 0.345 0.09310 N 1 B;P 0.35908 0.052;0.527 B;B 0.21360 0.004;0.034 T 0.01460 -1.1349 10 0.23302 T 0.38 1.5671 21.9879 0.99964 0.0:0.8332:0.1668:0.0 . 32;32 E9PHW5;Q99805 .;TM9S2_HUMAN Q 32 ENSP00000365567:R32Q ENSP00000365567:R32Q R + 2 0 TM9SF2 98951956 0.018000 0.18449 0.552000 0.28243 0.996000 0.88848 -0.549000 0.06041 -0.599000 0.05798 0.655000 0.94253 CGG TCGA-HZ-A9TJ-01A-11D-A40W-08 TM9SF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045602.3 0 0 0 6 396 1 56 0 1.306445e-03 0 195 1 56 13 0 0 0 0 0 2 0 1.034487e-03 6 378 1 53 22 -2.923173 1 1 0 0 1 2 2 4 2.218602 1 0.520000 3.450000 0.684211 0.090000 2.000000e-02 0.180000 0.080000 0.101143 0.090000 0 0.050000 0.140000 COL4A2 1284 broad.mit.edu 37 13 111102671 111102671 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr13:111102671G>A ENST00000360467.5 + 20 1515 c.1209G>A c.(1207-1209)ccG>ccA p.P403P NM_001846.2 NP_001837.2 P08572 CO4A2_HUMAN collagen, type IV, alpha 2 80 all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922) Breast(118;0.212) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151) GAGGCCTGCCGGGTGAGATGG 0.632000 0 SO:0001819 synonymous_variant ENST00000360467.5 1 1 hg19 CCDS41907.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 COL4A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045761.2 1 0 0 99 224 0 41 0 1 0 153 0 41 2 0 0 0 0 0 2 1 1 98 217 0 40 2 -7.973366 1 1 120848 5 37 1 2 2 4 2.218602 1 0.520000 3.450000 0.684211 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MRP63 0 broad.mit.edu 37 13 21751133 21751133 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr13:21751133C>T ENST00000309594.4 + 2 156 c.78C>T c.(76-78)ttC>ttT p.F26F SKA3_ENST00000314759.5_5'Flank|SKA3_ENST00000400018.3_5'Flank NM_024026.4 NP_076931.1 Q9BQC6 RT63_HUMAN 5 all_cancers(29;2.76e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147) GGCCGCGGTTCGTGTCGTTGC 0.662000 0 SO:0001819 synonymous_variant ENST00000309594.4 1 1 hg19 CCDS9296.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 MRP63-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044105.2 1 0 0 42 283 0 48 1 1 69 221 0 48 2 0 0 0 0 0 2 1 1 42 267 0 46 2 -20.000000 1 1 0 0 1 2 2 4 2.218602 1 0.520000 3.450000 0.684211 0.750000 5.500000e-01 0.980000 0.760000 0.766580 0.750000 0 0.650000 0.870000 EML1 2009 broad.mit.edu 37 14 100405553 100405553 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr14:100405553G>A ENST00000262233.6 + 21 2350 c.2211G>A c.(2209-2211)tcG>tcA p.S737S EML1_ENST00000327921.9_Silent_p.S725S|EML1_ENST00000334192.4_Silent_p.S756S NM_004434.2 NP_004425.2 O00423 EMAL1_HUMAN echinoderm microtubule associated protein like 1 42 Melanoma(154;0.0879)|all_epithelial(191;0.216) CAGAAGGCTCGGACGGAACCG 0.582000 0 SO:0001819 synonymous_variant ENST00000262233.6 1 1 hg19 CCDS32155.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 EML1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413943.1 1 0 1 42 237 0 63 0 1.147296e-01 0 4 0 63 2 0 0 0 0 0 2 1 1 40 230 0 61 2 -2.753200 1 1 121412 3 37 1 1 2 3 1.848437 1 0.520000 3.450000 0.619048 0.720000 5.400000e-01 0.940000 0.720000 0.739545 0.720000 0 0.630000 0.840000 XRCC3 7517 broad.mit.edu 37 14 104169592 104169592 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr14:104169592C>T ENST00000553264.1 - 5 1275 c.479G>A c.(478-480)cGg>cAg p.R160Q XRCC3_ENST00000554913.1_Missense_Mutation_p.R160Q|XRCC3_ENST00000554974.1_Intron|XRCC3_ENST00000555055.1_Missense_Mutation_p.R160Q|XRCC3_ENST00000445556.1_Missense_Mutation_p.R160Q|XRCC3_ENST00000352127.7_Missense_Mutation_p.R160Q|XRCC3_ENST00000555832.1_5'Flank O43542 XRCC3_HUMAN X-ray repair complementing defective repair in Chinese hamster cells 3 4 Melanoma(154;0.155)|all_epithelial(191;0.19) AGTGCGCAGCCGCGGCTGCTG 0.622000 Direct reversal of damage;Homologous recombination 0 SO:0001583 missense ENST00000553264.1 0 1 hg19 CCDS9984.1 . . . . . . . . . . C 8.476 0.858680 0.17178 . . ENSG00000126215 ENST00000554913;ENST00000352127;ENST00000553264;ENST00000555055;ENST00000445556 T;T;T;T;T 0.38560 1.13;1.13;1.13;1.13;1.13 4.7 -3.94 0.04130 DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1); 1.857050 0.02717 N 0.113582 T 0.30759 0.0775 N 0.22421 0.69 0.09310 N 1 B 0.18461 0.028 B 0.16289 0.015 T 0.24297 -1.0164 10 0.31617 T 0.26 -22.7782 12.9742 0.58529 0.0:0.165:0.0:0.835 . 160 O43542 XRCC3_HUMAN Q 160 ENSP00000451362:R160Q;ENSP00000343392:R160Q;ENSP00000451974:R160Q;ENSP00000452598:R160Q;ENSP00000412990:R160Q ENSP00000343392:R160Q R - 2 0 XRCC3 103239345 0.000000 0.05858 0.001000 0.08648 0.006000 0.05464 -1.699000 0.01906 -0.879000 0.04002 -0.367000 0.07326 CGG TCGA-HZ-A9TJ-01A-11D-A40W-08 XRCC3-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414631.1 1 0 1 7 33 0 14 1 5.169388e-01 3 6 0 14 2 0 0 0 0 0 2 1 9.824204e-01 7 32 0 14 2 -15.119890 1 1 117758 1 24 1 1 2 3 1.862466 1 0.520000 3.450000 0.619048 0.870000 4.100000e-01 1.000000 1.000000 0.832140 0.870000 1 0.610000 1.000000 DCAF5 8816 broad.mit.edu 37 14 69522129 69522129 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr14:69522129C>T ENST00000341516.5 - 9 1421 c.1274G>A c.(1273-1275)cGa>cAa p.R425Q DCAF5_ENST00000554215.1_Missense_Mutation_p.R343Q|DCAF5_ENST00000557386.1_Missense_Mutation_p.R424Q|DCAF5_ENST00000556847.1_Missense_Mutation_p.R343Q|DCAF5_ENST00000553293.1_5'UTR NM_001284206.1|NM_001284207.1|NM_003861.2 NP_001271135.1|NP_001271136.1|NP_003852.1 Q96JK2 DCAF5_HUMAN DDB1 and CUL4 associated factor 5 29 CTCGATCTCTCGGCGTACCAG 0.587000 0 SO:0001583 missense ENST00000341516.5 0 1 hg19 CCDS32106.1 . . . . . . . . . . C 21.4 4.141952 0.77775 . . ENSG00000139990 ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386 T;T;T;T 0.75938 -0.98;-0.81;-0.81;-0.3 5.68 5.68 0.88126 . 0.000000 0.85682 D 0.000000 T 0.72922 0.3521 L 0.34521 1.04 0.80722 D 1 P;P 0.49358 0.923;0.875 P;B 0.47891 0.56;0.357 T 0.71906 -0.4451 10 0.38643 T 0.18 -8.3451 19.7989 0.96497 0.0:1.0:0.0:0.0 . 424;425 G3V4J7;Q96JK2 .;DCAF5_HUMAN Q 425;343;343;424 ENSP00000341351:R425Q;ENSP00000451551:R343Q;ENSP00000452052:R343Q;ENSP00000451845:R424Q ENSP00000341351:R425Q R - 2 0 DCAF5 68591882 1.000000 0.71417 0.959000 0.39883 0.993000 0.82548 7.336000 0.79245 2.683000 0.91414 0.561000 0.74099 CGA TCGA-HZ-A9TJ-01A-11D-A40W-08 DCAF5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000414806.2 0 0 0 5 277 0 46 0 1.449018e-01 0 31 0 46 2 0 0 0 0 0 2 1 9.332525e-01 6 268 0 46 2 -3.286065 1 1 0 0 1 1 2 3 1.848437 1 0.520000 3.450000 0.619048 0.090000 2.000000e-02 0.190000 0.090000 0.102132 0.090000 0 0.050000 0.140000 PGF 5228 broad.mit.edu 37 14 75416111 75416111 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr14:75416111G>A ENST00000405431.2 - 3 263 c.264C>T c.(262-264)ggC>ggT p.G88G PGF_ENST00000553716.1_Silent_p.G88G|PGF_ENST00000238607.6_Silent_p.G87G|PGF_ENST00000555567.1_Silent_p.G88G P49763 PLGF_HUMAN placental growth factor 8 Aflibercept(DB08885) GATTCTCATCGCCGCAGCAGC 0.632000 GBM(127;389 2301 5452 48547) 0 SO:0001819 synonymous_variant ENST00000405431.2 1 1 hg19 CCDS9835.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 PGF-008 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000414064.1 1 0 0 12 243 0 45 1 6.128936e-01 3 39 0 45 2 0 0 0 0 0 2 1 9.990742e-01 11 239 0 43 2 -3.303761 1 1 121404 2 35 1 1 2 3 1.848437 1 0.520000 3.450000 0.619048 0.230000 1.200000e-01 0.380000 0.240000 0.244542 0.230000 0 0.170000 0.310000 PTPN21 11099 broad.mit.edu 37 14 89016677 89016677 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr14:89016677G>A ENST00000556564.1 - 2 369 c.85C>T c.(85-87)Ctg>Ttg p.L29L RP11-507K2.3_ENST00000556328.1_RNA|PTPN21_ENST00000328736.3_Silent_p.L29L|PTPN21_ENST00000554628.1_5'UTR NM_007039.3 NP_008970.2 Q16825 PTN21_HUMAN protein tyrosine phosphatase, non-receptor type 21 45 TTATTAAGCAGTTGGATCCGG 0.567000 0 SO:0001819 synonymous_variant ENST00000556564.1 1 1 hg19 CCDS9884.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 PTPN21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000410303.1 0 0 1 88 324 1 61 0 5.380857e-01 1 7 1 61 2 0 0 0 0 0 2 1 1 86 319 0 58 2 -20.000000 1 1 0 0 1 1 2 3 1.848437 1 0.520000 3.450000 0.619048 0.990000 8.400000e-01 1.000000 1.000000 0.978001 0.990000 1 0.930000 1.000000 MYO5A 4644 broad.mit.edu 37 15 52672018 52672018 + Splice_Site SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr15:52672018C>T ENST00000399231.3 - 17 2343 c.e17+1 MYO5A_ENST00000399233.2_Splice_Site|MYO5A_ENST00000553916.1_Splice_Site|MYO5A_ENST00000356338.6_Splice_Site|MYO5A_ENST00000358212.6_Splice_Site NM_000259.3 NP_000250 Q9Y4I1 MYO5A_HUMAN myosin VA (heavy chain 12, myoxin) 57 GCCAGGCTCACCGTGAGGGGA 0.453000 0 SO:0001630 splice_region_variant ENST00000399231.3 1 1 hg19 CCDS42037.1 . . . . . . . . . . C 23.2 4.385741 0.82792 . . ENSG00000197535 ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916 . . . 4.99 4.0 0.46444 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.1161 0.72404 0.0:0.8581:0.1419:0.0 . . . . . -1 . . . - . . MYO5A 50459310 1.000000 0.71417 0.997000 0.53966 0.971000 0.66376 7.818000 0.86416 2.464000 0.83262 0.650000 0.86243 . TCGA-HZ-A9TJ-01A-11D-A40W-08 MYO5A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000268102.1 1 0 1 75 422 1 58 0 0 0 1 58 2 0 0 0 0 0 2 1 9.999999e-01 75 419 1 56 26 -20.000000 1 1 0 0 1 1 3 4 1.900892 1 0.520000 3.450000 0.634146 0.790000 6.100000e-01 1.000000 0.770000 0.821572 0.790000 0 0.690000 1.000000 ZSCAN10 84891 broad.mit.edu 37 16 3140385 3140385 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr16:3140385C>T ENST00000252463.2 - 5 972 c.885G>A c.(883-885)gcG>gcA p.A295A ZSCAN10_ENST00000538082.2_Silent_p.A213A|ZSCAN10_ENST00000575108.1_5'UTR NM_032805.1 NP_116194.1 Q96SZ4 ZSC10_HUMAN zinc finger and SCAN domain containing 10 24 CCCCGCAGTCCGCGCAGATGA 0.632000 0 SO:0001819 synonymous_variant ENST00000252463.2 1 1 hg19 CCDS10493.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 ZSCAN10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437124.2 1 0 1 90 312 1 69 0 0 0 1 69 2 0 0 0 0 0 2 1 1 87 300 1 67 19 -3.838453 1 1 121256 1 32 1 2 4 6 1.959311 1 0.520000 3.450000 0.645390 0.990000 9.700000e-01 1.000000 1.000000 0.998228 0.990000 1 0.990000 1.000000 NLRC5 84166 broad.mit.edu 37 16 57092011 57092011 + Missense_Mutation SNP A A G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr16:57092011A>G ENST00000262510.6 + 28 4006 c.3781A>G c.(3781-3783)Aga>Gga p.R1261G NLRC5_ENST00000539144.1_Missense_Mutation_p.R1232G|NLRC5_ENST00000308149.7_Missense_Mutation_p.R1232G|NLRC5_ENST00000436936.1_Missense_Mutation_p.R1261G|RP11-322D14.2_ENST00000562970.1_RNA NM_032206.4 NP_115582.4 Q86WI3 NLRC5_HUMAN NLR family, CARD domain containing 5 75 all_neural(199;0.225) CAGCGGACTCAGATGCCTTCT 0.572000 0 SO:0001583 missense ENST00000262510.6 0 1 hg19 CCDS10773.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 7.659|7.659 0.684568|0.684568 0.14973|0.14973 .|. .|. ENSG00000140853|ENSG00000140853 ENST00000538805;ENST00000399221|ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110 .|T;T;T;T;T .|0.53423 .|0.62;5.54;0.62;5.54;0.62 4.68|4.68 2.39|2.39 0.29439|0.29439 .|. .|. .|. .|. .|. T|T 0.44371|0.44371 0.1290|0.1290 M|M 0.68952|0.68952 2.095|2.095 0.09310|0.09310 N|N 1|1 .|P;P;B;B .|0.36465 .|0.554;0.515;0.302;0.094 .|B;B;B;B .|0.35550 .|0.205;0.156;0.08;0.054 T|T 0.28004|0.28004 -1.0057|-1.0057 5|9 .|0.49607 .|T .|0.09 .|. 8.9296|8.9296 0.35661|0.35661 0.6488:0.3512:0.0:0.0|0.6488:0.3512:0.0:0.0 .|. .|945;1232;1261;1261 .|Q9H6Y0;Q86WI3-4;Q86WI3-6;Q86WI3 .|.;.;.;NLRC5_HUMAN R|G 1012;12|1261;1232;1261;704;1232;737 .|ENSP00000262510:R1261G;ENSP00000308886:R1232G;ENSP00000389739:R1261G;ENSP00000441727:R1232G;ENSP00000441597:R737G .|ENSP00000262510:R1261G Q|R +|+ 2|1 0|2 NLRC5|NLRC5 55649512|55649512 0.968000|0.968000 0.33430|0.33430 0.285000|0.285000 0.24819|0.24819 0.051000|0.051000 0.14879|0.14879 1.064000|1.064000 0.30579|0.30579 0.292000|0.292000 0.22492|0.22492 0.449000|0.449000 0.29647|0.29647 CAG|AGA TCGA-HZ-A9TJ-01A-11D-A40W-08 NLRC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257346.1 0 0 0 4 185 0 28 0 1.025561e-01 0 20 0 28 2 0 0 0 0 0 2 1 8.887450e-01 4 183 0 28 2 -5.915690 1 1 0 0 1 2 4 6 2.969935 1 0.520000 3.450000 0.764706 0.180000 4.000000e-02 0.400000 0.180000 0.204825 0.180000 0 0.100000 0.290000 CCDC135 0 broad.mit.edu 37 16 57764951 57764951 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr16:57764951C>T ENST00000360716.3 + 18 2721 c.2500C>T c.(2500-2502)Cgc>Tgc p.R834C CCDC135_ENST00000336825.8_Missense_Mutation_p.R769C|CCDC135_ENST00000394337.4_Missense_Mutation_p.R834C Q8IY82 CC135_HUMAN 30 GGCCATGTTCCGCATCCGCAT 0.597000 0 SO:0001583 missense ENST00000360716.3 1 1 hg19 CCDS10787.1 . . . . . . . . . . c 12.08 1.831476 0.32329 . . ENSG00000159625 ENST00000394337;ENST00000336825;ENST00000360716 T;T;T 0.55413 0.52;0.52;0.52 5.04 4.09 0.47781 . 0.274751 0.35646 N 0.003074 T 0.73613 0.3609 M 0.85197 2.74 0.58432 D 0.999999 B;D 0.89917 0.056;1.0 B;D 0.91635 0.026;0.999 T 0.77892 -0.2418 10 0.66056 D 0.02 -22.0214 12.618 0.56588 0.0:0.9179:0.0:0.0821 . 769;834 Q8IY82-2;Q8IY82 .;CC135_HUMAN C 834;769;834 ENSP00000377869:R834C;ENSP00000338938:R769C;ENSP00000353942:R834C ENSP00000338938:R769C R + 1 0 CCDC135 56322452 1.000000 0.71417 1.000000 0.80357 0.434000 0.31775 2.268000 0.43338 1.275000 0.44379 -0.156000 0.13503 CGC TCGA-HZ-A9TJ-01A-11D-A40W-08 CCDC135-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433323.2 1 0 1 108 224 0 53 0 0 0 1 0 53 2 0 0 0 0 0 2 1 1 107 221 0 49 2 -10.327270 1 1 121404 7 38 1 2 4 6 2.969935 1 0.520000 3.450000 0.764706 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CNGB1 1258 broad.mit.edu 37 16 57945695 57945695 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr16:57945695G>A ENST00000251102.8 - 25 2514 c.2454C>T c.(2452-2454)ctC>ctT p.L818L CNGB1_ENST00000564448.1_Silent_p.L812L NM_001297.4 NP_001288.3 Q14028 CNGB1_HUMAN cyclic nucleotide gated channel beta 1 54 GAGTGGAGCCGAGGCCCTGAT 0.547000 Colon(156;1293 1853 16336 28962 38659) 0 SO:0001819 synonymous_variant ENST00000251102.8 1 1 hg19 CCDS42169.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 CNGB1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000337167.2 1 0 1 86 172 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 1 84 168 0 24 2 -9.821425 1 1 120900 1 35 1 2 4 6 2.969935 1 0.520000 3.450000 0.764706 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 OSGIN1 29948 broad.mit.edu 37 16 83994666 83994666 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr16:83994666G>A ENST00000343939.2 + 6 1109 c.726G>A c.(724-726)caG>caA p.Q242Q OSGIN1_ENST00000565123.1_Silent_p.Q159Q|OSGIN1_ENST00000393306.1_Silent_p.Q159Q|OSGIN1_ENST00000361711.3_Silent_p.Q159Q Q9UJX0 OSGI1_HUMAN oxidative stress induced growth inhibitor 1 12 ACTGGATGCAGAAGAAGCGAA 0.572000 0 SO:0001819 synonymous_variant ENST00000343939.2 1 1 hg19 TCGA-HZ-A9TJ-01A-11D-A40W-08 OSGIN1-001 PUTATIVE basic protein_coding protein_coding OTTHUMT00000269081.1 1 0 1 58 246 0 52 1 9.991971e-01 19 29 0 52 2 0 0 0 0 0 2 1 1 57 239 0 51 2 -20.000000 1 1 121366 1 26 1 3 4 7 2.477696 1 0.520000 3.450000 0.717979 0.990000 9.900000e-01 1.000000 1.000000 0.998691 0.990000 1 0.990000 1.000000 TMEM132E 124842 broad.mit.edu 37 17 32953262 32953262 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr17:32953262C>T ENST00000321639.5 + 2 512 c.184C>T c.(184-186)Cgg>Tgg p.R62W NM_207313.1 NP_997196.1 Q6IEE7 T132E_HUMAN transmembrane protein 132E 57 GCGGGAGGCGCGGCCCCCGTC 0.731000 0 SO:0001583 missense ENST00000321639.5 0 1 hg19 CCDS11283.1 . . . . . . . . . . C 17.43 3.387866 0.61956 . . ENSG00000181291 ENST00000321639 T 0.11495 2.77 4.82 3.81 0.43845 . 0.445588 0.24391 N 0.038924 T 0.09512 0.0234 N 0.19112 0.55 0.21020 N 0.999805 D 0.60160 0.987 P 0.47705 0.555 T 0.11108 -1.0601 10 0.66056 D 0.02 -27.4389 8.5268 0.33309 0.1556:0.5772:0.2672:0.0 . 62 Q6IEE7 T132E_HUMAN W 62 ENSP00000316532:R62W ENSP00000316532:R62W R + 1 2 TMEM132E 29977375 0.834000 0.29399 0.889000 0.34880 0.942000 0.58702 1.415000 0.34748 0.913000 0.36797 0.478000 0.44815 CGG TCGA-HZ-A9TJ-01A-11D-A40W-08 TMEM132E-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256440.2 0 0 0 7 37 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 9.822264e-01 7 36 0 10 2 -14.857570 1 1 0 0 1 2 2 4 2.230651 1 0.520000 3.450000 0.684211 0.970000 4.500000e-01 1.000000 1.000000 0.875631 0.970000 1 0.680000 1.000000 TP53 7157 broad.mit.edu 37 17 7578406 7578406 + Missense_Mutation SNP C C T rs28934578 TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr17:7578406C>T ENST00000269305.4 - 5 713 c.524G>A c.(523-525)cGc>cAc p.R175H TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H 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.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GTGGGGGCAGCGCCTCACAAC 0.652000 R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY) 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 980 Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3) GRCh37 CM062017|CM951224 TP53 M rs28934578 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 . . . . . . . . . . C 31 5.079737 0.94050 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 D;D;D;D;D;D;D;D 0.99889 -7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55 5.41 5.41 0.78517 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.101149 0.64402 D 0.000008 D 0.99908 0.9956 M 0.92784 3.345 0.80722 A 1 D;P;D;D;P;B;D 0.89917 0.999;0.578;1.0;0.998;0.632;0.213;0.999 D;B;D;D;B;B;D 0.91635 0.985;0.26;0.999;0.921;0.378;0.144;0.939 D 0.96278 0.9204 9 0.87932 D 0 -11.8679 17.0767 0.86588 0.0:1.0:0.0:0.0 rs28934578 136;175;175;82;175;175;175 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. H 175;175;175;175;175;175;164;82;43;82;43 ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H ENSP00000269305:R175H R - 2 0 TP53 7519131 1.000000 0.71417 0.989000 0.46669 0.795000 0.44927 6.042000 0.70996 2.702000 0.92279 0.655000 0.94253 CGC TCGA-HZ-A9TJ-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 82 80 0 61 1 1 40 14 0 61 2 1 1 516 452 1 1065 6 1 1 82 78 0 59 2 -19.938370 1 1 121412 1 41 1 0 2 2 1.474757 1 0.520000 3.450000 0.520000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TEX19 400629 broad.mit.edu 37 17 80320465 80320465 + Missense_Mutation SNP T T C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr17:80320465T>C ENST00000333437.4 + 2 749 c.439T>C c.(439-441)Tgg>Cgg p.W147R NM_207459.3 NP_997342.1 Q8NA77 TEX19_HUMAN testis expressed 19 6 GGGTCTTCCCTGGAGATTTGA 0.597000 0 SO:0001583 missense ENST00000333437.4 1 1 hg19 CCDS11809.1 . . . . . . . . . . T 12.32 1.901393 0.33535 . . ENSG00000182459 ENST00000333437 . . . 3.55 3.55 0.40652 . . . . . T 0.58524 0.2128 L 0.34521 1.04 0.36261 D 0.85455 D 0.89917 1.0 D 0.87578 0.998 T 0.66376 -0.5939 8 0.87932 D 0 -12.8215 8.7547 0.34639 0.0:0.0:0.0:1.0 . 147 Q8NA77 TEX19_HUMAN R 147 . ENSP00000331500:W147R W + 1 0 TEX19 77913754 1.000000 0.71417 1.000000 0.80357 0.061000 0.15899 1.553000 0.36255 1.836000 0.53414 0.460000 0.39030 TGG TCGA-HZ-A9TJ-01A-11D-A40W-08 TEX19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256331.1 1 0 1 79 340 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1 78 332 0 63 2 -20.000000 1 1 0 0 1 0 4 4 2.260794 1 0.520000 3.450000 0.684211 0.990000 8.900000e-01 1.000000 1.000000 0.990828 0.990000 1 0.990000 1.000000 MIB1 57534 broad.mit.edu 37 18 19353645 19353645 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr18:19353645G>A ENST00000261537.6 + 4 856 c.592G>A c.(592-594)Gat>Aat p.D198N MIB1_ENST00000578646.1_3'UTR NM_020774.2 NP_065825.1 Q86YT6 MIB1_HUMAN mindbomb E3 ubiquitin protein ligase 1 27 STAD - Stomach adenocarcinoma(5;0.212) TGTCCTCTGGGATAATGGTGC 0.428000 0 SO:0001583 missense ENST00000261537.6 1 1 hg19 CCDS11871.1 . . . . . . . . . . G 27.0 4.795298 0.90453 . . ENSG00000101752 ENST00000261537 T 0.39406 1.08 5.36 5.36 0.76844 Mib-herc2 (2); 0.000000 0.85682 D 0.000000 T 0.66197 0.2765 M 0.79258 2.445 0.80722 D 1 D 0.69078 0.997 D 0.77004 0.989 T 0.63444 -0.6636 10 0.30078 T 0.28 -20.2918 19.0873 0.93209 0.0:0.0:1.0:0.0 . 198 Q86YT6 MIB1_HUMAN N 198 ENSP00000261537:D198N ENSP00000261537:D198N D + 1 0 MIB1 17607643 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.864000 0.99589 2.508000 0.84585 0.655000 0.94253 GAT TCGA-HZ-A9TJ-01A-11D-A40W-08 MIB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254675.1 0 0 0 23 544 0 38 0 2.378788e-01 0 22 0 38 2 0 0 0 0 0 2 1 9.999993e-01 23 539 0 38 2 -19.971710 1 1 0 0 1 1 9 10 4.179110 1 0.520000 3.450000 0.842022 0.480000 2.900000e-01 0.740000 0.490000 0.497724 0.480000 0 0.380000 0.600000 HDHD2 84064 broad.mit.edu 37 18 44661018 44661018 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr18:44661018C>T ENST00000300605.6 - 3 311 c.159G>A c.(157-159)aaG>aaA p.K53K HDHD2_ENST00000587841.1_Intron NM_032124.4 NP_115500.1 Q9H0R4 HDHD2_HUMAN haloacid dehalogenase-like hydrolase domain containing 2 6 ACAGGTCTTGCTTGCTCTCTT 0.403000 0 SO:0001819 synonymous_variant ENST00000300605.6 1 1 hg19 CCDS32829.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 HDHD2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450668.2 1 0 1 65 212 0 101 1 7.194426e-01 4 6 0 101 2 0 0 0 0 0 2 1 1 65 206 0 98 2 -20.000000 1 1 0 0 1 0 1 1 1.095673 1 0.520000 3.450000 0.351351 0.660000 5.200000e-01 0.800000 0.660000 0.668812 0.660000 0 0.590000 0.740000 ATF5 22809 broad.mit.edu 37 19 50436260 50436260 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr19:50436260G>A ENST00000423777.2 + 3 1137 c.760G>A c.(760-762)Gca>Aca p.A254T MIR4751_ENST00000578027.1_RNA|ATF5_ENST00000595125.1_Missense_Mutation_p.A254T|CTC-326K19.6_ENST00000451973.1_Intron NM_001193646.1 NP_001180575.1 Q9Y2D1 ATF5_HUMAN activating transcription factor 5 7 all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17) Pseudoephedrine(DB00852) GAAGGAACGGGCAGAGTCCGT 0.667000 GBM(48;768 989 9196 9511 26329) 0 SO:0001583 missense ENST00000423777.2 1 1 hg19 CCDS12789.1 . . . . . . . . . . G 18.96 3.734599 0.69189 2.27E-4 0.0 ENSG00000169136 ENST00000423777 T 0.56776 0.44 4.54 4.54 0.55810 Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1); 0.071375 0.53938 D 0.000044 T 0.66992 0.2846 M 0.69358 2.11 0.48511 D 0.999666 D 0.69078 0.997 D 0.72338 0.977 T 0.68880 -0.5292 10 0.56958 D 0.05 -6.7244 10.1231 0.42632 0.0:0.0:0.8:0.2 . 254 Q9Y2D1 ATF5_HUMAN T 254 ENSP00000396954:A254T ENSP00000396954:A254T A + 1 0 ATF5 55128072 1.000000 0.71417 0.950000 0.38849 0.353000 0.29299 7.197000 0.77814 2.079000 0.62486 0.448000 0.29417 GCA TCGA-HZ-A9TJ-01A-11D-A40W-08 ATF5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464915.2 1 0 1 12 218 0 22 1 9.551694e-01 12 87 0 22 2 0 0 0 0 0 2 1 9.989952e-01 11 211 0 22 2 -14.630450 1 1 121408 9 35 1 3 5 8 3.069081 1 0.520000 3.450000 0.773926 0.480000 2.400000e-01 1.000000 0.440000 0.562129 0.480000 0 0.340000 1.000000 ZNF28 7576 broad.mit.edu 37 19 53303834 53303834 + Missense_Mutation SNP A A T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr19:53303834A>T ENST00000457749.2 - 4 1383 c.1264T>A c.(1264-1266)Tat>Aat p.Y422N ZNF28_ENST00000414252.2_Missense_Mutation_p.Y369N|ZNF28_ENST00000360272.4_Missense_Mutation_p.Y369N|ZNF28_ENST00000438150.2_Missense_Mutation_p.Y369N NM_006969.3 NP_008900.3 P17035 ZNF28_HUMAN zinc finger protein 28 34 TATGAATTATATGCAAAAGCC 0.353000 0 SO:0001583 missense ENST00000457749.2 0 1 hg19 CCDS33093.2 . . . . . . . . . . - 3.848 -0.032494 0.07543 . . ENSG00000198538 ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783 T;T;T;T;T 0.08458 3.09;3.09;3.09;3.09;3.09 1.75 -3.5 0.04710 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.04998 0.0134 N 0.25647 0.755 0.09310 N 1 B 0.23128 0.08 B 0.25140 0.058 T 0.40213 -0.9575 9 0.30854 T 0.27 . 4.1215 0.10108 0.3639:0.3121:0.324:0.0 . 422 P17035 ZNF28_HUMAN N 369;422;369;369;369 ENSP00000412143:Y369N;ENSP00000397693:Y422N;ENSP00000353410:Y369N;ENSP00000444965:Y369N;ENSP00000375661:Y369N ENSP00000353410:Y369N Y - 1 0 ZNF28 57995646 0.000000 0.05858 0.000000 0.03702 0.132000 0.20833 -11.752000 0.00003 -1.516000 0.01782 0.165000 0.16767 TAT TCGA-HZ-A9TJ-01A-11D-A40W-08 ZNF28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336038.2 0 0 0 10 1165 0 158 0 2.406038e-02 1 24 0 158 2 0 0 0 0 0 2 1 9.966350e-01 10 1150 0 157 2 -3.315119 1 1 0 0 1 3 5 8 3.069081 1 0.520000 3.450000 0.773926 0.070000 1.000000e-02 1.000000 0.060000 0.249742 0.070000 0 0.030000 1.000000 NLRP12 91662 broad.mit.edu 37 19 54314230 54314230 + Missense_Mutation SNP T T C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr19:54314230T>C ENST00000324134.6 - 3 851 c.683A>G c.(682-684)cAc>cGc p.H228R NLRP12_ENST00000535162.1_Missense_Mutation_p.H228R|NLRP12_ENST00000354278.3_Missense_Mutation_p.H228R|NLRP12_ENST00000391772.1_Missense_Mutation_p.H228R|NLRP12_ENST00000345770.5_Missense_Mutation_p.H228R|NLRP12_ENST00000391773.1_Missense_Mutation_p.H228R|NLRP12_ENST00000351894.4_Missense_Mutation_p.H228R|NLRP12_ENST00000391775.3_Missense_Mutation_p.H228R NM_001277126.1|NM_144687.2 NP_001264055.1|NP_653288.1 P59046 NAL12_HUMAN NLR family, pyrin domain containing 12 80 Ovarian(34;0.19) CATCACCTTGTGTGCCAGCAT 0.577000 0 SO:0001583 missense ENST00000324134.6 1 1 hg19 CCDS12864.1 . . . . . . . . . . T 0.687 -0.795867 0.02862 . . ENSG00000142405 ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772 T;T;T;T;T;T;T 0.76709 -1.04;-1.04;-1.04;-1.04;-1.04;-1.04;-1.04 4.47 1.18 0.20946 NACHT nucleoside triphosphatase (1); 0.313100 0.23263 N 0.050104 T 0.42359 0.1199 N 0.01493 -0.835 0.80722 D 1 B;B;B;B 0.26935 0.134;0.064;0.134;0.164 B;B;B;B 0.26517 0.031;0.031;0.031;0.07 T 0.45101 -0.9284 10 0.02654 T 1 . 7.0128 0.24871 0.0:0.2972:0.0:0.7028 . 228;228;228;228 F2Z321;A8K407;A8MTQ2;P59046 .;.;.;NAL12_HUMAN R 228 ENSP00000319377:H228R;ENSP00000438030:H228R;ENSP00000340473:H228R;ENSP00000346231:H228R;ENSP00000375655:H228R;ENSP00000375653:H228R;ENSP00000375652:H228R ENSP00000319377:H228R H - 2 0 NLRP12 59006042 0.996000 0.38824 0.973000 0.42090 0.891000 0.51852 0.716000 0.25836 0.224000 0.20940 0.254000 0.18369 CAC TCGA-HZ-A9TJ-01A-11D-A40W-08 NLRP12-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000134340.1 0 0 0 14 463 1 58 0 0 0 1 58 2 0 0 0 0 0 2 0 4.776192e-02 14 461 1 56 25 -13.396060 1 0 0 0 1 3 5 8 3.069081 1 0.520000 3.450000 0.773926 0.260000 1.300000e-01 1.000000 0.250000 0.399713 0.260000 0 0.180000 1.000000 ZNF543 125919 broad.mit.edu 37 19 57839619 57839619 + Silent SNP T T C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr19:57839619T>C ENST00000321545.4 + 4 1134 c.789T>C c.(787-789)gcT>gcC p.A263A NM_213598.3 NP_998763.2 Q08ER8 ZN543_HUMAN zinc finger protein 543 28 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221) GTGGGAAGGCTTTTAACCGCA 0.522000 0 SO:0001819 synonymous_variant ENST00000321545.4 0 1 hg19 CCDS33130.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 ZNF543-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465780.1 0 0 0 5 468 0 49 0 6.160546e-03 0 9 0 49 2 0 0 0 0 0 2 1 9.353779e-01 5 461 0 47 2 -2.588949 1 1 121412 1 33 1 3 5 8 3.109811 1 0.520000 3.450000 0.777200 0.100000 1.000000e-02 1.000000 0.070000 0.267594 0.100000 0 0.050000 1.000000 FUT6 2528 broad.mit.edu 37 19 5831521 5831521 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr19:5831521C>T ENST00000318336.4 - 3 2252 c.1058G>A c.(1057-1059)gGc>gAc p.G353D FUT6_ENST00000592563.1_Intron|FUT6_ENST00000527106.1_Missense_Mutation_p.G353D|FUT6_ENST00000524754.1_Missense_Mutation_p.G353D|FUT6_ENST00000286955.5_Missense_Mutation_p.G353D NM_000150.2 NP_000141.1 P51993 FUT6_HUMAN fucosyltransferase 6 (alpha (1,3) fucosyltransferase) 6 AGCCGCTATGCCGCGTGTCTG 0.632000 0 SO:0001583 missense ENST00000318336.4 0 1 hg19 CCDS12152.1 . . . . . . . . . . C 11.12 1.544153 0.27563 . . ENSG00000156413 ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955 T;T;T;T 0.20332 2.08;2.08;2.08;2.08 3.23 3.23 0.37069 . . . . . T 0.04634 0.0126 N 0.00182 -1.905 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.15350 -1.0440 9 0.06236 T 0.91 . 12.6777 0.56903 0.0:1.0:0.0:0.0 . 353 P51993 FUT6_HUMAN D 353 ENSP00000431708:G353D;ENSP00000432954:G353D;ENSP00000313398:G353D;ENSP00000286955:G353D ENSP00000286955:G353D G - 2 0 FUT6 5782521 0.004000 0.15560 0.326000 0.25389 0.012000 0.07955 0.883000 0.28200 1.743000 0.51761 0.436000 0.28706 GGC TCGA-HZ-A9TJ-01A-11D-A40W-08 FUT6-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394218.2 0 0 0 6 411 0 92 0 1.048388e-01 0 32 0 92 2 0 0 0 0 0 2 1 9.573416e-01 6 384 0 84 2 -1.912481 0 1 0 0 1 0 4 4 1.734322 1 0.520000 3.450000 0.593909 0.070000 2.000000e-02 1.000000 0.060000 0.278948 0.070000 0 0.040000 1.000000 COL11A1 1301 broad.mit.edu 37 1 103400665 103400665 + Missense_Mutation SNP G G C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:103400665G>C ENST00000370096.3 - 45 3755 c.3443C>G c.(3442-3444)cCt>cGt p.P1148R COL11A1_ENST00000512756.1_Missense_Mutation_p.P1032R|COL11A1_ENST00000358392.2_Missense_Mutation_p.P1160R|COL11A1_ENST00000353414.4_Missense_Mutation_p.P1109R NM_001854.3 NP_001845.3 P12107 COBA1_HUMAN collagen, type XI, alpha 1 258 all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181) GGGACCGGGAGGGCCCTGCAG 0.448000 0 SO:0001583 missense ENST00000370096.3 1 1 hg19 CCDS778.1 . . . . . . . . . . G 16.61 3.171191 0.57584 . . ENSG00000060718 ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756 D;D;D;D 0.98684 -5.07;-5.07;-5.07;-5.07 5.52 5.52 0.82312 . 0.000000 0.85682 D 0.000000 D 0.98560 0.9519 L 0.41492 1.28 0.80722 D 1 D;D;D;D;D 0.89917 1.0;0.989;1.0;1.0;0.999 D;D;D;D;D 0.91635 0.996;0.967;0.999;0.997;0.997 D 0.99935 1.1349 10 0.87932 D 0 . 19.4476 0.94854 0.0:0.0:1.0:0.0 . 1032;1109;1160;1148;368 E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5 .;.;.;COBA1_HUMAN;. R 1148;1160;1109;368;1032 ENSP00000359114:P1148R;ENSP00000351163:P1160R;ENSP00000302551:P1109R;ENSP00000426533:P1032R ENSP00000302551:P1109R P - 2 0 COL11A1 103173253 1.000000 0.71417 1.000000 0.80357 0.565000 0.35776 9.813000 0.99286 2.588000 0.87417 0.655000 0.94253 CCT TCGA-HZ-A9TJ-01A-11D-A40W-08 COL11A1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000029997.1 1 0 1 15 113 0 25 0 3.060848e-01 0 9 0 25 2 0 0 0 0 0 2 1 9.998797e-01 14 110 0 23 2 -19.999440 1 1 0 0 1 2 2 4 2.124937 1 0.520000 3.450000 0.673025 0.690000 4.000000e-01 1.000000 1.000000 0.714249 0.690000 0 0.530000 0.920000 VPS13D 55187 broad.mit.edu 37 1 12364627 12364627 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:12364627C>T ENST00000358136.3 + 26 6411 c.6281C>T c.(6280-6282)aCg>aTg p.T2094M VPS13D_ENST00000356315.4_Missense_Mutation_p.T2094M NM_015378.2 NP_056193.2 vacuolar protein sorting 13 homolog D (S. cerevisiae) 130 Ovarian(185;0.249) Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) ACGACAAGCACGGAGGAGCCC 0.522000 0 SO:0001583 missense ENST00000358136.3 1 1 hg19 CCDS30588.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 3.278|3.278 -0.147578|-0.147578 0.06627|0.06627 .|. .|. ENSG00000048707|ENSG00000048707 ENST00000011700|ENST00000356315;ENST00000358136 .|T;T .|0.53206 .|0.63;0.64 5.94|5.94 1.31|1.31 0.21738|0.21738 .|. .|1.074530 .|0.07029 .|N .|0.828020 T|T 0.27798|0.27798 0.0684|0.0684 N|N 0.08118|0.08118 0|0 0.09310|0.09310 N|N 1|1 .|B;B .|0.13145 .|0.007;0.002 .|B;B .|0.09377 .|0.004;0.002 T|T 0.21655|0.21655 -1.0239|-1.0239 5|10 .|0.33940 .|T .|0.23 .|. 8.7283|8.7283 0.34483|0.34483 0.0:0.6002:0.0:0.3998|0.0:0.6002:0.0:0.3998 .|. .|2094;2094 .|Q5THJ4-2;Q5THJ4 .|.;VP13D_HUMAN W|M 917|2094 .|ENSP00000348666:T2094M;ENSP00000350854:T2094M .|ENSP00000348666:T2094M R|T +|+ 1|2 2|0 VPS13D|VPS13D 12287214|12287214 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.010000|0.010000 0.07245|0.07245 0.256000|0.256000 0.18351|0.18351 0.362000|0.362000 0.24319|0.24319 -0.224000|-0.224000 0.12420|0.12420 CGG|ACG TCGA-HZ-A9TJ-01A-11D-A40W-08 VPS13D-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036897.2 1 0 1 26 160 0 25 0 1.551381e-01 0 5 0 25 2 0 0 0 0 0 2 1 9.999999e-01 26 156 0 24 2 -20.000000 1 1 0 0 1 2 2 4 2.143394 1 0.520000 3.450000 0.675325 0.810000 5.400000e-01 1.000000 1.000000 0.818492 0.810000 0 0.670000 1.000000 CENPF 1063 broad.mit.edu 37 1 214815002 214815002 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:214815002G>A ENST00000366955.3 + 12 3489 c.3321G>A c.(3319-3321)caG>caA p.Q1107Q NM_016343.3 NP_057427.3 P49454 CENPF_HUMAN centromere protein F, 350/400kDa 126 AGACAGTGCAGCAAGCTCTGA 0.373000 Colon(80;575 1284 11000 14801 43496) 0 SO:0001819 synonymous_variant ENST00000366955.3 0 1 hg19 CCDS31023.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 CENPF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000089749.1 0 0 0 5 367 0 39 0 7.702465e-03 0 8 0 39 2 0 0 0 0 0 2 1 9.357022e-01 5 362 0 39 2 -3.325794 1 1 0 0 1 2 3 5 2.588351 1 0.520000 3.450000 0.730337 0.090000 1.000000e-02 0.210000 0.100000 0.108930 0.090000 0 0.050000 0.160000 TP53BP2 7159 broad.mit.edu 37 1 223986037 223986037 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:223986037C>T ENST00000343537.7 - 12 2119 c.1828G>A c.(1828-1830)Gtg>Atg p.V610M TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.V481M|TP53BP2_ENST00000391879.2_Intron NM_001031685.2 NP_001026855.2 Q13625 ASPP2_HUMAN tumor protein p53 binding protein 2 29 CTTGCTGCCACGGTCTGGGGT 0.527000 0 SO:0001583 missense ENST00000343537.7 1 1 hg19 CCDS44319.1 . . . . . . . . . . C 22.0 4.229638 0.79688 . . ENSG00000143514 ENST00000391878;ENST00000343537 T;T 0.56941 0.43;0.62 5.88 5.88 0.94601 . 0.055023 0.64402 D 0.000001 T 0.67477 0.2897 L 0.43152 1.355 0.80722 D 1 D;D 0.89917 1.0;0.985 D;P 0.85130 0.997;0.49 T 0.61352 -0.7080 10 0.33940 T 0.23 . 20.2422 0.98381 0.0:1.0:0.0:0.0 . 610;604 B4DG66;Q13625 .;ASPP2_HUMAN M 481;610 ENSP00000375750:V481M;ENSP00000341957:V610M ENSP00000341957:V610M V - 1 0 TP53BP2 222052660 0.997000 0.39634 0.966000 0.40874 0.972000 0.66771 3.655000 0.54460 2.782000 0.95742 0.655000 0.94253 GTG TCGA-HZ-A9TJ-01A-11D-A40W-08 TP53BP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090985.3 1 0 0 30 761 0 110 1 8.394246e-01 5 81 0 110 2 1 1 79 1853 0 993 2 1 1 30 748 0 107 2 -3.849560 1 1 0 0 1 2 3 5 2.588351 1 0.520000 3.450000 0.730337 0.250000 1.600000e-01 0.370000 0.250000 0.267459 0.250000 0 0.210000 0.320000 OR2M4 26245 broad.mit.edu 37 1 248403055 248403055 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:248403055G>A ENST00000306687.1 + 1 825 c.825G>A c.(823-825)tcG>tcA p.S275S NM_017504.1 NP_059974.1 Q96R27 OR2M4_HUMAN olfactory receptor, family 2, subfamily M, member 4 50 all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0245) AGATGGTGTCGGCCTTCTACA 0.488000 0 SO:0001819 synonymous_variant ENST00000306687.1 1 1 hg19 CCDS31108.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 OR2M4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097352.1 1 0 1 54 298 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1 53 294 0 46 2 -2.565258 1 1 0 0 1 3 4 7 2.496828 1 0.520000 3.450000 0.720117 0.990000 7.900000e-01 1.000000 1.000000 0.969736 0.990000 1 0.910000 1.000000 FCN3 8547 broad.mit.edu 37 1 27697110 27697110 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:27697110C>T ENST00000270879.4 - 7 640 c.635G>A c.(634-636)gGc>gAc p.G212D FCN3_ENST00000354982.2_Missense_Mutation_p.G201D NM_003665.2 NP_003656.2 O75636 FCN3_HUMAN ficolin (collagen/fibrinogen domain containing) 3 7 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) TGAGAACTTGCCCAGTGCCAG 0.582000 0 SO:0001583 missense ENST00000270879.4 0 1 hg19 CCDS300.1 . . . . . . . . . . C 21.5 4.159905 0.78226 . . ENSG00000142748 ENST00000270879;ENST00000354982;ENST00000498393 T;T 0.76186 -1.0;-1.0 4.84 2.93 0.34026 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1); 0.324971 0.25288 N 0.031759 T 0.81432 0.4821 L 0.56769 1.78 0.25196 N 0.990097 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.992 T 0.70916 -0.4742 10 0.59425 D 0.04 . 10.1394 0.42725 0.0:0.8212:0.0:0.1788 . 201;212 Q6UXM4;O75636 .;FCN3_HUMAN D 212;201;90 ENSP00000270879:G212D;ENSP00000347077:G201D ENSP00000270879:G212D G - 2 0 FCN3 27569697 0.046000 0.20272 0.975000 0.42487 0.386000 0.30323 0.596000 0.24044 1.198000 0.43158 0.558000 0.71614 GGC TCGA-HZ-A9TJ-01A-11D-A40W-08 FCN3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000015667.1 0 0 0 6 440 0 71 0 1.619075e-03 0 4 0 71 2 0 0 0 0 0 2 1 9.624207e-01 6 430 0 70 2 -2.070124 0 1 0 0 1 2 2 4 2.124937 1 0.520000 3.450000 0.673025 0.080000 1.000000e-02 1.000000 0.080000 0.161743 0.080000 0 0.040000 0.140000 GPR3 2827 broad.mit.edu 37 1 27720926 27720926 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:27720926C>T ENST00000374024.3 + 2 723 c.624C>T c.(622-624)atC>atT p.I208I NM_005281.3 NP_005272.1 P46089 GPR3_HUMAN G protein-coupled receptor 3 8 Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157) TGTTTGGCATCATGCTGCAGC 0.577000 0 SO:0001819 synonymous_variant ENST00000374024.3 1 1 hg19 CCDS303.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 GPR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000009522.1 0 0 0 14 429 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 9.997344e-01 14 423 0 95 2 -3.222301 1 1 0 0 1 2 2 4 2.124937 1 0.520000 3.450000 0.673025 0.180000 9.000000e-02 1.000000 0.190000 0.255630 0.180000 0 0.130000 0.260000 LRRC7 57554 broad.mit.edu 37 1 70257750 70257750 + Nonsense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:70257750C>T ENST00000035383.5 + 2 244 c.214C>T c.(214-216)Cga>Tga p.R72* LRRC7_ENST00000370958.1_Nonsense_Mutation_p.R110*|LRRC7_ENST00000310961.5_Nonsense_Mutation_p.R77*|LRRC7_ENST00000415775.2_5'UTR NM_020794.2 NP_065845.1 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 p.R72G(1) 162 TCAAGCTCTACGAAAACTAAG 0.294000 1 Substitution - Missense(1) SO:0001587 stop_gained ENST00000035383.5 0 1 hg19 CCDS645.1 . . . . . . . . . . C 37 6.592986 0.97688 . . ENSG00000033122 ENST00000310961;ENST00000370958;ENST00000035383;ENST00000335298 . . . 5.68 2.7 0.31948 . 0.148908 0.46758 D 0.000280 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 13.3006 0.60324 0.4547:0.5453:0.0:0.0 . . . . X 77;110;72;72 . ENSP00000035383:R72X R + 1 2 LRRC7 70030338 0.999000 0.42202 0.999000 0.59377 0.997000 0.91878 2.305000 0.43664 0.277000 0.22141 0.561000 0.74099 CGA TCGA-HZ-A9TJ-01A-11D-A40W-08 LRRC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131261.1 1 0 1 134 352 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 1 134 350 1 81 20 -20.000000 1 1 0 0 1 2 2 4 2.124937 1 0.520000 3.450000 0.673025 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 LRRC7 57554 broad.mit.edu 37 1 70541973 70541973 + Missense_Mutation SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr1:70541973C>A ENST00000035383.5 + 22 4360 c.4330C>A c.(4330-4332)Cca>Aca p.P1444T LRRC7_ENST00000310961.5_Missense_Mutation_p.P1402T|LRRC7_ENST00000415775.2_Missense_Mutation_p.P728T NM_020794.2 NP_065845.1 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 162 GGATGGATATCCAGAGCAGGT 0.463000 0 SO:0001583 missense ENST00000035383.5 1 1 hg19 CCDS645.1 . . . . . . . . . . C 18.22 3.575374 0.65878 . . ENSG00000033122 ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957 T;T;T 0.36520 1.25;1.31;2.41 6.16 6.16 0.99307 PDZ/DHR/GLGF (1); 0.129386 0.53938 D 0.000049 T 0.20414 0.0491 N 0.08118 0 0.54753 D 0.999982 P;P;P 0.44429 0.787;0.835;0.608 B;P;B 0.47645 0.372;0.553;0.18 T 0.04930 -1.0917 10 0.37606 T 0.19 . 19.848 0.96722 0.0:1.0:0.0:0.0 . 728;1397;1444 F8WE45;Q96NW7-2;Q96NW7 .;.;LRRC7_HUMAN T 1402;1444;728;1220 ENSP00000309245:P1402T;ENSP00000035383:P1444T;ENSP00000394867:P728T ENSP00000035383:P1444T P + 1 0 LRRC7 70314561 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 6.176000 0.71955 2.937000 0.99478 0.650000 0.86243 CCA TCGA-HZ-A9TJ-01A-11D-A40W-08 LRRC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131261.1 1 0 1 32 198 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 1 32 195 0 25 2 -20.000000 1 1 0 0 1 2 2 4 2.124937 1 0.520000 3.450000 0.673025 0.800000 5.600000e-01 1.000000 1.000000 0.813251 0.800000 0 0.670000 0.980000 NKX2-4 644524 broad.mit.edu 37 20 21376877 21376877 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr20:21376877C>T ENST00000351817.4 - 2 1365 c.737G>A c.(736-738)cGg>cAg p.R246Q RP11-227D2.3_ENST00000419666.2_RNA|RP11-227D2.3_ENST00000552439.1_RNA NM_033176.1 NP_149416.1 Q9H2Z4 NKX24_HUMAN NK2 homeobox 4 3 CTTGGCCTGCCGTTTCATCTT 0.711000 0 SO:0001583 missense ENST00000351817.4 1 1 hg19 CCDS42855.1 . . . . . . . . . . C 23.3 4.394647 0.83011 . . ENSG00000125816 ENST00000351817 D 0.96396 -4.0 3.49 3.49 0.39957 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.000000 0.56097 U 0.000036 D 0.97885 0.9305 M 0.84156 2.68 0.58432 D 0.999993 D 0.69078 0.997 D 0.72982 0.979 D 0.98753 1.0721 10 0.87932 D 0 . 14.7591 0.69593 0.0:1.0:0.0:0.0 . 246 Q9H2Z4 NKX24_HUMAN Q 246 ENSP00000345147:R246Q ENSP00000345147:R246Q R - 2 0 NKX2-4 21324877 1.000000 0.71417 0.998000 0.56505 0.688000 0.40055 7.095000 0.76952 1.781000 0.52344 0.484000 0.47621 CGG TCGA-HZ-A9TJ-01A-11D-A40W-08 NKX2-4-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078270.2 1 0 0 11 46 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 9.984898e-01 11 43 0 19 2 -19.943030 1 1 121008 1 27 1 2 2 4 1.603688 1 0.520000 3.450000 0.565217 0.880000 4.700000e-01 1.000000 1.000000 0.844835 0.880000 1 0.650000 1.000000 SLC12A5 57468 broad.mit.edu 37 20 44685548 44685548 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr20:44685548C>T ENST00000454036.2 + 24 3241 c.3192C>T c.(3190-3192)aaC>aaT p.N1064N SLC12A5_ENST00000243964.3_Silent_p.N1041N NM_001134771.1 NP_001128243.1 Q9H2X9 S12A5_HUMAN solute carrier family 12 (potassium/chloride transporter), member 5 80 Myeloproliferative disorder(115;0.0122) Bumetanide(DB00887)|Potassium Chloride(DB00761) AGTGGGAGAACTTGTAAGTGC 0.493000 0 SO:0001819 synonymous_variant ENST00000454036.2 1 1 hg19 CCDS46610.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 SLC12A5-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000471538.1 1 0 1 54 353 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1 53 348 0 68 2 -20.000000 1 1 0 0 1 3 4 7 2.450645 1 0.520000 3.450000 0.715808 0.910000 6.700000e-01 1.000000 1.000000 0.897559 0.910000 1 0.770000 1.000000 SLC2A10 81031 broad.mit.edu 37 20 45354423 45354423 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr20:45354423G>A ENST00000359271.2 + 2 998 c.748G>A c.(748-750)Gtg>Atg p.V250M NM_030777.3 NP_110404.1 O95528 GTR10_HUMAN solute carrier family 2 (facilitated glucose transporter), member 10 34 Myeloproliferative disorder(115;0.0122) GCAGCCCAACGTGCTGTGCTA 0.622000 0 SO:0001583 missense ENST00000359271.2 1 1 hg19 CCDS13402.1 . . . . . . . . . . G 18.27 3.586473 0.66105 . . ENSG00000197496 ENST00000359271 T 0.76448 -1.02 5.86 4.89 0.63831 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.057050 0.64402 D 0.000002 D 0.86146 0.5863 M 0.76170 2.325 0.49798 D 0.999825 D 0.89917 1.0 D 0.76071 0.987 D 0.87084 0.2168 10 0.87932 D 0 -18.7043 10.4704 0.44633 0.0688:0.0:0.7961:0.1351 . 250 O95528 GTR10_HUMAN M 250 ENSP00000352216:V250M ENSP00000352216:V250M V + 1 0 SLC2A10 44787830 1.000000 0.71417 0.996000 0.52242 0.955000 0.61496 4.571000 0.60879 1.432000 0.47375 0.655000 0.94253 GTG TCGA-HZ-A9TJ-01A-11D-A40W-08 SLC2A10-001 KNOWN mRNA_end_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079578.2 1 0 1 83 603 0 102 0 5.219725e-01 0 14 0 102 2 0 0 0 0 0 2 1 1 83 593 0 100 2 -20.000000 1 1 121412 3 40 1 3 4 7 2.450645 1 0.520000 3.450000 0.715808 0.810000 6.300000e-01 1.000000 0.790000 0.842551 0.810000 0 0.720000 1.000000 TIAM1 7074 broad.mit.edu 37 21 32493062 32493062 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr21:32493062G>A ENST00000286827.3 - 29 4871 c.4400C>T c.(4399-4401)cCg>cTg p.P1467L TIAM1_ENST00000541036.1_Missense_Mutation_p.P1407L NM_003253.2 NP_003244.2 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 115 CTCTTTCTCCGGGCTGCTTGC 0.577000 0 SO:0001583 missense ENST00000286827.3 1 1 hg19 CCDS13609.1 . . . . . . . . . . G 27.0 4.789061 0.90367 . . ENSG00000156299 ENST00000286827;ENST00000541036 T;T 0.42131 0.98;1.01 5.14 5.14 0.70334 . 0.126543 0.53938 D 0.000041 T 0.49525 0.1562 L 0.50333 1.59 0.80722 D 1 D;D 0.58970 0.981;0.984 P;B 0.49637 0.617;0.413 T 0.51012 -0.8759 10 0.51188 T 0.08 . 18.6336 0.91369 0.0:0.0:1.0:0.0 . 1407;1467 F5GZ53;Q13009 .;TIAM1_HUMAN L 1467;1407 ENSP00000286827:P1467L;ENSP00000441570:P1407L ENSP00000286827:P1467L P - 2 0 TIAM1 31414933 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 7.421000 0.80204 2.377000 0.81083 0.655000 0.94253 CCG TCGA-HZ-A9TJ-01A-11D-A40W-08 TIAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192552.1 1 0 1 38 227 0 42 0 2.730592e-01 0 7 0 42 2 0 0 0 0 0 2 1 1 37 219 0 41 2 -2.545005 1 1 121412 11 43 1 1 2 3 1.721172 1 0.520000 3.450000 0.598326 0.680000 4.800000e-01 1.000000 0.660000 0.728872 0.680000 0 0.570000 1.000000 TIAM1 7074 broad.mit.edu 37 21 32589921 32589921 + Missense_Mutation SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr21:32589921C>A ENST00000286827.3 - 10 2561 c.2090G>T c.(2089-2091)tGg>tTg p.W697L TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Missense_Mutation_p.W697L NM_003253.2 NP_003244.2 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 115 ATCCAGACCCCACAGAGAAGA 0.532000 0 SO:0001583 missense ENST00000286827.3 1 1 hg19 CCDS13609.1 . . . . . . . . . . C 19.86 3.906475 0.72868 . . ENSG00000156299 ENST00000286827;ENST00000399841;ENST00000541036 T;T 0.32988 1.43;1.43 5.41 5.41 0.78517 . 0.124926 0.64402 D 0.000016 T 0.33556 0.0867 L 0.54323 1.7 0.80722 D 1 B;B;B;B 0.32573 0.101;0.061;0.376;0.104 B;B;B;B 0.30401 0.098;0.045;0.115;0.11 T 0.08953 -1.0697 10 0.46703 T 0.11 . 19.3868 0.94560 0.0:1.0:0.0:0.0 . 697;697;538;697 F5GZ53;B7ZLR6;E9PD83;Q13009 .;.;.;TIAM1_HUMAN L 697;538;697 ENSP00000286827:W697L;ENSP00000441570:W697L ENSP00000286827:W697L W - 2 0 TIAM1 31511792 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 7.569000 0.82380 2.803000 0.96430 0.655000 0.94253 TGG TCGA-HZ-A9TJ-01A-11D-A40W-08 TIAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192552.1 0 0 1 57 374 0 112 0 1.820968e-02 0 2 0 112 2 0 0 0 0 0 2 1 1 57 364 0 107 2 -2.619883 1 1 0 0 1 1 2 3 1.721172 1 0.520000 3.450000 0.598326 0.620000 4.700000e-01 1.000000 0.610000 0.683808 0.620000 0 0.540000 1.000000 COL18A1 80781 broad.mit.edu 37 21 46932271 46932271 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr21:46932271G>A ENST00000359759.4 + 41 5245 c.5224G>A c.(5224-5226)Gtg>Atg p.V1742M SLC19A1_ENST00000567670.1_Intron|SLC19A1_ENST00000468508.1_5'Flank|COL18A1_ENST00000355480.5_Missense_Mutation_p.V1507M|COL18A1_ENST00000400337.2_Missense_Mutation_p.V1327M P39060 COIA1_HUMAN collagen, type XVIII, alpha 1 25 CGCCTACATCGTGCTCTGCAT 0.692000 0 SO:0001583 missense ENST00000359759.4 0 1 hg19 . . . . . . . . . . G 16.15 3.041922 0.55003 . . ENSG00000182871 ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220 T;T;T;T 0.59638 0.25;0.25;0.25;0.25 4.41 3.52 0.40303 Collagenase NC10/endostatin (1);C-type lectin fold (1);C-type lectin-like (1); 0.000000 0.85682 U 0.000000 T 0.77418 0.4127 M 0.88979 2.995 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.83275 0.996;0.99;0.996;0.994 T 0.80417 -0.1391 10 0.87932 D 0 . 10.9067 0.47084 0.0934:0.0:0.9066:0.0 . 1742;1324;1507;1327 P39060;D3DSM4;P39060-1;P39060-2 COIA1_HUMAN;.;.;. M 1327;1327;1507;1742;1742;675 ENSP00000383191:V1327M;ENSP00000347665:V1507M;ENSP00000352798:V1742M;ENSP00000339118:V675M ENSP00000339118:V675M V + 1 0 COL18A1 45756699 1.000000 0.71417 0.357000 0.25798 0.012000 0.07955 5.167000 0.64972 1.005000 0.39183 0.549000 0.68633 GTG TCGA-HZ-A9TJ-01A-11D-A40W-08 COL18A1-201 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000206827.1 1 0 0 7 107 0 21 1 9.999822e-01 14 437 0 21 2 0 0 0 0 0 2 1 9.811088e-01 7 106 0 20 2 -10.821990 1 1 120986 3 31 1 2 2 4 2.120256 1 0.520000 3.450000 0.671862 0.380000 1.600000e-01 1.000000 0.340000 0.440891 0.380000 0 0.250000 0.590000 CELSR1 9620 broad.mit.edu 37 22 46931761 46931761 + Missense_Mutation SNP G G C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr22:46931761G>C ENST00000262738.3 - 1 1306 c.1307C>G c.(1306-1308)cCg>cGg p.P436R CELSR1_ENST00000395964.1_Missense_Mutation_p.P436R|CELSR1_ENST00000497509.1_5'Flank NM_014246.1 NP_055061.1 Q9NYQ6 CELR1_HUMAN cadherin, EGF LAG seven-pass G-type receptor 1 95 Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766) GAGCGGGCCCGGATTGCGCCC 0.667000 0 SO:0001583 missense ENST00000262738.3 1 1 hg19 CCDS14076.1 . . . . . . . . . . G 14.61 2.585708 0.46110 . . ENSG00000075275 ENST00000262738;ENST00000395964 T;T 0.51574 0.7;0.7 4.65 3.62 0.41486 Cadherin (4);Cadherin-like (1); 0.000000 0.64402 U 0.000004 T 0.68072 0.2961 M 0.78637 2.42 0.39149 D 0.96218 D 0.89917 1.0 D 0.97110 1.0 T 0.74137 -0.3762 10 0.66056 D 0.02 . 13.7659 0.62995 0.0:0.0:0.8449:0.1551 . 436 Q9NYQ6 CELR1_HUMAN R 436 ENSP00000262738:P436R;ENSP00000379293:P436R ENSP00000262738:P436R P - 2 0 CELSR1 45310425 1.000000 0.71417 0.997000 0.53966 0.534000 0.34807 9.205000 0.95048 0.943000 0.37553 0.462000 0.41574 CCG TCGA-HZ-A9TJ-01A-11D-A40W-08 CELSR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318037.1 1 0 1 22 99 0 30 1 7.062757e-01 6 7 0 30 2 0 0 0 0 0 2 1 9.999991e-01 21 96 0 27 2 -20.000000 1 1 0 0 1 2 2 4 1.612139 1 0.520000 3.450000 0.569275 0.820000 5.200000e-01 1.000000 1.000000 0.823533 0.820000 0 0.650000 1.000000 GLI2 2736 broad.mit.edu 37 2 121742187 121742187 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:121742187G>A ENST00000452319.1 + 12 1884 c.1824G>A c.(1822-1824)ccG>ccA p.P608P GLI2_ENST00000361492.4_Silent_p.P608P|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Silent_p.P280P GLI family zinc finger 2 64 Renal(3;0.0496) Prostate(154;0.0623) TCCGCACACCGCTGCTCAAAG 0.652000 0 SO:0001819 synonymous_variant ENST00000452319.1 1 1 hg19 CCDS33283.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 GLI2-009 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000332293.3 1 0 1 41 302 0 52 0 1.504223e-02 0 2 0 52 2 0 0 0 1 0 0 2 1 1 40 301 0 50 2 -16.738570 1 1 121410 3 35 1 3 4 7 2.341448 1 0.520000 3.450000 0.702048 0.780000 5.500000e-01 1.000000 0.740000 0.812330 0.780000 0 0.650000 1.000000 NCKAP5 344148 broad.mit.edu 37 2 133540781 133540781 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:133540781G>A ENST00000409261.1 - 14 3976 c.3603C>T c.(3601-3603)atC>atT p.I1201I NCKAP5_ENST00000317721.6_Silent_p.I1201I|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank NM_207363.2 NP_997246.2 O14513 NCKP5_HUMAN NCK-associated protein 5 118 CACCCGCTGTGATCTCCATGC 0.478000 0 SO:0001819 synonymous_variant ENST00000409261.1 1 1 hg19 CCDS46418.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 NCKAP5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000331663.1 1 0 1 44 227 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 1 44 221 0 49 2 -20.000000 1 1 0 0 1 3 4 7 2.341448 1 0.520000 3.450000 0.702048 0.990000 7.600000e-01 1.000000 1.000000 0.964995 0.990000 1 0.900000 1.000000 THSD7B 80731 broad.mit.edu 37 2 138400061 138400061 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:138400061G>A ENST00000409968.1 + 21 3981 c.3803G>A c.(3802-3804)cGa>cAa p.R1268Q THSD7B_ENST00000272643.3_Missense_Mutation_p.R1271Q|THSD7B_ENST00000413152.2_Missense_Mutation_p.R1240Q|THSD7B_ENST00000543459.1_Intron Q9C0I4 THS7B_HUMAN thrombospondin, type I, domain containing 7B 134 ATTTTAGGTCGAATGAGCCGG 0.478000 0 SO:0001583 missense ENST00000409968.1 1 1 hg19 . . . . . . . . . . G 11.34 1.609124 0.28623 . . ENSG00000144229 ENST00000409968;ENST00000272643;ENST00000413152 T;T;T 0.51325 0.71;0.71;0.71 5.29 -0.929 0.10444 . 1.100800 0.06637 N 0.760367 T 0.21103 0.0508 N 0.03281 -0.365 0.80722 D 1 B 0.06786 0.001 B 0.04013 0.001 T 0.46582 -0.9181 10 0.02654 T 1 . 10.7598 0.46258 0.6294:0.0:0.3706:0.0 . 1240 C9JKN6 . Q 1268;1271;1240 ENSP00000387145:R1268Q;ENSP00000272643:R1271Q;ENSP00000413841:R1240Q ENSP00000272643:R1271Q R + 2 0 THSD7B 138116531 0.970000 0.33590 0.992000 0.48379 0.992000 0.81027 -0.041000 0.12084 -0.106000 0.12110 -0.258000 0.10820 CGA TCGA-HZ-A9TJ-01A-11D-A40W-08 THSD7B-001 NOVEL not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000331769.2 0 0 1 161 353 0 56 0 0 0 1 0 56 2 0 0 0 0 0 2 1 1 158 349 0 56 2 -12.574930 1 1 120828 1 36 1 3 4 7 2.341448 1 0.520000 3.450000 0.702048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TTN 7273 broad.mit.edu 37 2 179397543 179397543 + Nonsense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:179397543C>T ENST00000591111.1 - 308 99100 c.98876G>A c.(98875-98877)tGg>tAg p.W32959* TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.W32032*|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.W25535*|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.W34600*|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.W25727*|TTN_ENST00000359218.5_Nonsense_Mutation_p.W25660*|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000450692.2_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) GAACTGTTCCCATCTTGAAAG 0.428000 0 SO:0001587 stop_gained ENST00000591111.1 0 1 hg19 . . . . . . . . . . C 73 115.725762 0.99999 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 . . . 5.81 5.81 0.92471 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.87932 D 0 . 19.6737 0.95921 0.0:1.0:0.0:0.0 . . . . X 32032;25535;25727;25660;25532 . ENSP00000340554:W25727X W - 2 0 TTN 179105789 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.794000 0.85869 2.757000 0.94681 0.462000 0.41574 TGG TCGA-HZ-A9TJ-01A-11D-A40W-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 80 163 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 1 79 159 0 52 2 -8.959370 1 1 0 0 1 3 4 7 2.341448 1 0.520000 3.450000 0.702048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PID1 55022 broad.mit.edu 37 2 229890591 229890591 + Silent SNP G G A rs139231184 byFrequency TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:229890591G>A ENST00000354069.6 - 3 540 c.510C>T c.(508-510)acC>acT p.T170T PID1_ENST00000482518.2_Intron|PID1_ENST00000392054.3_Silent_p.T168T|PID1_ENST00000409462.1_Silent_p.T88T|PID1_ENST00000392055.3_Silent_p.T137T Q7Z2X4 PCLI1_HUMAN phosphotyrosine interaction domain containing 1 26 Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171) TGTGGTCGGCGGTGCAGTAGG 0.582000 0 SO:0001819 synonymous_variant ENST00000354069.6 0 1 hg19 TCGA-HZ-A9TJ-01A-11D-A40W-08 PID1-005 KNOWN basic protein_coding protein_coding OTTHUMT00000331810.2 0 0 0 5 435 1 51 0 8.772374e-03 0 10 1 51 2 0 0 0 0 0 2 0 3.166707e-07 5 429 2 49 35 -2.267164 0 1 121412 19 46 1 3 4 7 2.238105 1 0.520000 3.450000 0.689521 0.080000 1.000000e-02 1.000000 0.080000 0.296901 0.080000 0 0.040000 1.000000 PER2 8864 broad.mit.edu 37 2 239185809 239185809 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:239185809C>T ENST00000254657.3 - 3 535 c.256G>A c.(256-258)Gca>Aca p.A86T PER2_ENST00000254658.3_Missense_Mutation_p.A86T|PER2_ENST00000440245.1_Missense_Mutation_p.A86T|PER2_ENST00000355768.2_Missense_Mutation_p.A86T NM_022817.2 NP_073728.1 O15055 PER2_HUMAN period circadian clock 2 p.A86T(1) 37 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244) TCAGATTTTGCCATCATCAGG 0.383000 1 Substitution - Missense(1) SO:0001583 missense ENST00000254657.3 0 1 hg19 CCDS2528.1 . . . . . . . . . . C 0.421 -0.908299 0.02434 . . ENSG00000132326 ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768;ENST00000431832 T;T;T;T;T 0.53423 2.72;0.68;1.71;0.68;0.62 4.96 2.12 0.27331 . 0.345872 0.34110 N 0.004259 T 0.34308 0.0893 L 0.34521 1.04 0.20074 N 0.999938 B;B;B;B 0.10296 0.003;0.0;0.001;0.0 B;B;B;B 0.12837 0.008;0.001;0.005;0.001 T 0.18053 -1.0349 10 0.31617 T 0.26 -1.2378 11.0032 0.47618 0.0:0.7639:0.0:0.2361 . 86;86;86;86 F5GYD5;B4DH14;O15055-2;O15055 .;.;.;PER2_HUMAN T 86 ENSP00000254657:A86T;ENSP00000254658:A86T;ENSP00000397516:A86T;ENSP00000348013:A86T;ENSP00000405891:A86T ENSP00000254657:A86T A - 1 0 PER2 238850548 0.693000 0.27728 0.002000 0.10522 0.041000 0.13682 0.717000 0.25851 -0.004000 0.14419 -0.797000 0.03246 GCA TCGA-HZ-A9TJ-01A-11D-A40W-08 PER2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257167.1 0 0 0 9 1570 1 293 0 3.797202e-02 0 47 1 293 2 0 0 0 0 0 2 0 4.091860e-02 9 1558 1 291 19 -1.723641 0 1 0 0 1 2 3 5 2.294524 1 0.520000 3.450000 0.694151 0.040000 0 1.000000 0.040000 0.223318 0.040000 0 0.020000 1.000000 FARP2 9855 broad.mit.edu 37 2 242312551 242312551 + Missense_Mutation SNP T T A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:242312551T>A ENST00000264042.3 + 2 199 c.29T>A c.(28-30)gTc>gAc p.V10D FARP2_ENST00000373287.4_Missense_Mutation_p.V10D|FARP2_ENST00000479427.1_3'UTR|FARP2_ENST00000545004.1_Missense_Mutation_p.V10D NM_014808.2 NP_055623.1 O94887 FARP2_HUMAN FERM, RhoGEF and pleckstrin domain protein 2 43 all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238) ACATACAGAGTCCTGCAGACT 0.463000 0 SO:0001583 missense ENST00000264042.3 1 1 hg19 CCDS33424.1 . . . . . . . . . . T 12.23 1.876107 0.33162 . . ENSG00000006607 ENST00000264042;ENST00000545004;ENST00000373287;ENST00000418082;ENST00000445489 T;D;D;T;T 0.83591 -1.11;-1.73;-1.74;-0.31;-1.13 5.65 -2.92 0.05615 . 0.515409 0.19294 N 0.117813 T 0.80737 0.4680 L 0.57536 1.79 0.27964 N 0.936655 P;P;P 0.46512 0.879;0.773;0.664 P;P;B 0.48270 0.572;0.572;0.235 T 0.76250 -0.3028 10 0.49607 T 0.09 . 11.2139 0.48815 0.0:0.4967:0.0:0.5033 . 10;10;10 O94887-2;F5GZ84;O94887 .;.;FARP2_HUMAN D 10 ENSP00000264042:V10D;ENSP00000443876:V10D;ENSP00000362384:V10D;ENSP00000393376:V10D;ENSP00000388167:V10D ENSP00000264042:V10D V + 2 0 FARP2 241961224 0.907000 0.30839 0.057000 0.19452 0.532000 0.34746 1.218000 0.32467 -0.815000 0.04346 0.460000 0.39030 GTC TCGA-HZ-A9TJ-01A-11D-A40W-08 FARP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323153.1 1 0 1 99 178 0 32 1 9.929730e-01 6 11 0 32 2 0 0 0 0 0 2 1 1 98 173 0 32 2 -20.000000 1 1 0 0 1 2 3 5 2.294524 1 0.520000 3.450000 0.694151 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FARP2 9855 broad.mit.edu 37 2 242373703 242373703 + Missense_Mutation SNP T T A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:242373703T>A ENST00000264042.3 + 10 1168 c.998T>A c.(997-999)gTc>gAc p.V333D FARP2_ENST00000373287.4_Missense_Mutation_p.V333D|FARP2_ENST00000545004.1_Missense_Mutation_p.V333D NM_014808.2 NP_055623.1 O94887 FARP2_HUMAN FERM, RhoGEF and pleckstrin domain protein 2 43 all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238) GCAAAAGCCGTCTTCTTCAGC 0.468000 0 SO:0001583 missense ENST00000264042.3 1 1 hg19 CCDS33424.1 . . . . . . . . . . T 22.9 4.347971 0.82132 . . ENSG00000006607 ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432 D;D;D;D 0.85629 -2.01;-2.01;-2.01;-2.01 5.2 5.2 0.72013 FERM adjacent (FA) (1); 0.066906 0.64402 D 0.000010 D 0.91828 0.7414 M 0.80982 2.52 0.80722 D 1 D;D;D 0.89917 1.0;0.999;0.999 D;D;D 0.72625 0.978;0.968;0.978 D 0.91344 0.5099 10 0.35671 T 0.21 . 15.0632 0.71970 0.0:0.0:0.0:1.0 . 333;333;333 O94887-2;F5GZ84;O94887 .;.;FARP2_HUMAN D 333;333;333;20 ENSP00000264042:V333D;ENSP00000443876:V333D;ENSP00000362384:V333D;ENSP00000412772:V20D ENSP00000264042:V333D V + 2 0 FARP2 242022376 1.000000 0.71417 0.158000 0.22627 0.695000 0.40330 6.019000 0.70818 1.956000 0.56807 0.455000 0.32223 GTC TCGA-HZ-A9TJ-01A-11D-A40W-08 FARP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323153.1 1 0 1 52 304 0 53 1 9.804798e-01 8 31 0 53 2 0 0 0 0 0 2 1 1 50 300 0 52 2 -19.999950 1 0 0 0 1 2 3 5 2.294524 1 0.520000 3.450000 0.694151 0.910000 6.800000e-01 1.000000 1.000000 0.903476 0.910000 1 0.780000 1.000000 OTOF 9381 broad.mit.edu 37 2 26689975 26689975 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:26689975G>A ENST00000272371.2 - 35 4480 c.4354C>T c.(4354-4356)Cgc>Tgc p.R1452C OTOF_ENST00000402415.3_Missense_Mutation_p.R762C|OTOF_ENST00000339598.3_Missense_Mutation_p.R685C|OTOF_ENST00000338581.6_Missense_Mutation_p.R685C|OTOF_ENST00000403946.3_Missense_Mutation_p.R1452C NM_194248.2 NP_919224.1 Q9HC10 OTOF_HUMAN otoferlin 106 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) ACCTTGAAGCGTCCCACAATG 0.642000 GBM(102;732 1451 20652 24062 31372) 0 SO:0001583 missense ENST00000272371.2 1 1 hg19 CCDS1725.1 . . . . . . . . . . G 14.65 2.597730 0.46318 . . ENSG00000115155 ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946 T;T;T;T;T 0.80480 -1.13;-1.13;-1.12;-1.38;-1.38 4.69 -0.734 0.11140 . 0.045494 0.85682 D 0.000000 T 0.68504 0.3008 L 0.41236 1.265 0.80722 D 1 B;B;B;B 0.33171 0.397;0.026;0.4;0.026 B;B;B;B 0.20955 0.013;0.032;0.03;0.032 T 0.66172 -0.5990 10 0.59425 D 0.04 -20.9378 14.53 0.67917 0.0:0.0:0.3367:0.6633 . 1452;685;762;685 Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4 OTOF_HUMAN;.;.;. C 685;685;762;1452;1452 ENSP00000345137:R685C;ENSP00000344521:R685C;ENSP00000383906:R762C;ENSP00000272371:R1452C;ENSP00000385255:R1452C ENSP00000272371:R1452C R - 1 0 OTOF 26543479 0.984000 0.35163 0.971000 0.41717 0.920000 0.55202 0.944000 0.29043 0.077000 0.16863 0.561000 0.74099 CGC TCGA-HZ-A9TJ-01A-11D-A40W-08 OTOF-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000214047.3 1 0 1 36 178 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 1 34 173 0 49 2 -20.000000 1 1 121412 1 34 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.990000 7.700000e-01 1.000000 1.000000 0.971698 0.990000 1 0.920000 1.000000 PLEKHH2 130271 broad.mit.edu 37 2 43937444 43937444 + Missense_Mutation SNP G G T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:43937444G>T ENST00000282406.4 + 13 2299 c.2189G>T c.(2188-2190)gGt>gTt p.G730V NM_172069.3 NP_742066.2 Q8IVE3 PKHH2_HUMAN pleckstrin homology domain containing, family H (with MyTH4 domain) member 2 56 all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17) CTTAAAGGTGGTGAATTACTT 0.363000 0 SO:0001583 missense ENST00000282406.4 1 1 hg19 CCDS1812.1 . . . . . . . . . . G 19.46 3.832003 0.71258 . . ENSG00000152527 ENST00000282406 T 0.76578 -1.03 5.02 4.11 0.48088 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.056676 0.64402 D 0.000001 D 0.88429 0.6434 M 0.82433 2.59 0.80722 D 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.97110 0.99;1.0;0.999 D 0.90058 0.4154 10 0.87932 D 0 -10.151 15.0911 0.72195 0.0:0.1426:0.8574:0.0 . 730;167;730 Q8IVE3;Q8IVE3-2;Q8IVE3-3 PKHH2_HUMAN;.;. V 730 ENSP00000282406:G730V ENSP00000282406:G730V G + 2 0 PLEKHH2 43790948 1.000000 0.71417 0.997000 0.53966 0.979000 0.70002 6.354000 0.73036 1.043000 0.40175 0.563000 0.77884 GGT TCGA-HZ-A9TJ-01A-11D-A40W-08 PLEKHH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250537.1 1 0 1 108 379 0 67 1 8.747230e-01 8 7 0 67 2 0 0 0 0 0 2 1 1 107 374 0 66 2 -20.000000 1 1 0 0 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.990000 9.900000e-01 1.000000 1.000000 0.999995 0.990000 1 0.990000 1.000000 ABCG8 64241 broad.mit.edu 37 2 44102445 44102445 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:44102445C>T ENST00000272286.2 + 11 1739 c.1649C>T c.(1648-1650)gCg>gTg p.A550V NM_022437.2 NP_071882.1 Q9H221 ABCG8_HUMAN ATP-binding cassette, sub-family G (WHITE), member 8 45 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) Ezetimibe(DB00973) CTGGCCGCCGCGGCCCTGCTC 0.617000 0 SO:0001583 missense ENST00000272286.2 1 1 hg19 CCDS1815.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 15.22 2.768002 0.49680 . . ENSG00000143921 ENST00000272286 T 0.74947 -0.89 4.73 3.85 0.44370 ABC-2 type transporter (1); 0.167185 0.52532 D 0.000066 T 0.81650 0.4867 M 0.65975 2.015 0.22968 N 0.998499 D;D 0.71674 0.998;0.998 P;P 0.61658 0.827;0.892 T 0.73528 -0.3954 10 0.42905 T 0.14 . 12.9331 0.58299 0.0:0.9209:0.0:0.0791 . 549;550 Q9H221-2;Q9H221 .;ABCG8_HUMAN V 550 ENSP00000272286:A550V ENSP00000272286:A550V A + 2 0 ABCG8 43955949 0.954000 0.32549 0.001000 0.08648 0.001000 0.01503 5.484000 0.66844 0.984000 0.38629 0.462000 0.41574 GCG TCGA-HZ-A9TJ-01A-11D-A40W-08 ABCG8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250671.1 1 0 1 113 238 0 56 0 1.049119e-01 0 2 0 56 2 0 0 0 1 0 0 2 1 1 111 235 0 52 2 -20.000000 1 1 121412 2 36 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PSME4 23198 broad.mit.edu 37 2 54133825 54133825 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:54133825C>T ENST00000404125.1 - 26 2908 c.2853G>A c.(2851-2853)cgG>cgA p.R951R PSME4_ENST00000421748.2_Silent_p.R95R NM_014614.2 NP_055429.2 Q14997 PSME4_HUMAN proteasome (prosome, macropain) activator subunit 4 60 Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181) CAGTTAGTGTCCGTAGCTAAG 0.308000 0 SO:0001819 synonymous_variant ENST00000404125.1 1 1 hg19 CCDS33197.2 TCGA-HZ-A9TJ-01A-11D-A40W-08 PSME4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324163.1 0 0 0 14 370 0 51 0 3.380292e-01 1 30 0 51 2 0 0 0 0 0 2 1 9.997571e-01 14 368 0 50 2 -3.408037 1 1 0 0 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.250000 1.300000e-01 1.000000 0.220000 0.424000 0.250000 0 0.180000 1.000000 SOX11 6664 broad.mit.edu 37 2 5833216 5833216 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:5833216G>A ENST00000322002.3 + 1 418 c.363G>A c.(361-363)cgG>cgA p.R121R AC108025.2_ENST00000420221.1_RNA|AC108025.2_ENST00000453678.1_RNA|AC107057.2_ENST00000458264.1_RNA NM_003108.3 NP_003099.1 P35716 SOX11_HUMAN SRY (sex determining region Y)-box 11 13 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) ACCGGCCCCGGAAAAAGCCCA 0.692000 0 SO:0001819 synonymous_variant ENST00000322002.3 0 1 hg19 CCDS1654.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 SOX11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206698.1 0 0 0 4 136 0 26 0 0 0 0 26 2 0 0 0 0 0 2 1 8.863296e-01 4 133 0 24 2 -6.722651 1 1 0 0 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.240000 6.000000e-02 1.000000 0.180000 0.406537 0.240000 0 0.130000 1.000000 ZNF638 27332 broad.mit.edu 37 2 71629120 71629120 + Missense_Mutation SNP A A G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:71629120A>G ENST00000409544.1 + 16 3362 c.2732A>G c.(2731-2733)aAt>aGt p.N911S ZNF638_ENST00000264447.4_Missense_Mutation_p.N911S|ZNF638_ENST00000355812.3_Missense_Mutation_p.N911S NM_001252612.1 NP_001239541.1 Q14966 ZN638_HUMAN zinc finger protein 638 63 CTTGTCTCTAATTTGCCTAAT 0.269000 0 SO:0001583 missense ENST00000409544.1 1 1 hg19 CCDS1917.1 . . . . . . . . . . A 15.94 2.981481 0.53827 . . ENSG00000075292 ENST00000394137;ENST00000355812;ENST00000264447;ENST00000409544 T;T;T 0.56275 0.47;1.49;1.49 5.69 5.69 0.88448 . 0.272209 0.41500 D 0.000865 T 0.50769 0.1635 M 0.65975 2.015 0.80722 D 1 B;B;P;B 0.35272 0.361;0.287;0.493;0.361 B;B;B;B 0.33454 0.079;0.085;0.164;0.079 T 0.51132 -0.8744 10 0.33940 T 0.23 -4.9239 13.8977 0.63783 1.0:0.0:0.0:0.0 . 911;911;911;911 A8K583;Q14966-4;Q14966-3;Q14966 .;.;.;ZN638_HUMAN S 490;911;911;911 ENSP00000348066:N911S;ENSP00000264447:N911S;ENSP00000386433:N911S ENSP00000264447:N911S N + 2 0 ZNF638 71482628 1.000000 0.71417 1.000000 0.80357 0.945000 0.59286 5.314000 0.65804 2.167000 0.68274 0.477000 0.44152 AAT TCGA-HZ-A9TJ-01A-11D-A40W-08 ZNF638-002 NOVEL alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000327431.1 1 0 0 13 223 0 39 0 1.368502e-01 1 10 0 39 2 0 0 0 0 0 2 1 9.995261e-01 13 219 0 38 2 -16.376160 1 1 0 0 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.390000 2.000000e-01 1.000000 0.350000 0.517522 0.390000 0 0.280000 1.000000 CD8B 926 broad.mit.edu 37 2 87085345 87085345 + Missense_Mutation SNP T T G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr2:87085345T>G ENST00000390655.6 - 2 296 c.238A>C c.(238-240)Atc>Ctc p.I80L CD8B_ENST00000349455.3_Missense_Mutation_p.I80L|CD8B_ENST00000393761.2_Missense_Mutation_p.I80L|CD8B_ENST00000431506.2_Intron|CD8B_ENST00000393759.2_Missense_Mutation_p.I80L|CD8B_ENST00000331469.2_Missense_Mutation_p.I80L NM_004931.4 NP_004922.1 P10966 CD8B_HUMAN CD8b molecule 13 TCACCGTGGATAGTCCCTTTT 0.552000 0 SO:0001583 missense ENST00000390655.6 1 1 hg19 CCDS1997.1 . . . . . . . . . . T 8.426 0.847470 0.17034 . . ENSG00000172116 ENST00000393761;ENST00000393759;ENST00000349455;ENST00000331469;ENST00000390655;ENST00000445248 T;T;T;T;T 0.65178 -0.14;-0.14;-0.14;-0.14;-0.14 4.35 -6.41 0.01938 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 3.220850 0.00873 N 0.002047 T 0.41096 0.1144 N 0.17474 0.49 0.09310 N 1 B;B;B;B;B;B 0.24132 0.016;0.001;0.004;0.002;0.001;0.098 B;B;B;B;B;B 0.15484 0.007;0.003;0.004;0.002;0.003;0.013 T 0.20042 -1.0287 10 0.28530 T 0.3 0.0063 7.5745 0.27928 0.1156:0.284:0.0:0.6004 . 80;80;80;80;80;80 Q496E2;Q53QL8;P10966;P10966-3;P10966-2;P10966-6 .;.;CD8B_HUMAN;.;.;. L 80 ENSP00000377358:I80L;ENSP00000377356:I80L;ENSP00000340592:I80L;ENSP00000331172:I80L;ENSP00000375070:I80L ENSP00000331172:I80L I - 1 0 CD8B 86938856 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.673000 0.01951 -1.420000 0.02009 -2.142000 0.00338 ATC TCGA-HZ-A9TJ-01A-11D-A40W-08 CD8B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330402.1 1 0 1 48 388 0 68 0 3.527135e-02 1 2 0 68 2 0 0 0 0 0 2 1 1 43 342 0 70 2 -20.000000 1 1 0 0 1 3 4 7 2.336558 1 0.520000 3.450000 0.702048 0.720000 5.200000e-01 1.000000 0.690000 0.766754 0.720000 0 0.610000 1.000000 ALCAM 214 broad.mit.edu 37 3 105290748 105290748 + Missense_Mutation SNP A A G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:105290748A>G ENST00000306107.5 + 15 2217 c.1717A>G c.(1717-1719)Aag>Gag p.K573E ALCAM_ENST00000389927.4_Missense_Mutation_p.K295E|ALCAM_ENST00000486979.2_Missense_Mutation_p.K522E|ALCAM_ENST00000472644.2_Missense_Mutation_p.K560E NM_001627.3 NP_001618.2 Q13740 CD166_HUMAN activated leukocyte cell adhesion molecule 28 AGAAAACAAAAAGTTAGAAGA 0.353000 0 SO:0001583 missense ENST00000306107.5 1 1 hg19 CCDS33810.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 18.78|18.78 3.696782|3.696782 0.68386|0.68386 .|. .|. ENSG00000170017|ENSG00000170017 ENST00000306107;ENST00000472644;ENST00000486979;ENST00000389927|ENST00000465413 T;T;T;T|T 0.58060|0.25579 0.42;0.58;0.36;1.15|1.79 5.42|5.42 5.42|5.42 0.78866|0.78866 .|. 0.000000|0.000000 0.85682|0.85682 D|D 0.000000|0.000000 T|T 0.31451|0.31451 0.0797|0.0797 L|L 0.36672|0.36672 1.1|1.1 0.53688|0.53688 D|D 0.999979|0.999979 D;D;D|. 0.63880|. 0.993;0.993;0.993|. D;D;D|. 0.70935|. 0.956;0.956;0.971|. T|T 0.02282|0.02282 -1.1183|-1.1183 10|8 0.44086|0.29301 T|T 0.13|0.29 -17.4549|-17.4549 15.7464|15.7464 0.77949|0.77949 1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0 .|. 295;560;573|. Q6ZS95;B4DTU0;Q13740|. .;.;CD166_HUMAN|. E|R 573;560;522;295|333 ENSP00000305988:K573E;ENSP00000419236:K560E;ENSP00000418213:K522E;ENSP00000374577:K295E|ENSP00000418937:K333R ENSP00000305988:K573E|ENSP00000418937:K333R K|K +|+ 1|2 0|0 ALCAM|ALCAM 106773438|106773438 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.996000|0.996000 0.88848|0.88848 6.000000|6.000000 0.70678|0.70678 2.176000|2.176000 0.68965|0.68965 0.455000|0.455000 0.32223|0.32223 AAG|AAA TCGA-HZ-A9TJ-01A-11D-A40W-08 ALCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353764.1 1 0 1 31 245 0 54 1 9.372080e-01 5 34 0 54 2 0 0 0 0 0 2 1 1 31 243 0 53 2 -13.006490 1 1 0 0 1 1 3 4 2.115187 1 0.520000 3.450000 0.670692 0.640000 4.400000e-01 1.000000 0.640000 0.678496 0.640000 0 0.530000 0.810000 SLC6A1 6529 broad.mit.edu 37 3 11067497 11067497 + Silent SNP C C T rs144034291 TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:11067497C>T ENST00000287766.4 + 9 1309 c.888C>T c.(886-888)taC>taT p.Y296Y SLC6A1_ENST00000536032.1_Silent_p.Y118Y NM_003042.3 NP_003033.3 P30531 SC6A1_HUMAN solute carrier family 6 (neurotransmitter transporter), member 1 26 Ovarian(110;0.0392) Clobazam(DB00349)|Tiagabine(DB00906) TCTTCTCATACGGGCTGGGCC 0.532000 0 SO:0001819 synonymous_variant ENST00000287766.4 1 1 hg19 CCDS2603.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 SLC6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102767.2 1 0 1 63 375 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1 63 366 0 73 2 -3.319375 1 1 121412 2 38 1 1 3 4 2.097128 1 0.520000 3.450000 0.668325 0.810000 6.300000e-01 1.000000 0.800000 0.829110 0.810000 0 0.710000 0.960000 BFSP2 8419 broad.mit.edu 37 3 133119141 133119141 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:133119141C>T ENST00000302334.2 + 1 303 c.214C>T c.(214-216)Cgt>Tgt p.R72C NM_003571.2 NP_003562.1 Q13515 BFSP2_HUMAN beaded filament structural protein 2, phakinin 13 CTTGGGTGCCCGTGTGACCCG 0.667000 0 SO:0001583 missense ENST00000302334.2 1 1 hg19 CCDS33859.1 . . . . . . . . . . C 34 5.344701 0.95807 . . ENSG00000170819 ENST00000302334 D 0.84223 -1.82 5.95 5.95 0.96441 . 0.205916 0.34507 N 0.003911 D 0.90752 0.7097 M 0.66939 2.045 0.80722 D 1 D 0.76494 0.999 P 0.60173 0.87 D 0.88493 0.3077 10 0.35671 T 0.21 -9.7541 20.3789 0.98926 0.0:1.0:0.0:0.0 . 72 Q13515 BFSP2_HUMAN C 72 ENSP00000304987:R72C ENSP00000304987:R72C R + 1 0 BFSP2 134601831 1.000000 0.71417 0.933000 0.37362 0.992000 0.81027 6.977000 0.76141 2.826000 0.97356 0.563000 0.77884 CGT TCGA-HZ-A9TJ-01A-11D-A40W-08 BFSP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357031.1 1 0 1 47 267 0 40 0 0 0 0 40 2 0 0 0 0 0 2 1 1 46 261 0 38 2 -2.546063 1 1 0 0 1 1 3 4 2.115187 1 0.520000 3.450000 0.670692 0.850000 6.300000e-01 1.000000 1.000000 0.859407 0.850000 1 0.730000 1.000000 SLC9A9 285195 broad.mit.edu 37 3 143100949 143100949 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:143100949C>T ENST00000316549.6 - 13 1685 c.1477G>A c.(1477-1479)Gtg>Atg p.V493M SLC9A9-AS2_ENST00000490153.1_RNA NM_173653.3 NP_775924.1 Q8IVB4 SL9A9_HUMAN solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9 57 TCCAGGTCCACGCCAACTCTG 0.438000 0 SO:0001583 missense ENST00000316549.6 1 1 hg19 CCDS33872.1 . . . . . . . . . . C 16.10 3.026124 0.54683 . . ENSG00000181804 ENST00000316549 T 0.30714 1.52 5.11 4.24 0.50183 . 0.350509 0.24330 N 0.039471 T 0.33177 0.0854 M 0.80332 2.49 0.46542 D 0.999099 P 0.38420 0.63 B 0.33750 0.169 T 0.29336 -1.0015 10 0.66056 D 0.02 . 9.1529 0.36973 0.0:0.9029:0.0:0.0971 . 493 Q8IVB4 SL9A9_HUMAN M 493 ENSP00000320246:V493M ENSP00000320246:V493M V - 1 0 SLC9A9 144583639 0.990000 0.36364 0.987000 0.45799 0.986000 0.74619 1.403000 0.34612 1.376000 0.46267 0.655000 0.94253 GTG TCGA-HZ-A9TJ-01A-11D-A40W-08 SLC9A9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354994.1 0 0 0 105 530 0 108 0 2.790805e-02 0 2 0 108 2 0 0 0 0 0 2 1 1 103 523 0 106 2 -20.000000 1 1 121412 10 45 1 1 3 4 2.115187 1 0.520000 3.450000 0.670692 0.930000 7.700000e-01 1.000000 1.000000 0.929360 0.930000 1 0.840000 1.000000 MCF2L2 23101 broad.mit.edu 37 3 183017842 183017842 + Missense_Mutation SNP T T A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:183017842T>A ENST00000328913.3 - 11 1553 c.1256A>T c.(1255-1257)aAa>aTa p.K419I MCF2L2_ENST00000473233.1_Missense_Mutation_p.K419I|MCF2L2_ENST00000414362.2_Missense_Mutation_p.K419I|MCF2L2_ENST00000447025.2_Missense_Mutation_p.K419I NM_015078.2 NP_055893 Q86YR7 MF2L2_HUMAN MCF.2 cell line derived transforming sequence-like 2 72 all_cancers(143;1.26e-12)|Ovarian(172;0.0355) all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21) AATGTCCCATTTTTTCTTGTT 0.458000 0 SO:0001583 missense ENST00000328913.3 1 1 hg19 CCDS3243.1 . . . . . . . . . . T 15.08 2.726819 0.48833 . . ENSG00000053524 ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362 T;T;T;T 0.32515 1.45;1.45;1.45;1.45 4.59 0.741 0.18336 . 0.117224 0.56097 D 0.000033 T 0.47116 0.1428 M 0.82630 2.6 0.32472 N 0.542635 P;D 0.63880 0.904;0.993 P;P 0.57371 0.465;0.819 T 0.58561 -0.7615 10 0.56958 D 0.05 . 8.7236 0.34456 0.0:0.2264:0.0:0.7736 . 419;419 Q86YR7-2;Q86YR7 .;MF2L2_HUMAN I 419;419;419;19;419 ENSP00000328118:K419I;ENSP00000420070:K419I;ENSP00000388190:K419I;ENSP00000414131:K419I ENSP00000328118:K419I K - 2 0 MCF2L2 184500536 0.996000 0.38824 0.541000 0.28102 0.201000 0.24016 2.616000 0.46376 -0.021000 0.14009 -0.290000 0.09829 AAA TCGA-HZ-A9TJ-01A-11D-A40W-08 MCF2L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350868.1 1 0 0 28 322 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1 28 321 0 74 2 -9.043142 1 1 0 0 1 1 2 3 1.723513 1 0.520000 3.450000 0.595687 0.380000 2.500000e-01 1.000000 0.360000 0.496381 0.380000 0 0.310000 1.000000 PFKFB4 5210 broad.mit.edu 37 3 48563059 48563059 + Missense_Mutation SNP T T A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:48563059T>A ENST00000232375.3 - 10 1143 c.1031A>T c.(1030-1032)tAt>tTt p.Y344F PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000416568.1_Missense_Mutation_p.Y337F|PFKFB4_ENST00000541519.1_Missense_Mutation_p.Y310F|PFKFB4_ENST00000536104.1_Missense_Mutation_p.Y333F|PFKFB4_ENST00000545984.1_3'UTR|PFKFB4_ENST00000383734.2_Intron NM_004567.2 NP_004558.1 Q16877 F264_HUMAN 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 14 CTCCAGTGGATAATTATCCTG 0.557000 0 SO:0001583 missense ENST00000232375.3 1 1 hg19 CCDS2771.1 . . . . . . . . . . T 12.05 1.822425 0.32237 . . ENSG00000114268 ENST00000232375;ENST00000536104;ENST00000416568;ENST00000541519 T;T;T;T 0.71341 -0.56;-0.56;-0.56;-0.56 4.1 4.1 0.47936 Histidine phosphatase superfamily, clade-1 (2); 0.252467 0.41097 D 0.000943 T 0.48960 0.1529 N 0.12663 0.25 0.80722 D 1 B;B;B 0.06786 0.001;0.0;0.001 B;B;B 0.17722 0.019;0.001;0.017 T 0.44787 -0.9305 10 0.37606 T 0.19 -5.5052 7.0254 0.24936 0.2025:0.0:0.0:0.7974 . 333;337;344 B7Z5C3;Q66S35;Q16877 .;.;F264_HUMAN F 344;333;337;310 ENSP00000232375:Y344F;ENSP00000438908:Y333F;ENSP00000388394:Y337F;ENSP00000437446:Y310F ENSP00000232375:Y344F Y - 2 0 PFKFB4 48538063 0.498000 0.26075 1.000000 0.80357 0.990000 0.78478 3.035000 0.49759 1.844000 0.53588 0.383000 0.25322 TAT TCGA-HZ-A9TJ-01A-11D-A40W-08 PFKFB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257503.2 1 0 0 14 142 0 29 0 2.663005e-02 0 3 0 29 2 0 0 0 0 0 2 1 9.997703e-01 14 139 0 29 2 -19.802350 1 1 0 0 1 1 3 4 2.097128 1 0.520000 3.450000 0.668325 0.530000 2.900000e-01 1.000000 0.490000 0.579526 0.530000 0 0.400000 0.750000 UBA7 7318 broad.mit.edu 37 3 49842859 49842859 + Missense_Mutation SNP A A T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:49842859A>T ENST00000333486.3 - 24 3079 c.2921T>A c.(2920-2922)cTg>cAg p.L974Q MIR5193_ENST00000584510.1_RNA NM_003335.2 NP_003326.2 P41226 UBA7_HUMAN ubiquitin-like modifier activating enzyme 7 33 CTGCTGAACCAGTTCTGTCAC 0.617000 0 SO:0001583 missense ENST00000333486.3 1 1 hg19 CCDS2805.1 . . . . . . . . . . A 16.92 3.255794 0.59321 . . ENSG00000182179 ENST00000333486 T 0.57752 0.38 5.36 5.36 0.76844 Ubiquitin-activating enzyme e1, C-terminal (1); 0.261023 0.25634 N 0.029323 T 0.72358 0.3450 M 0.80183 2.485 0.45150 D 0.998165 D 0.89917 1.0 D 0.83275 0.996 T 0.76377 -0.2981 10 0.87932 D 0 -1.9099 11.7536 0.51862 1.0:0.0:0.0:0.0 . 974 P41226 UBA7_HUMAN Q 974 ENSP00000333266:L974Q ENSP00000333266:L974Q L - 2 0 UBA7 49817863 0.105000 0.21958 0.392000 0.26245 0.872000 0.50106 2.681000 0.46926 2.026000 0.59711 0.460000 0.39030 CTG TCGA-HZ-A9TJ-01A-11D-A40W-08 UBA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350503.1 1 0 1 94 119 0 27 1 1 115 74 0 27 2 0 0 0 0 0 2 1 1 92 118 0 27 2 -20.000000 1 1 0 0 1 1 3 4 2.097128 1 0.520000 3.450000 0.668325 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CADM2 253559 broad.mit.edu 37 3 85961592 85961592 + Missense_Mutation SNP G G A rs150681488 TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr3:85961592G>A ENST00000407528.2 + 5 634 c.572G>A c.(571-573)cGa>cAa p.R191Q CADM2_ENST00000405615.2_Missense_Mutation_p.R193Q|CADM2_ENST00000383699.3_Missense_Mutation_p.R200Q NM_001167674.1 NP_001161146.1 Q8N3J6 CADM2_HUMAN cell adhesion molecule 2 38 Lung NSC(201;0.0148) CTGGACTTCCGAGTGGACCGG 0.433000 0 SO:0001583 missense ENST00000407528.2 1 1 hg19 CCDS54614.1 . . . . . . . . . . G 9.166 1.020020 0.19433 0.0 1.16E-4 ENSG00000175161 ENST00000383699;ENST00000407528;ENST00000405615 T;T;T 0.76578 -1.03;-1.03;-1.03 5.5 4.62 0.57501 CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.280225 0.38058 N 0.001838 T 0.43411 0.1246 N 0.01874 -0.695 0.32061 N 0.595716 B;B;B 0.11235 0.002;0.003;0.004 B;B;B 0.08055 0.002;0.002;0.003 T 0.49606 -0.8922 10 0.07030 T 0.85 . 3.7449 0.08544 0.2201:0.0:0.5739:0.206 . 193;200;191 Q8N3J6-3;G3XHN4;Q8N3J6 .;.;CADM2_HUMAN Q 200;191;193 ENSP00000373200:R200Q;ENSP00000384575:R191Q;ENSP00000384193:R193Q ENSP00000373200:R200Q R + 2 0 CADM2 86044282 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.202000 0.58446 2.583000 0.87209 0.591000 0.81541 CGA TCGA-HZ-A9TJ-01A-11D-A40W-08 CADM2-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352822.1 1 0 1 72 143 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1 70 139 0 45 2 -9.060599 1 1 121412 2 36 1 1 3 4 2.115187 1 0.520000 3.450000 0.670692 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 LRBA 987 broad.mit.edu 37 4 151738335 151738335 + Missense_Mutation SNP A A G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr4:151738335A>G ENST00000357115.3 - 31 5489 c.5246T>C c.(5245-5247)gTc>gCc p.V1749A LRBA_ENST00000510413.1_Missense_Mutation_p.V1749A|LRBA_ENST00000507224.1_Missense_Mutation_p.V1749A|LRBA_ENST00000535741.1_Missense_Mutation_p.V1749A NM_006726.4 NP_006717.2 P50851 LRBA_HUMAN LPS-responsive vesicle trafficking, beach and anchor containing 91 all_hematologic(180;0.151) AACCACACTGACAGCATTGGT 0.398000 0 SO:0001583 missense ENST00000357115.3 1 1 hg19 CCDS3773.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 23.2|23.2 4.384896|4.384896 0.82792|0.82792 .|. .|. ENSG00000198589|ENSG00000198589 ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224 .|T;T;T;T .|0.58060 .|0.77;0.92;0.77;0.36 5.95|5.95 5.95|5.95 0.96441|0.96441 .|. .|0.860939 .|0.10195 .|N .|0.704143 T|T 0.72875|0.72875 0.3515|0.3515 M|M 0.72479|0.72479 2.2|2.2 0.58432|0.58432 D|D 0.999994|0.999994 .|P;D .|0.67145 .|0.745;0.996 .|B;D .|0.76071 .|0.251;0.987 T|T 0.63184|0.63184 -0.6694|-0.6694 5|10 .|0.27082 .|T .|0.32 .|. 16.4323|16.4323 0.83853|0.83853 1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0 .|. .|1749;1749 .|P50851;P50851-2 .|LRBA_HUMAN;. P|A 402|1749 .|ENSP00000446299:V1749A;ENSP00000421552:V1749A;ENSP00000349629:V1749A;ENSP00000422180:V1749A .|ENSP00000349629:V1749A S|V -|- 1|2 0|0 LRBA|LRBA 151957785|151957785 0.999000|0.999000 0.42202|0.42202 0.971000|0.971000 0.41717|0.41717 0.980000|0.980000 0.70556|0.70556 4.766000|4.766000 0.62279|0.62279 2.281000|2.281000 0.76405|0.76405 0.528000|0.528000 0.53228|0.53228 TCA|GTC TCGA-HZ-A9TJ-01A-11D-A40W-08 LRBA-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000364939.1 1 0 1 84 260 0 66 1 9.757865e-01 6 15 0 66 2 0 0 0 0 0 2 1 1 84 255 1 64 18 -20.000000 1 1 0 0 1 1 2 3 1.835097 1 0.520000 3.450000 0.619048 0.990000 9.600000e-01 1.000000 1.000000 0.998214 0.990000 1 0.990000 1.000000 SLC12A2 6558 broad.mit.edu 37 5 127487026 127487026 + Missense_Mutation SNP C C G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr5:127487026C>G ENST00000262461.2 + 14 2390 c.2201C>G c.(2200-2202)gCt>gGt p.A734G SLC12A2_ENST00000343225.4_Missense_Mutation_p.A734G NM_001046.2 NP_001037.1 P55011 S12A2_HUMAN solute carrier family 12 (sodium/potassium/chloride transporter), member 2 48 all_cancers(142;0.0972)|Prostate(80;0.151) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325) AACTGGTGGGCTGCATTGCTA 0.378000 0 SO:0001583 missense ENST00000262461.2 1 1 hg19 CCDS4144.1 . . . . . . . . . . C 21.6 4.168369 0.78339 . . ENSG00000064651 ENST00000262461;ENST00000343225 D;D 0.98968 -5.28;-5.28 4.7 4.7 0.59300 Amino acid permease domain (1); 0.124211 0.53938 D 0.000048 D 0.99017 0.9664 M 0.90252 3.1 0.80722 D 1 D;D 0.56746 0.971;0.977 P;P 0.54544 0.641;0.755 D 0.99734 1.1013 10 0.87932 D 0 . 18.2088 0.89864 0.0:1.0:0.0:0.0 . 734;734 P55011-3;P55011 .;S12A2_HUMAN G 734 ENSP00000262461:A734G;ENSP00000340878:A734G ENSP00000262461:A734G A + 2 0 SLC12A2 127514925 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.651000 0.83577 2.626000 0.88956 0.655000 0.94253 GCT TCGA-HZ-A9TJ-01A-11D-A40W-08 SLC12A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250972.1 1 0 1 55 320 0 79 1 9.610810e-01 3 30 0 79 2 0 0 0 0 0 2 1 1 54 319 0 79 2 -20.000000 1 1 0 0 1 1 2 3 1.848393 1 0.520000 3.450000 0.619048 0.700000 5.400000e-01 0.890000 0.720000 0.718624 0.700000 0 0.620000 0.800000 PCDHGB4 8641 broad.mit.edu 37 5 140769477 140769477 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr5:140769477C>T ENST00000519479.1 + 1 2026 c.2026C>T c.(2026-2028)Cgc>Tgc p.R676C PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_5'Flank NM_003736.2|NM_018925.2|NM_032098.1 NP_003727.1|NP_061748.1|NP_115269.1 Q9UN71 PCDGG_HUMAN protocadherin gamma subfamily B, 4 37 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TATCACTGACCGCCCCGACCC 0.622000 0 SO:0001583 missense ENST00000519479.1 1 0 hg19 CCDS54928.1 . . . . . . . . . . . 14.95 2.687676 0.48097 . . ENSG00000253953 ENST00000519479 T 0.51574 0.7 5.4 -1.69 0.08186 . . . . . T 0.59046 0.2165 M 0.79258 2.445 0.09310 N 1 D;D 0.69078 0.991;0.997 P;P 0.55615 0.78;0.489 T 0.56829 -0.7914 9 0.41790 T 0.15 . 12.3444 0.55111 0.2819:0.24:0.4781:0.0 . 676;676 Q9UN71-2;Q9UN71 .;PCDGG_HUMAN C 676 ENSP00000428288:R676C ENSP00000428288:R676C R + 1 0 PCDHGB4 140749661 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -0.066000 0.11598 -0.317000 0.08677 0.563000 0.77884 CGC TCGA-HZ-A9TJ-01A-11D-A40W-08 PCDHGB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374745.1 0 0 1 92 410 2 116 0 0 0 2 116 2 0 0 0 0 0 2 1 1 92 403 1 115 16 -3.230914 1 1 0 0 1 1 2 3 1.848393 1 0.520000 3.450000 0.619048 0.880000 7.200000e-01 1.000000 1.000000 0.888580 0.880000 1 0.800000 0.970000 RBM27 54439 broad.mit.edu 37 5 145651191 145651191 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr5:145651191G>A ENST00000265271.5 + 19 3108 c.2942G>A c.(2941-2943)gGa>gAa p.G981E RBM27_ENST00000506502.1_Missense_Mutation_p.G926E NM_018989.1 NP_061862.1 Q9P2N5 RBM27_HUMAN RNA binding motif protein 27 39 KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) CTAACAGTTGGAGGATTCATT 0.443000 0 SO:0001583 missense ENST00000265271.5 1 1 hg19 CCDS43378.1 . . . . . . . . . . G 13.40 2.225732 0.39300 . . ENSG00000091009 ENST00000265271 T 0.41065 1.01 4.93 3.02 0.34903 . 0.351548 0.27019 N 0.021331 T 0.26048 0.0635 N 0.22421 0.69 0.32293 N 0.566076 B 0.19583 0.037 B 0.13407 0.009 T 0.18935 -1.0321 10 0.30854 T 0.27 -10.6489 10.0237 0.42059 0.0:0.1252:0.635:0.2397 . 981 Q9P2N5 RBM27_HUMAN E 981 ENSP00000265271:G981E ENSP00000265271:G981E G + 2 0 RBM27 145631384 0.676000 0.27567 1.000000 0.80357 0.993000 0.82548 2.866000 0.48420 2.445000 0.82738 0.650000 0.86243 GGA TCGA-HZ-A9TJ-01A-11D-A40W-08 RBM27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000373420.1 1 0 1 31 244 0 63 1 7.703714e-01 3 21 0 63 2 0 0 0 0 0 2 1 1 31 240 0 62 2 -3.221916 1 1 0 0 1 1 2 3 1.848393 1 0.520000 3.450000 0.619048 0.540000 3.800000e-01 0.740000 0.540000 0.558597 0.540000 0 0.460000 0.650000 GRIA1 2890 broad.mit.edu 37 5 153026597 153026597 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr5:153026597G>A ENST00000285900.5 + 3 673 c.330G>A c.(328-330)acG>acA p.T110T GRIA1_ENST00000518142.1_Intron|GRIA1_ENST00000340592.5_Silent_p.T110T|GRIA1_ENST00000448073.4_Silent_p.T120T|GRIA1_ENST00000521843.2_Silent_p.T41T|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000518783.1_Silent_p.T120T NM_000827.3|NM_001258019.1 NP_000818.2|NP_001244948.1 P42261 GRIA1_HUMAN glutamate receptor, ionotropic, AMPA 1 p.T110T(2) 81 Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21) Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236) GCTTCATTACGCCGAGCTTTC 0.498000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000285900.5 1 1 hg19 CCDS4322.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 GRIA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252456.3 1 0 1 109 348 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1 109 346 0 73 2 -20.000000 1 1 0 0 1 1 2 3 1.848393 1 0.520000 3.450000 0.619048 0.990000 9.600000e-01 1.000000 1.000000 0.998293 0.990000 1 0.990000 1.000000 C5orf42 65250 broad.mit.edu 37 5 37187926 37187926 + Missense_Mutation SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr5:37187926C>A ENST00000508244.1 - 21 3923 c.3830G>T c.(3829-3831)tGt>tTt p.C1277F C5orf42_ENST00000274258.7_Missense_Mutation_p.C158F|C5orf42_ENST00000425232.2_Missense_Mutation_p.C1277F Q9H799 CE042_HUMAN chromosome 5 open reading frame 42 79 all_lung(31;0.000616) COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202) ACACAGAGCACAAAGTTCTCT 0.358000 0 SO:0001583 missense ENST00000508244.1 1 1 hg19 CCDS34146.2 . . . . . . . . . . C 25.5 4.644168 0.87859 . . ENSG00000197603 ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739 T;T;T;T 0.75367 -0.77;-0.77;-0.93;-0.85 5.49 5.49 0.81192 . 0.000000 0.85682 D 0.000000 T 0.81697 0.4877 L 0.32530 0.975 0.54753 D 0.999985 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 T 0.83156 -0.0101 10 0.87932 D 0 . 19.7365 0.96208 0.0:1.0:0.0:0.0 . 1277;158 E9PH94;Q9H799 .;CE042_HUMAN F 1277;1277;158;325;158 ENSP00000421690:C1277F;ENSP00000389014:C1277F;ENSP00000274258:C158F;ENSP00000424223:C325F ENSP00000274258:C158F C - 2 0 C5orf42 37223683 1.000000 0.71417 1.000000 0.80357 0.889000 0.51656 6.568000 0.73987 2.749000 0.94314 0.491000 0.48974 TGT TCGA-HZ-A9TJ-01A-11D-A40W-08 C5orf42-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360806.1 1 0 0 9 117 0 29 0 6.661822e-03 0 2 0 29 2 0 0 0 0 0 2 1 9.945717e-01 9 116 0 29 2 -13.689020 1 1 0 0 1 0 5 5 1.749031 1 0.520000 3.450000 0.600931 0.370000 1.700000e-01 1.000000 0.330000 0.477581 0.370000 0 0.250000 1.000000 HCN1 348980 broad.mit.edu 37 5 45262241 45262241 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr5:45262241C>T ENST00000303230.4 - 8 2512 c.2455G>A c.(2455-2457)Gtg>Atg p.V819M NM_021072.3 NP_066550.2 O60741 HCN1_HUMAN hyperpolarization activated cyclic nucleotide-gated potassium channel 1 156 ACCGCCGTCACGGGTTGAGGG 0.677000 0 SO:0001583 missense ENST00000303230.4 0 1 hg19 CCDS3952.1 . . . . . . . . . . C 3.532 -0.095427 0.07010 . . ENSG00000164588 ENST00000303230 D 0.97430 -4.38 5.02 3.2 0.36748 . 0.562530 0.16681 N 0.203943 D 0.91851 0.7421 N 0.19112 0.55 0.09310 N 1 B 0.13145 0.007 B 0.06405 0.002 D 0.85041 0.0923 10 0.62326 D 0.03 . 6.1826 0.20480 0.0:0.6436:0.1339:0.2225 . 819 O60741 HCN1_HUMAN M 819 ENSP00000307342:V819M ENSP00000307342:V819M V - 1 0 HCN1 45297998 0.033000 0.19621 0.118000 0.21660 0.722000 0.41435 1.321000 0.33678 0.596000 0.29794 0.655000 0.94253 GTG TCGA-HZ-A9TJ-01A-11D-A40W-08 HCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253847.1 0 0 0 10 111 1 18 0 0 0 1 18 2 0 0 0 0 0 2 0 5.435040e-02 8 106 1 17 18 -15.543950 1 1 0 0 1 1 2 3 1.854437 1 0.520000 3.450000 0.619048 0.410000 2.100000e-01 0.680000 0.390000 0.431201 0.410000 0 0.300000 0.550000 PLEKHG1 57480 broad.mit.edu 37 6 151054871 151054871 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr6:151054871G>A ENST00000358517.2 + 2 265 c.54G>A c.(52-54)tcG>tcA p.S18S PLEKHG1_ENST00000367328.1_Silent_p.S18S Q9ULL1 PKHG1_HUMAN pleckstrin homology domain containing, family G (with RhoGef domain) member 1 53 BRCA - Breast invasive adenocarcinoma(37;0.0923) CATCATCCTCGGCCTCTTCCC 0.542000 0 SO:0001819 synonymous_variant ENST00000358517.2 0 1 hg19 CCDS34552.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 PLEKHG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042691.1 0 0 0 6 410 0 69 0 5.152734e-02 0 21 0 69 2 0 0 0 1 0 0 2 1 9.630802e-01 6 402 0 69 2 -2.655910 1 1 0 0 1 2 2 4 2.056728 0 0.520000 3.450000 0.661017 0.090000 2.000000e-02 1.000000 0.070000 0.228851 0.090000 0 0.050000 0.190000 TIAM2 26230 broad.mit.edu 37 6 155450620 155450620 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr6:155450620G>A ENST00000461783.3 + 6 1536 c.263G>A c.(262-264)gGt>gAt p.G88D TIAM2_ENST00000360366.4_Missense_Mutation_p.G88D|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000318981.5_Missense_Mutation_p.G88D|TIAM2_ENST00000456144.1_Missense_Mutation_p.G88D|TIAM2_ENST00000529824.2_Missense_Mutation_p.G88D Q8IVF5 TIAM2_HUMAN T-cell lymphoma invasion and metastasis 2 65 Ovarian(120;0.196) GTCTCCAGAGGTGTTGCCTAC 0.552000 0 SO:0001583 missense ENST00000461783.3 1 1 hg19 CCDS34558.1 . . . . . . . . . . G 9.868 1.198064 0.22037 . . ENSG00000146426 ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000535583;ENST00000360366;ENST00000529824 T;T;T;T;T;T 0.06933 3.33;3.24;3.3;3.33;3.32;3.3 5.33 4.46 0.54185 . 0.114029 0.64402 N 0.000011 T 0.03915 0.0110 M 0.62723 1.935 0.80722 D 1 B 0.30021 0.265 B 0.24006 0.05 T 0.15263 -1.0443 10 0.51188 T 0.08 . 7.9497 0.30008 0.0808:0.0:0.7604:0.1588 . 88 Q8IVF5 TIAM2_HUMAN D 88;334;88;88;88;88;88;88 ENSP00000437188:G88D;ENSP00000434901:G88D;ENSP00000407746:G88D;ENSP00000327315:G88D;ENSP00000353528:G88D;ENSP00000433348:G88D ENSP00000327315:G88D G + 2 0 TIAM2 155492312 0.975000 0.34042 0.131000 0.22000 0.014000 0.08584 2.069000 0.41481 1.230000 0.43646 0.561000 0.74099 GGT TCGA-HZ-A9TJ-01A-11D-A40W-08 TIAM2-005 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000387980.2 1 0 0 14 172 0 30 0 1.905473e-02 1 2 0 30 2 0 0 0 0 0 2 1 9.997830e-01 14 171 0 30 2 -18.966090 1 1 0 0 1 2 2 4 2.056728 0 0.520000 3.450000 0.661017 0.440000 2.400000e-01 1.000000 0.400000 0.519246 0.440000 0 0.330000 0.720000 RNF39 80352 broad.mit.edu 37 6 30043491 30043491 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr6:30043491C>T ENST00000244360.6 - 1 173 c.76G>A c.(76-78)Gca>Aca p.A26T RNF39_ENST00000376751.3_Missense_Mutation_p.A26T NM_025236.3 NP_079512.2 Q9H2S5 RNF39_HUMAN ring finger protein 39 TTAACTTTTGCCGCTTTCCGC 0.602000 NSCLC(8;188 360 1520 20207 31481) 0 SO:0001583 missense ENST00000244360.6 0 1 hg19 CCDS4673.1 . . . . . . . . . . c 17.05 3.290422 0.59976 . . ENSG00000204618 ENST00000376751;ENST00000244360;ENST00000376746 T;T 0.70749 -0.03;-0.51 3.51 0.223 0.15292 . . . . . T 0.23492 0.0568 N 0.08118 0 0.09310 N 1 B;B 0.10296 0.002;0.003 B;B 0.09377 0.002;0.004 T 0.17137 -1.0379 9 0.66056 D 0.02 . 2.3362 0.04248 0.1257:0.4139:0.293:0.1674 . 26;26 Q9H2S5;Q9H2S5-2 RNF39_HUMAN;. T 26 ENSP00000365942:A26T;ENSP00000244360:A26T ENSP00000244360:A26T A - 1 0 RNF39 30151470 0.000000 0.05858 0.000000 0.03702 0.834000 0.47266 -0.148000 0.10219 0.251000 0.21505 0.436000 0.28706 GCA TCGA-HZ-A9TJ-01A-11D-A40W-08 RNF39-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000076625.3 0 0 0 6 373 1 79 0 1.241839e-02 0 9 1 79 2 0 0 0 0 0 2 0 1.452191e-02 6 368 1 76 17 -2.312564 0 1 0 0 1 2 2 4 2.044431 0 0.520000 3.450000 0.659768 0.100000 2.000000e-02 1.000000 0.080000 0.241452 0.100000 0 0.050000 0.240000 COL19A1 1310 broad.mit.edu 37 6 70831785 70831785 + Missense_Mutation SNP T T C TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr6:70831785T>C ENST00000322773.4 + 17 1394 c.1292T>C c.(1291-1293)aTa>aCa p.I431T COL19A1_ENST00000393344.1_Missense_Mutation_p.I53T NM_001858.4 NP_001849.2 Q14993 COJA1_HUMAN collagen, type XIX, alpha 1 109 CCTCCTGGAATACAAGGAATA 0.269000 0 SO:0001583 missense ENST00000322773.4 0 1 hg19 CCDS4970.1 . . . . . . . . . . T 9.437 1.087165 0.20390 . . ENSG00000082293 ENST00000322773;ENST00000393344;ENST00000455415 D;T;T 0.96136 -3.92;1.4;1.4 5.32 1.21 0.21127 . 1.367040 0.04335 N 0.353095 T 0.80602 0.4654 L 0.35542 1.07 0.09310 N 1 B 0.02656 0.0 B 0.06405 0.002 T 0.72475 -0.4282 10 0.10636 T 0.68 . 2.6339 0.04952 0.1426:0.0899:0.1479:0.6195 . 431 Q14993 COJA1_HUMAN T 431;53;5 ENSP00000316030:I431T;ENSP00000377013:I53T;ENSP00000416556:I5T ENSP00000316030:I431T I + 2 0 COL19A1 70888506 0.027000 0.19231 0.069000 0.20011 0.880000 0.50808 0.635000 0.24629 0.501000 0.28013 0.533000 0.62120 ATA TCGA-HZ-A9TJ-01A-11D-A40W-08 COL19A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041127.1 0 0 0 7 517 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 9.792159e-01 7 506 0 90 2 -3.323001 1 1 0 0 1 2 2 4 2.056728 0 0.520000 3.450000 0.661017 0.080000 1.000000e-02 1.000000 0.070000 0.221878 0.080000 0 0.050000 0.170000 DSP 1832 broad.mit.edu 37 6 7571743 7571743 + Missense_Mutation SNP C C G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr6:7571743C>G ENST00000379802.3 + 14 2170 c.1829C>G c.(1828-1830)tCt>tGt p.S610C DSP_ENST00000418664.2_Missense_Mutation_p.S610C NM_004415.2 NP_004406.2 P15924 DESP_HUMAN desmoplakin 101 Ovarian(93;0.0584) all_hematologic(90;0.236) AAAATACAGTCTCAGTTCACC 0.488000 0 SO:0001583 missense ENST00000379802.3 1 1 hg19 CCDS4501.1 . . . . . . . . . . C 15.97 2.988573 0.53934 . . ENSG00000096696 ENST00000379802;ENST00000418664;ENST00000397483 T;T 0.75050 -0.57;-0.9 5.64 5.64 0.86602 . 0.352625 0.24412 N 0.038749 T 0.51126 0.1656 N 0.14661 0.345 0.35388 D 0.790495 B;B 0.28055 0.199;0.199 B;B 0.26864 0.074;0.074 T 0.58707 -0.7589 10 0.72032 D 0.01 . 19.7154 0.96115 0.0:1.0:0.0:0.0 . 657;610 Q4LE79;P15924 .;DESP_HUMAN C 610;610;415 ENSP00000369129:S610C;ENSP00000396591:S610C ENSP00000369129:S610C S + 2 0 DSP 7516742 0.998000 0.40836 0.964000 0.40570 0.988000 0.76386 3.766000 0.55280 2.664000 0.90586 0.655000 0.94253 TCT TCGA-HZ-A9TJ-01A-11D-A40W-08 DSP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039786.2 1 0 0 42 682 0 124 0 9.252693e-01 1 72 0 124 2 0 0 0 0 0 2 1 1 42 673 0 123 2 -7.284908 1 1 0 0 1 2 2 4 2.044431 0 0.520000 3.450000 0.659768 0.320000 2.200000e-01 1.000000 0.320000 0.428115 0.320000 0 0.270000 0.470000 MUC17 140453 broad.mit.edu 37 7 100679220 100679220 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr7:100679220C>T ENST00000306151.4 + 3 4587 c.4523C>T c.(4522-4524)aCg>aTg p.T1508M NM_001040105.1 NP_001035194.1 Q685J3 MUC17_HUMAN mucin 17, cell surface associated 343 Lung NSC(181;0.136)|all_lung(186;0.182) GCAATCTCAACGCCTAGTGAA 0.473000 0 SO:0001583 missense ENST00000306151.4 1 1 hg19 CCDS34711.1 . . . . . . . . . . c 0.032 -1.330977 0.01298 2.27E-4 1.16E-4 ENSG00000169876 ENST00000306151 T 0.03330 3.97 0.922 -0.0705 0.13747 . . . . . T 0.04092 0.0114 N 0.19112 0.55 0.09310 N 1 D 0.64830 0.994 P 0.53185 0.72 T 0.45454 -0.9260 9 0.32370 T 0.25 . 4.9293 0.13909 0.0:0.6094:0.3906:0.0 . 1508 Q685J3 MUC17_HUMAN M 1508 ENSP00000302716:T1508M ENSP00000302716:T1508M T + 2 0 MUC17 100465940 0.000000 0.05858 0.001000 0.08648 0.003000 0.03518 0.062000 0.14389 0.011000 0.14865 -1.865000 0.00557 ACG TCGA-HZ-A9TJ-01A-11D-A40W-08 MUC17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347161.1 1 0 0 100 1257 0 196 0 5.565760e-03 0 2 0 196 2 0 0 0 0 0 2 1 1 99 1152 0 184 2 -18.445280 1 0 121374 23 48 1 3 5 8 2.700920 1 0.520000 3.450000 0.741658 0.540000 4.200000e-01 1.000000 0.530000 0.643524 0.540000 0 0.480000 1.000000 NUP205 23165 broad.mit.edu 37 7 135304378 135304378 + Missense_Mutation SNP A A G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr7:135304378A>G ENST00000285968.6 + 29 4197 c.4171A>G c.(4171-4173)Att>Gtt p.I1391V NM_015135.2 NP_055950 Q92621 NU205_HUMAN nucleoporin 205kDa 93 TTTTGCTTCTATTGGAGATTC 0.368000 0 SO:0001583 missense ENST00000285968.6 1 1 hg19 CCDS34759.1 . . . . . . . . . . A 6.227 0.410051 0.11812 . . ENSG00000155561 ENST00000285968 T 0.29142 1.58 5.67 2.02 0.26589 . 0.133675 0.64402 N 0.000002 T 0.12347 0.0300 N 0.08118 0 0.80722 D 1 B 0.06786 0.001 B 0.04013 0.001 T 0.14755 -1.0461 10 0.14656 T 0.56 -22.4023 6.4248 0.21764 0.6149:0.1191:0.266:0.0 . 1391 Q92621 NU205_HUMAN V 1391 ENSP00000285968:I1391V ENSP00000285968:I1391V I + 1 0 NUP205 134954918 1.000000 0.71417 0.984000 0.44739 0.990000 0.78478 4.161000 0.58170 0.107000 0.17824 0.397000 0.26171 ATT TCGA-HZ-A9TJ-01A-11D-A40W-08 NUP205-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340358.1 1 0 0 13 163 0 43 1 1.571301e-01 2 7 0 43 2 0 0 0 0 0 2 1 9.995314e-01 13 159 0 42 2 -18.283880 1 0 0 0 1 0 1 1 1.358100 1 0.520000 3.450000 0.464286 0.250000 1.400000e-01 0.410000 0.260000 0.269284 0.250000 0 0.190000 0.330000 PTPRN2 5799 broad.mit.edu 37 7 157370783 157370783 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr7:157370783G>A ENST00000389418.4 - 18 2555 c.2546C>T c.(2545-2547)gCg>gTg p.A849V PTPRN2_ENST00000389413.3_Missense_Mutation_p.A820V|PTPRN2_ENST00000409483.1_Missense_Mutation_p.A811V|PTPRN2_ENST00000404321.2_Missense_Mutation_p.A872V|PTPRN2_ENST00000389416.4_Missense_Mutation_p.A832V NM_002847.3 NP_002838.2 Q92932 PTPR2_HUMAN protein tyrosine phosphatase, receptor type, N polypeptide 2 86 all_neural(206;0.181) all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132) OV - Ovarian serous cystadenocarcinoma(82;0.00463) GCCGTTCTCCGCGAGGGGTGT 0.622000 0 SO:0001583 missense ENST00000389418.4 1 1 hg19 CCDS5947.1 . . . . . . . . . . G 2.966 -0.213558 0.06140 . . ENSG00000155093 ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321 D;D;D;D;D 0.82711 -1.64;-1.64;-1.64;-1.64;-1.64 5.33 5.33 0.75918 Protein-tyrosine phosphatase, receptor/non-receptor type (3); 0.607774 0.16155 N 0.227082 T 0.48114 0.1482 N 0.00134 -2.025 0.09310 N 1 B;B;B;B;B 0.17667 0.02;0.009;0.003;0.023;0.009 B;B;B;B;B 0.08055 0.002;0.003;0.002;0.002;0.003 T 0.26744 -1.0094 10 0.02654 T 1 . 14.2668 0.66123 0.0732:0.0:0.9268:0.0 . 872;811;820;832;849 Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932 .;.;.;.;PTPR2_HUMAN V 811;820;832;849;872 ENSP00000387114:A811V;ENSP00000374064:A820V;ENSP00000374067:A832V;ENSP00000374069:A849V;ENSP00000385464:A872V ENSP00000374064:A820V A - 2 0 PTPRN2 157063544 0.929000 0.31497 0.190000 0.23270 0.069000 0.16628 5.203000 0.65174 2.488000 0.83962 0.655000 0.94253 GCG TCGA-HZ-A9TJ-01A-11D-A40W-08 PTPRN2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000353214.1 1 0 0 10 145 0 51 0 1.557914e-01 0 10 0 51 2 0 0 0 0 0 2 1 9.964335e-01 10 138 0 50 2 -13.738760 1 1 0 0 1 0 2 2 1.385510 1 0.520000 3.450000 0.520000 0.270000 1.300000e-01 1.000000 0.240000 0.406292 0.270000 0 0.190000 1.000000 DNAH11 8701 broad.mit.edu 37 7 21599227 21599227 + Silent SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr7:21599227G>A ENST00000409508.3 + 4 730 c.699G>A c.(697-699)ccG>ccA p.P233P DNAH11_ENST00000328843.6_Silent_p.P233P NM_001277115.1 NP_001264044.1 Q96DT5 DYH11_HUMAN dynein, axonemal, heavy chain 11 230 GTAGGCCACCGTCAAACGAAA 0.308000 Kartagener syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000409508.3 1 1 hg19 TCGA-HZ-A9TJ-01A-11D-A40W-08 DNAH11-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000326582.6 0 0 1 14 129 0 29 0 0 1 0 0 29 2 0 0 0 0 0 2 1 9.997843e-01 14 127 0 29 2 -7.815694 1 1 120704 3 32 1 1 4 5 2.427488 1 0.520000 3.450000 0.711365 0.670000 3.700000e-01 1.000000 1.000000 0.698269 0.670000 0 0.500000 0.950000 CCL24 6369 broad.mit.edu 37 7 75441265 75441265 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr7:75441265C>T ENST00000416943.1 - 4 302 c.209G>A c.(208-210)gGc>gAc p.G70D CCL24_ENST00000222902.2_Missense_Mutation_p.G70D NM_002991.2 NP_002982.2 O00175 CCL24_HUMAN chemokine (C-C motif) ligand 24 3 GAACTGCTGGCCCTTCTTGGT 0.612000 0 SO:0001583 missense ENST00000416943.1 0 1 hg19 CCDS34670.1 . . . . . . . . . . C 9.453 1.091082 0.20471 . . ENSG00000106178 ENST00000222902;ENST00000416943 T;T 0.05925 3.37;3.37 4.15 3.26 0.37387 Chemokine interleukin-8-like domain (3); 0.680432 0.13196 N 0.406384 T 0.08670 0.0215 L 0.61036 1.89 0.27743 N 0.944416 B 0.29716 0.255 B 0.30716 0.119 T 0.15235 -1.0444 10 0.36615 T 0.2 . 8.3206 0.32126 0.0:0.8859:0.0:0.1141 . 70 O00175 CCL24_HUMAN D 70 ENSP00000222902:G70D;ENSP00000400533:G70D ENSP00000222902:G70D G - 2 0 CCL24 75279201 0.659000 0.27411 0.245000 0.24217 0.370000 0.29829 1.945000 0.40273 0.862000 0.35528 0.555000 0.69702 GGC TCGA-HZ-A9TJ-01A-11D-A40W-08 CCL24-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344886.1 0 0 0 6 255 0 57 0 4.924807e-02 0 13 0 57 2 0 0 0 0 0 2 1 9.637746e-01 6 251 0 56 2 -6.821953 1 1 0 0 1 2 2 4 2.209518 1 0.520000 3.450000 0.684211 0.140000 5.000000e-02 0.280000 0.130000 0.155358 0.140000 0 0.090000 0.210000 FZD1 8321 broad.mit.edu 37 7 90894600 90894600 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr7:90894600C>T ENST00000287934.2 + 1 818 c.405C>T c.(403-405)ccC>ccT p.P135P NM_003505.1 NP_003496.1 Q9UP38 FZD1_HUMAN frizzled class receptor 1 24 all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215) STAD - Stomach adenocarcinoma(171;0.0134) CCATCATGCCCAACCTGCTGG 0.617000 0 SO:0001819 synonymous_variant ENST00000287934.2 1 1 hg19 CCDS5620.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 FZD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059367.2 0 0 0 23 530 0 45 0 1.081264e-01 0 13 0 45 2 0 0 0 0 0 2 1 9.999992e-01 23 519 0 42 2 -2.741919 1 1 0 0 1 3 6 9 2.774697 1 0.520000 3.450000 0.748691 0.330000 1.900000e-01 1.000000 0.320000 0.482991 0.330000 0 0.250000 1.000000 FAM135B 51059 broad.mit.edu 37 8 139165088 139165088 + Nonsense_Mutation SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr8:139165088C>A ENST00000395297.1 - 13 1800 c.1630G>T c.(1630-1632)Gag>Tag p.E544* NM_015912.3 NP_056996.2 Q49AJ0 F135B_HUMAN family with sequence similarity 135, member B 238 all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0805) TGTCCATCCTCTGGACCTGGA 0.512000 HNSCC(54;0.14) 0 SO:0001587 stop_gained ENST00000395297.1 0 1 hg19 CCDS6375.2 . . . . . . . . . . C 40 8.288310 0.98745 . . ENSG00000147724 ENST00000395297 . . . 5.45 4.57 0.56435 . 0.787170 0.12180 N 0.492215 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.13108 T 0.6 -4.7828 13.4045 0.60903 0.0:0.9248:0.0:0.0752 . . . . X 544 . ENSP00000276737:E544X E - 1 0 FAM135B 139234270 0.116000 0.22171 0.386000 0.26170 0.934000 0.57294 1.547000 0.36190 1.446000 0.47643 0.655000 0.94253 GAG TCGA-HZ-A9TJ-01A-11D-A40W-08 FAM135B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313590.3 1 0 0 22 239 0 57 0 0 0 0 57 2 0 0 0 0 0 2 1 9.999990e-01 22 238 0 57 2 -3.221886 1 1 0 0 1 1 2 3 1.883033 1 0.520000 3.450000 0.619048 0.410000 2.600000e-01 0.590000 0.420000 0.422811 0.410000 0 0.330000 0.500000 DLGAP2 9228 broad.mit.edu 37 8 1645335 1645335 + Missense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr8:1645335C>T ENST00000421627.2 + 11 2713 c.2579C>T c.(2578-2580)cCg>cTg p.P860L NM_004745.3 NP_004736.2 Q9P1A6 DLGP2_HUMAN discs, large (Drosophila) homolog-associated protein 2 41 Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846) ATGCCGAGGCCGACGTCGCAG 0.667000 0 SO:0001583 missense ENST00000421627.2 1 1 hg19 CCDS47760.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 19.12|19.12 3.766620|3.766620 0.69878|0.69878 0.0|0.0 2.41E-4|2.41E-4 ENSG00000198010|ENSG00000198010 ENST00000356067;ENST00000421627|ENST00000520901 T|. 0.22945|. 1.93|. 4.91|4.91 4.91|4.91 0.64330|0.64330 .|. 0.000000|. 0.85682|. D|. 0.000000|. D|. 0.83695|. 0.5310|. M|M 0.88105|0.88105 2.93|2.93 0.80722|0.80722 D|D 1|1 D;D|. 0.89917|. 1.0;0.992|. D;D|. 0.97110|. 1.0;0.976|. D|. 0.86683|. 0.1918|. 10|. 0.87932|. D|. 0|. -12.8537|-12.8537 18.0887|18.0887 0.89466|0.89466 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 925;939|. Q9P1A6-2;Q9P1A6|. .;DLGP2_HUMAN|. L|X 891;860|863 ENSP00000400258:P860L|. ENSP00000348366:P891L|. P|R +|+ 2|1 0|2 DLGAP2|DLGAP2 1632742|1632742 1.000000|1.000000 0.71417|0.71417 0.060000|0.060000 0.19600|0.19600 0.254000|0.254000 0.26022|0.26022 7.404000|7.404000 0.79996|0.79996 2.270000|2.270000 0.75569|0.75569 0.561000|0.561000 0.74099|0.74099 CCG|CGA TCGA-HZ-A9TJ-01A-11D-A40W-08 DLGAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374478.1 1 0 1 13 88 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 9.995480e-01 13 84 0 25 2 -19.982970 1 1 120886 4 34 1 2 2 4 1.551692 0 0.520000 3.450000 0.552573 0.560000 3.100000e-01 1.000000 0.530000 0.605760 0.560000 0 0.420000 0.790000 RP1 6101 broad.mit.edu 37 8 55533656 55533656 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr8:55533656G>A ENST00000220676.1 + 2 278 c.130G>A c.(130-132)Gga>Aga p.G44R NM_006269.1 NP_006260.1 P56715 RP1_HUMAN retinitis pigmentosa 1 (autosomal dominant) 169 all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123) OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285) CTACAAGAGCGGAGACCCCCA 0.547000 Colon(91;1014 1389 7634 14542 40420) 0 SO:0001583 missense ENST00000220676.1 1 1 hg19 CCDS6160.1 . . . . . . . . . . G 32 5.162331 0.94727 . . ENSG00000104237 ENST00000220676 D 0.95272 -3.66 5.44 5.44 0.79542 Doublecortin domain (4); 0.000000 0.56097 D 0.000023 D 0.98182 0.9399 H 0.94462 3.54 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.99164 1.0862 10 0.87932 D 0 -18.28 19.2628 0.93974 0.0:0.0:1.0:0.0 . 44 P56715 RP1_HUMAN R 44 ENSP00000220676:G44R ENSP00000220676:G44R G + 1 0 RP1 55696209 1.000000 0.71417 1.000000 0.80357 0.896000 0.52359 9.790000 0.99075 2.545000 0.85829 0.650000 0.86243 GGA TCGA-HZ-A9TJ-01A-11D-A40W-08 RP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378532.2 1 0 0 13 294 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 9.994793e-01 13 287 0 74 2 -3.013260 1 1 0 0 1 1 2 3 1.801915 1 0.520000 3.450000 0.619048 0.200000 1.100000e-01 0.340000 0.210000 0.219123 0.200000 0 0.150000 0.270000 NECAB1 64168 broad.mit.edu 37 8 91929840 91929840 + Nonsense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr8:91929840C>T ENST00000417640.2 + 6 815 c.478C>T c.(478-480)Caa>Taa p.Q160* NM_022351.4 NP_071746.1 Q8N987 NECA1_HUMAN N-terminal EF-hand calcium binding protein 1 12 BRCA - Breast invasive adenocarcinoma(11;0.0499) TACTGAGGAGCAAACCCGTCA 0.383000 0 SO:0001587 stop_gained ENST00000417640.2 0 1 hg19 CCDS47889.1 . . . . . . . . . . C 39 7.736388 0.98462 . . ENSG00000123119 ENST00000417640 . . . 5.16 5.16 0.70880 . 0.110120 0.64402 D 0.000006 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 -5.9093 18.6331 0.91368 0.0:1.0:0.0:0.0 . . . . X 160 . ENSP00000387380:Q160X Q + 1 0 NECAB1 91999016 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 6.953000 0.75995 2.386000 0.81285 0.467000 0.42956 CAA TCGA-HZ-A9TJ-01A-11D-A40W-08 NECAB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376728.1 1 0 0 15 209 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 9.998848e-01 15 208 0 42 2 -6.173016 1 1 0 0 1 1 2 3 1.792031 1 0.520000 3.450000 0.614272 0.330000 1.900000e-01 1.000000 0.320000 0.368991 0.330000 0 0.250000 0.440000 COL15A1 1306 broad.mit.edu 37 9 101802811 101802811 + Silent SNP C C T rs146647282 TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr9:101802811C>T ENST00000375001.3 + 23 2907 c.2484C>T c.(2482-2484)gaC>gaT p.D828D NM_001855.3 NP_001846.3 P39059 COFA1_HUMAN collagen, type XV, alpha 1 107 Acute lymphoblastic leukemia(62;0.0562) AGGGGCCGGACGGGTTGCCTG 0.587000 0 SO:0001819 synonymous_variant ENST00000375001.3 1 1 hg19 CCDS35081.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 COL15A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053386.3 0 0 1 169 144 0 70 0 1 0 100 0 70 2 0 0 0 0 0 2 1 1 167 143 0 70 2 -3.075755 1 1 121412 57 51 1 0 3 3 1.817473 1 0.520000 3.450000 0.619048 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ASTN2 23245 broad.mit.edu 37 9 119976795 119976795 + Missense_Mutation SNP T T A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr9:119976795T>A ENST00000313400.4 - 3 957 c.857A>T c.(856-858)gAg>gTg p.E286V ASTN2_ENST00000373996.3_Missense_Mutation_p.E286V|ASTN2_ENST00000361209.2_Missense_Mutation_p.E286V|ASTN2_ENST00000361477.3_5'UTR O75129 ASTN2_HUMAN astrotactin 2 102 GATGGGAGTCTCCCGGATGGG 0.617000 0 SO:0001583 missense ENST00000313400.4 1 1 hg19 . . . . . . . . . . T 17.28 3.349878 0.61183 . . ENSG00000148219 ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209 T;T;T;T 0.22743 2.09;2.08;2.13;1.94 5.16 5.16 0.70880 . 0.000000 0.64402 D 0.000002 T 0.31544 0.0800 N 0.24115 0.695 0.58432 D 0.999995 D;D;D 0.89917 1.0;0.999;0.998 D;D;D 0.83275 0.996;0.991;0.96 T 0.05616 -1.0874 9 . . . -22.8697 14.6696 0.68934 0.0:0.0:0.0:1.0 . 286;286;286 O75129-2;O75129;O75129-3 .;ASTN2_HUMAN;. V 286;286;13;286 ENSP00000314038:E286V;ENSP00000363108:E286V;ENSP00000363098:E13V;ENSP00000354504:E286V . E - 2 0 ASTN2 119016616 1.000000 0.71417 1.000000 0.80357 0.824000 0.46624 7.662000 0.83803 1.935000 0.56089 0.533000 0.62120 GAG TCGA-HZ-A9TJ-01A-11D-A40W-08 ASTN2-201 KNOWN basic protein_coding protein_coding 0 0 0 17 212 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 9.999605e-01 16 205 0 38 2 -19.995220 1 1 0 0 1 0 3 3 1.826005 1 0.520000 3.450000 0.619048 0.360000 2.100000e-01 0.550000 0.360000 0.376610 0.360000 0 0.280000 0.460000 GPR21 2844 broad.mit.edu 37 9 125797611 125797611 + Nonsense_Mutation SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr9:125797611C>T ENST00000373642.1 + 1 806 c.766C>T c.(766-768)Cga>Tga p.R256* RABGAP1_ENST00000373647.4_Intron|RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373643.5_Intron NM_005294.1 NP_005285.1 Q99679 GPR21_HUMAN G protein-coupled receptor 21 15 GGTCCTGTTTCGAATCACTAG 0.507000 0 SO:0001587 stop_gained ENST00000373642.1 0 1 hg19 CCDS6849.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 22.0|22.0 4.225223|4.225223 0.79576|0.79576 0.0|0.0 1.16E-4|1.16E-4 ENSG00000188394|ENSG00000188394 ENST00000373642|ENST00000412269 .|. .|. .|. 5.93|5.93 5.03|5.03 0.67393|0.67393 .|. 0.000000|. 0.64402|. U|. 0.000006|. .|T .|0.66356 .|0.2781 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.61456 .|-0.7059 .|5 0.30854|0.19590 T|T 0.27|0.45 -4.8434|-4.8434 16.7619|16.7619 0.85514|0.85514 0.1297:0.8703:0.0:0.0|0.1297:0.8703:0.0:0.0 .|. .|. .|. .|. X|L 256|248 .|. ENSP00000362746:R256X|ENSP00000389239:S248L R|S +|+ 1|2 2|0 GPR21|GPR21 124837432|124837432 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.982000|0.982000 0.71751|0.71751 3.714000|3.714000 0.54889|0.54889 1.491000|1.491000 0.48482|0.48482 0.591000|0.591000 0.81541|0.81541 CGA|TCG TCGA-HZ-A9TJ-01A-11D-A40W-08 GPR21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053965.1 1 0 0 33 558 1 94 0 0 0 1 94 2 0 0 0 0 0 2 1 9.633839e-01 33 555 1 91 21 -5.803027 1 1 121412 1 27 1 0 3 3 1.826005 1 0.520000 3.450000 0.619048 0.260000 1.800000e-01 0.370000 0.270000 0.277564 0.260000 0 0.220000 0.320000 NTNG2 84628 broad.mit.edu 37 9 135102349 135102349 + Missense_Mutation SNP G G A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chr9:135102349G>A ENST00000393229.3 + 4 1747 c.971G>A c.(970-972)cGc>cAc p.R324H NTNG2_ENST00000372179.3_Missense_Mutation_p.R324H|NTNG2_ENST00000393228.4_Missense_Mutation_p.R324H|NTNG2_ENST00000360670.3_Missense_Mutation_p.R324H NM_032536.2 NP_115925.2 Q96CW9 NTNG2_HUMAN netrin G2 29 AAGAATTTCCGCACCCGGTCC 0.677000 0 SO:0001583 missense ENST00000393229.3 0 1 hg19 CCDS6946.1 . . . . . . . . . . G 15.70 2.910498 0.52439 . . ENSG00000196358 ENST00000393229;ENST00000393228;ENST00000360670;ENST00000372179 T;T;T;T 0.61392 0.11;0.11;0.11;0.11 4.75 4.75 0.60458 EGF-like, laminin (3); 0.249770 0.32852 N 0.005578 T 0.25975 0.0633 N 0.01473 -0.845 0.42692 D 0.99358 P 0.50066 0.931 B 0.36608 0.229 T 0.34329 -0.9833 10 0.10636 T 0.68 . 16.7144 0.85394 0.0:0.0:1.0:0.0 . 324 Q96CW9 NTNG2_HUMAN H 324 ENSP00000376921:R324H;ENSP00000376920:R324H;ENSP00000353888:R324H;ENSP00000361252:R324H ENSP00000353888:R324H R + 2 0 NTNG2 134092170 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 7.158000 0.77470 2.184000 0.69523 0.313000 0.20887 CGC TCGA-HZ-A9TJ-01A-11D-A40W-08 NTNG2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000054779.1 1 0 1 15 93 0 18 0 0 0 1 0 18 2 0 0 0 0 0 2 1 9.998537e-01 14 87 0 18 2 -19.999960 1 1 121348 7 37 1 0 3 3 1.826005 1 0.520000 3.450000 0.619048 0.680000 4.000000e-01 1.000000 1.000000 0.697501 0.680000 0 0.530000 0.860000 KIAA1210 57481 broad.mit.edu 37 X 118284525 118284525 + Silent SNP C C A TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chrX:118284525C>A ENST00000402510.2 - 1 17 c.18G>T c.(16-18)acG>acT p.T6T NM_020721.1 NP_065772.1 Q9ULL0 K1210_HUMAN KIAA1210 p.T6T(1) 64 AGCCTCGAGGCGTCCAGCCGG 0.652000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000402510.2 1 1 hg19 CCDS48156.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 KIAA1210-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371251.2 1 0 1 131 67 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 1 129 66 0 30 2 -20.000000 1 1 0 0 1 0 1 1 0.520000 3.450000 0.520000 0.980000 9.400000e-01 1.000000 0.990000 0.988033 0.980000 1 0.970000 1.000000 L1CAM 3897 broad.mit.edu 37 X 153138054 153138054 + Missense_Mutation SNP C C G TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chrX:153138054C>G ENST00000370060.1 - 4 379 c.190G>C c.(190-192)Gaa>Caa p.E64Q L1CAM_ENST00000361981.3_Missense_Mutation_p.E59Q|L1CAM_ENST00000361699.4_Missense_Mutation_p.E64Q|L1CAM_ENST00000538883.1_Missense_Mutation_p.E66Q|L1CAM_ENST00000370055.1_Missense_Mutation_p.E59Q|L1CAM_ENST00000370057.3_Missense_Mutation_p.E64Q|L1CAM_ENST00000543994.1_Missense_Mutation_p.E66Q NM_001278116.1 NP_001265045.1 P32004 L1CAM_HUMAN L1 cell adhesion molecule 81 all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CACTGCACTTCGGGCTTGCCA 0.602000 0 SO:0001583 missense ENST00000370060.1 1 1 hg19 CCDS14733.1 . . . . . . . . . . C 10.36 1.329577 0.24167 . . ENSG00000198910 ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699;ENST00000439496;ENST00000407935;ENST00000420165;ENST00000458029 T;T;T;T;T;T;T;T;T;T;T 0.12774 2.65;2.65;2.65;2.65;2.65;2.65;2.65;2.65;2.65;2.65;2.65 4.69 1.83 0.25207 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.182154 0.37095 N 0.002256 T 0.11196 0.0273 N 0.21240 0.645 0.09310 N 1 B;B;B 0.18741 0.03;0.008;0.01 B;B;B 0.30179 0.112;0.046;0.076 T 0.26849 -1.0091 10 0.35671 T 0.21 . 13.9763 0.64275 0.0:0.3682:0.6318:0.0 . 59;64;64 G3XAF4;P32004-2;P32004 .;.;L1CAM_HUMAN Q 64;66;64;66;59;59;64;64;59;59;64 ENSP00000359077:E64Q;ENSP00000438430:E66Q;ENSP00000359074:E64Q;ENSP00000439645:E66Q;ENSP00000354712:E59Q;ENSP00000359072:E59Q;ENSP00000355380:E64Q;ENSP00000402407:E64Q;ENSP00000384902:E59Q;ENSP00000392524:E59Q;ENSP00000396079:E64Q ENSP00000355380:E64Q E - 1 0 L1CAM 152791248 0.001000 0.12720 0.195000 0.23364 0.913000 0.54294 -0.399000 0.07250 0.066000 0.16515 0.529000 0.55759 GAA TCGA-HZ-A9TJ-01A-11D-A40W-08 L1CAM-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000061094.2 1 0 1 64 146 0 24 0 2.255235e-01 1 2 0 24 2 1 1 267 493 0 528 2 1 1 64 145 0 23 2 -6.848788 1 1 0 0 1 0 1 1 0.520000 3.450000 0.520000 0.580000 4.600000e-01 0.700000 0.580000 0.587045 0.580000 0 0.520000 0.650000 PCDH11X 27328 broad.mit.edu 37 X 91132649 91132649 + Silent SNP C C T TCGA-HZ-A9TJ-01A-11D-A40W-08 TCGA-HZ-A9TJ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec6e4492-5846-4ef8-bfb8-0db49299854f 24e4448a-09eb-432b-aa22-61c71daa11f6 g.chrX:91132649C>T ENST00000373094.1 + 2 2255 c.1410C>T c.(1408-1410)ttC>ttT p.F470F PCDH11X_ENST00000298274.8_Silent_p.F470F|PCDH11X_ENST00000361724.1_Silent_p.F470F|PCDH11X_ENST00000373088.1_Silent_p.F470F|PCDH11X_ENST00000395337.2_Silent_p.F470F|PCDH11X_ENST00000504220.2_Silent_p.F470F|PCDH11X_ENST00000361655.2_Silent_p.F470F|PCDH11X_ENST00000406881.1_Silent_p.F470F|PCDH11X_ENST00000373097.1_Silent_p.F470F NM_032968.3 NP_116750.1 Q9BZA7 PC11X_HUMAN protocadherin 11 X-linked 159 CCCAGTCTTTCGTAACTGTTT 0.433000 NSCLC(38;925 1092 2571 38200 45895) 0 SO:0001819 synonymous_variant ENST00000373094.1 1 1 hg19 CCDS14461.1 TCGA-HZ-A9TJ-01A-11D-A40W-08 PCDH11X-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057436.1 0 0 0 146 78 1 42 0 0 0 1 42 2 0 0 0 0 0 2 1 1 129 71 1 55 13 -20.000000 1 1 121410 3 34 1 0 1 1 0.520000 3.450000 0.520000 0.980000 9.400000e-01 1.000000 0.990000 0.988797 0.980000 1 0.970000 1.000000