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 UBC 7316 broad.mit.edu 37 12 125396390 125396393 + Frame_Shift_Del DEL CCTT CCTT - rs144126075 by1000genomes TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 CCTT - CCTT CCTT Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:125396390_125396393delCCTT ENST00000538617.1 - 4 1101_1104 c.785_788delAAGG c.(784-789)gaaggcfs p.EG262fs UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Frame_Shift_Del_p.EG642fs|UBC_ENST00000536769.1_Frame_Shift_Del_p.EG642fs|UBC_ENST00000546120.1_Frame_Shift_Del_p.EG566fs P0CG48 UBC_HUMAN ubiquitin C 36 all_neural(191;0.101)|Medulloblastoma(191;0.163) AGGAGGGATGCCTTCCTTATCTTG 0.510000 0 SO:0001589 frameshift_variant ENST00000538617.1 1 0 hg19 TCGA-S4-A8RM-01A-11D-A377-08 UBC-003 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000400179.1 1 0 0 188 1089 0 257 1 1 47 7932 0 257 2 0 0 0 0 1 1.000000 227 974 10 266 64 0 0 0 0 0 0 -20.000000 1 0 0 0 1 0 0 0 1.993499 0 0.640000 1.980000 0.637681 0.450000 3.900000e-01 0.520000 0.460000 0.458624 0.450000 0 4.200000e-01 0.490000 SMAD4 4089 broad.mit.edu 37 18 48604715 48604716 + Frame_Shift_Ins INS - - A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 - A - - Valid Somatic Phase_I WXS targeted Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr18:48604715_48604716insA ENST00000342988.3 + 12 2075_2076 c.1537_1538insA c.(1537-1539)tacfs p.Y513fs SMAD4_ENST00000588745.1_Frame_Shift_Ins_p.Y417fs|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Ins_p.Y513fs NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) GGGACCGGATTACCCAAGACAG 0.480000 38 Whole gene deletion(36)|Unknown(2) SO:0001589 frameshift_variant ENST00000342988.3 0 1 hg19 CCDS11950.1 TCGA-S4-A8RM-01A-11D-A377-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 0 93 254 0 62 0 1 1 83 0 62 2 1 1 267 660 0 508 2 1 1.000000 93 248 0 61 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.440698 1 0.640000 1.980000 0.473068 0.560000 4.700000e-01 0.670000 0.570000 0.573204 0.560000 0 5.100000e-01 0.620000 ZNF468 90333 broad.mit.edu 37 19 53344850 53344850 + Frame_Shift_Del DEL G G - TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G - G G Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr19:53344850delG ENST00000595646.1 - 4 817 c.697delC c.(697-699)catfs p.H233fs ZNF468_ENST00000396409.4_Frame_Shift_Del_p.H180fs|ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000390651.4_Frame_Shift_Del_p.H180fs|ZNF28_ENST00000594602.1_Intron Q5VIY5 ZN468_HUMAN zinc finger protein 468 23 ATTATCTGATGTTTTTTTAAG 0.353000 0 SO:0001589 frameshift_variant ENST00000595646.1 1 1 hg19 CCDS33094.1 TCGA-S4-A8RM-01A-11D-A377-08 ZNF468-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463098.1 1 0 0 98 379 0 155 1 9.900293e-01 3 27 0 155 2 0 0 0 0 1 1.000000 99 376 1 156 12 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.032905 0 0.640000 1.980000 0.641148 0.640000 5.300000e-01 0.770000 0.640000 0.647184 0.640000 0 5.800000e-01 0.710000 A4GNT 51146 broad.mit.edu 37 3 137849766 137849767 + Frame_Shift_Ins INS - - A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr3:137849766_137849767insA ENST00000236709.3 - 2 533_534 c.332_333insT c.(331-333)atafs p.I111fs NM_016161.2 NP_057245.1 Q9UNA3 A4GCT_HUMAN alpha-1,4-N-acetylglucosaminyltransferase 16 AAACGTTGTCTATTGCTGACAG 0.421000 0 SO:0001589 frameshift_variant ENST00000236709.3 0 1 hg19 CCDS3097.1 TCGA-S4-A8RM-01A-11D-A377-08 A4GNT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357557.1 1 0 0 124 460 0 80 0 9.788509e-01 0 25 0 80 2 0 0 0 0 1 1.000000 127 454 0 80 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 2.015211 0 0.640000 1.980000 0.640000 0.650000 5.500000e-01 0.770000 0.660000 0.665948 0.650000 0 6.000000e-01 0.720000 LMLN 89782 broad.mit.edu 37 3 197687308 197687309 + Frame_Shift_Del DEL TG TG - TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr3:197687308_197687309delTG ENST00000330198.4 + 1 238_239 c.216_217delTG c.(214-219)actgagfs p.E73fs LMLN_ENST00000420910.2_Frame_Shift_Del_p.E73fs|IQCG_ENST00000480302.1_5'Flank|LMLN_ENST00000482695.1_Intron|LMLN_ENST00000332636.5_Intron|IQCG_ENST00000265239.6_5'Flank NM_033029.3 NP_149018.2 Q96KR4 LMLN_HUMAN leishmanolysin-like (metallopeptidase M8 family) 25 all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976) Lung NSC(153;0.132) Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07) CCTCTGACACTGAGGTAGGGCG 0.639000 0 SO:0001589 frameshift_variant ENST00000330198.4 0 1 hg19 CCDS3332.1 TCGA-S4-A8RM-01A-11D-A377-08 LMLN-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000339701.1 1 0 0 28 231 0 28 0 9.986996e-02 0 5 0 28 2 0 0 0 0 1 1.000000 30 225 0 28 2 0 0 0 0 0 0 -3.221905 1 1 0 0 1 1 2 3 2.028014 0 0.640000 1.980000 0.641148 0.330000 2.300000e-01 0.480000 0.340000 0.347583 0.330000 0 2.800000e-01 0.410000 SEMA3F 6405 broad.mit.edu 37 3 50222213 50222214 + In_Frame_Ins INS - - GACGGGCGT TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr3:50222213_50222214insGACGGGCGT ENST00000002829.3 + 13 1906_1907 c.1422_1423insGACGGGCGT c.(1423-1425)gac>GACGGGCGTgac p.475_475D>DGRD SEMA3F_ENST00000434342.1_In_Frame_Ins_p.444_444D>DGRD|SEMA3F_ENST00000413852.1_In_Frame_Ins_p.376_376D>DGRD NM_004186.3 NP_004177.3 Q13275 SEM3F_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F 17 TGGATGCAGCCGACGGGCGCTA 0.673000 0 SO:0001652 inframe_insertion ENST00000002829.3 0 1 hg19 CCDS2811.1 TCGA-S4-A8RM-01A-11D-A377-08 SEMA3F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345929.1 1 0 0 12 191 0 22 0 4.258142e-01 0 23 0 22 2 0 0 0 0 1 0.999597 33 193 0 23 2 0 0 0 0 0 0 -15.382830 1 1 0 0 1 0 0 0 2.015211 0 0.640000 1.980000 0.640000 0.180000 1.000000e-01 0.300000 0.180000 0.197608 0.180000 0 1.300000e-01 0.250000 SFMBT2 57713 broad.mit.edu 37 10 7218087 7218087 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr10:7218087G>A ENST00000361972.4 - 17 1939 c.1849C>T c.(1849-1851)Cgg>Tgg p.R617W SFMBT2_ENST00000397167.1_Missense_Mutation_p.R617W NM_001018039.1 NP_001018049.1 Q5VUG0 SMBT2_HUMAN Scm-like with four mbt domains 2 p.R617G(1) 99 TCAGATGTCCGTACGATTTTG 0.468000 1 Substitution - Missense(1) SO:0001583 missense ENST00000361972.4 0 1 hg19 CCDS31138.1 . . . . . . . . . . G 18.55 3.648095 0.67358 . . ENSG00000198879 ENST00000361972;ENST00000397167 T;T 0.47528 0.84;0.84 5.96 5.04 0.67666 . 0.000000 0.85682 D 0.000000 T 0.68522 0.3010 M 0.70275 2.135 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.72868 -0.4162 10 0.72032 D 0.01 . 16.3303 0.83006 0.0:0.0:0.8669:0.1331 . 617 Q5VUG0 SMBT2_HUMAN W 617 ENSP00000355109:R617W;ENSP00000380353:R617W ENSP00000355109:R617W R - 1 2 SFMBT2 7258093 1.000000 0.71417 0.041000 0.18516 0.283000 0.27025 5.140000 0.64807 1.468000 0.48064 0.655000 0.94253 CGG TCGA-S4-A8RM-01A-11D-A377-08 SFMBT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046673.1 0 0 0 7 609 0 84 0 1.101637e-03 0 4 0 84 2 0 0 0 0 0 2 1 0.978666 6 593 0 82 2 0 0 0 0 84 2 -2.221656 0 1 121412 1 31 1 1 2 3 2.029876 0 0.640000 1.980000 0.641148 0.030000 0 0.080000 0.040000 0.040412 0.030000 0 1.000000e-02 0.060000 ARHGEF12 23365 broad.mit.edu 37 11 120348235 120348235 + Splice_Site SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr11:120348235G>T ENST00000397843.2 + 36 3698 c.3532G>T c.(3532-3534)Gac>Tac p.D1178Y ARHGEF12_ENST00000532993.1_Splice_Site_p.D1075Y|ARHGEF12_ENST00000356641.3_Splice_Site_p.D1159Y NM_015313.2 NP_056128.1 Q9NZN5 ARHGC_HUMAN Rho guanine nucleotide exchange factor (GEF) 12 61 Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112) GCAGAGTCCAGGTACACTCTT 0.413000 T MLL AML Dom yes 11 11q23.3 23365 RHO guanine nucleotide exchange factor (GEF) 12 (LARG) L 0 SO:0001630 splice_region_variant ENST00000397843.2 1 0 hg19 CCDS41727.1 . . . . . . . . . . G 20.8 4.045601 0.75846 . . ENSG00000196914 ENST00000397843;ENST00000356641;ENST00000532993 T;T;T 0.72505 -0.55;-0.66;-0.53 4.85 4.85 0.62838 . 0.141481 0.32357 N 0.006209 T 0.74794 0.3763 L 0.29908 0.895 0.46586 D 0.999111 D;D 0.71674 0.998;0.997 D;P 0.63192 0.912;0.819 T 0.77638 -0.2513 10 0.59425 D 0.04 -5.4223 16.4829 0.84162 0.0:0.0:1.0:0.0 . 1159;1178 Q9NZN5-2;Q9NZN5 .;ARHGC_HUMAN Y 1178;1159;1075 ENSP00000380942:D1178Y;ENSP00000349056:D1159Y;ENSP00000432984:D1075Y ENSP00000349056:D1159Y D + 1 0 ARHGEF12 119853445 1.000000 0.71417 1.000000 0.80357 0.684000 0.39900 5.638000 0.67861 2.392000 0.81423 0.585000 0.79938 GAC TCGA-S4-A8RM-01A-11D-A377-08 ARHGEF12-001 PUTATIVE basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388052.1 1 0 1 71 165 0 42 1 1 19 84 0 42 2 0 0 0 0 0 2 1 1.000000 70 161 0 42 2 0 0 0 0 42 2 -7.089722 1 1 0 0 1 1 2 3 2.027490 0 0.640000 1.980000 0.641148 0.930000 7.600000e-01 1.000000 1.000000 0.929513 0.930000 1 8.400000e-01 1.000000 NFRKB 4798 broad.mit.edu 37 11 129739654 129739654 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr11:129739654C>T ENST00000446488.3 - 23 3369 c.3266G>A c.(3265-3267)cGc>cAc p.R1089H NFRKB_ENST00000524746.1_Missense_Mutation_p.R1089H|NFRKB_ENST00000524794.1_Missense_Mutation_p.R1114H|NFRKB_ENST00000304521.5_Missense_Mutation_p.R1089H NM_001143835.1 NP_001137307.1 Q6P4R8 NFRKB_HUMAN nuclear factor related to kappaB binding protein 32 all_hematologic(175;0.0537) Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186) CTGCACGATGCGGATCGTGGC 0.597000 0 SO:0001583 missense ENST00000446488.3 0 1 hg19 CCDS44770.1 . . . . . . . . . . C 31 5.063126 0.93898 0.0 1.16E-4 ENSG00000170322 ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746 . . . 5.31 5.31 0.75309 . 0.000000 0.85682 D 0.000000 T 0.68540 0.3012 L 0.32530 0.975 0.58432 D 0.999999 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.996;0.998;0.997 T 0.69975 -0.4999 9 0.52906 T 0.07 -11.2341 18.9658 0.92695 0.0:1.0:0.0:0.0 . 1089;1088;1114 Q6P4R8;Q6P4R8-3;Q6P4R8-2 NFRKB_HUMAN;.;. H 1089;1089;1114;1089 . ENSP00000303800:R1089H R - 2 0 NFRKB 129244864 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.487000 0.81328 2.474000 0.83562 0.655000 0.94253 CGC TCGA-S4-A8RM-01A-11D-A377-08 NFRKB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000386063.2 0 0 0 5 522 0 94 0 5.854911e-02 0 33 0 94 2 0 0 0 0 0 2 1 0.935596 5 515 0 94 2 0 0 0 0 94 2 -2.111172 0 1 121412 2 36 1 1 2 3 2.027490 0 0.640000 1.980000 0.641148 0.020000 0 0.070000 0.030000 0.034854 0.020000 0 1.000000e-02 0.050000 KCNA4 3739 broad.mit.edu 37 11 30033579 30033579 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr11:30033579C>T ENST00000328224.6 - 2 1880 c.647G>A c.(646-648)cGc>cAc p.R216H KCNA4_ENST00000526518.1_5'Flank NM_002233.3 NP_002224.1 P22459 KCNA4_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 4 78 Dalfampridine(DB06637) ATACTCATTGCGCAAAGGGTC 0.478000 0 SO:0001583 missense ENST00000328224.6 1 1 hg19 CCDS41629.1 . . . . . . . . . . C 23.4 4.410513 0.83340 . . ENSG00000182255 ENST00000328224 T 0.77358 -1.09 4.94 4.94 0.65067 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); 0.000000 0.85682 D 0.000000 D 0.84297 0.5441 M 0.84156 2.68 0.80722 D 1 D 0.69078 0.997 P 0.49332 0.607 D 0.87784 0.2614 10 0.72032 D 0.01 . 18.1944 0.89817 0.0:1.0:0.0:0.0 . 216 P22459 KCNA4_HUMAN H 216 ENSP00000328511:R216H ENSP00000328511:R216H R - 2 0 KCNA4 29990155 1.000000 0.71417 0.981000 0.43875 0.887000 0.51463 7.787000 0.85759 2.297000 0.77311 0.655000 0.94253 CGC TCGA-S4-A8RM-01A-11D-A377-08 KCNA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388074.2 1 0 0 32 434 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 1.000000 32 429 0 72 2 0 0 0 0 72 2 -8.455999 1 1 0 0 1 1 2 3 2.027490 0 0.640000 1.980000 0.641148 0.210000 1.400000e-01 0.300000 0.220000 0.220793 0.210000 0 1.700000e-01 0.260000 DUSP16 80824 broad.mit.edu 37 12 12639992 12639992 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:12639992G>A ENST00000228862.2 - 5 1292 c.661C>T c.(661-663)Ccg>Tcg p.P221S DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_5'UTR|RP11-253I19.3_ENST00000544086.1_lincRNA NM_030640.2 NP_085143.1 Q9BY84 DUS16_HUMAN dual specificity phosphatase 16 26 Prostate(47;0.0687) TCCAACCACGGCAAAATTTTC 0.458000 Ovarian(158;443 1896 15437 36069 46477) 0 SO:0001583 missense ENST00000228862.2 0 1 hg19 CCDS8650.1 . . . . . . . . . . G 29.0 4.968201 0.92855 . . ENSG00000111266 ENST00000228862 D 0.85339 -1.97 5.27 5.27 0.74061 Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2); 0.128209 0.53938 D 0.000056 D 0.89525 0.6740 L 0.39326 1.205 0.80722 D 1 D;D 0.63880 0.993;0.966 D;D 0.72338 0.977;0.948 D 0.89322 0.3641 10 0.49607 T 0.09 . 19.2465 0.93904 0.0:0.0:1.0:0.0 . 221;221 Q9BY84;Q96N49 DUS16_HUMAN;. S 221 ENSP00000228862:P221S ENSP00000228862:P221S P - 1 0 DUSP16 12531259 1.000000 0.71417 0.734000 0.30879 0.975000 0.68041 9.516000 0.98017 2.621000 0.88768 0.561000 0.74099 CCG TCGA-S4-A8RM-01A-11D-A377-08 DUSP16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400311.1 0 0 0 5 524 0 106 0 1.723071e-01 0 65 0 106 2 0 0 0 0 0 2 1 0.936243 5 519 0 106 2 0 0 0 0 106 2 -1.930126 0 1 0 0 1 1 2 3 2.030759 0 0.640000 1.980000 0.641148 0.020000 0 0.070000 0.030000 0.034714 0.020000 0 1.000000e-02 0.050000 DDX47 51202 broad.mit.edu 37 12 12974195 12974195 + Missense_Mutation SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:12974195G>T ENST00000358007.3 + 3 257 c.235G>T c.(235-237)Gct>Tct p.A79S DDX47_ENST00000352940.4_Missense_Mutation_p.A79S|DDX47_ENST00000392155.2_3'UTR NM_016355.3 NP_057439.2 Q9H0S4 DDX47_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 16 Prostate(47;0.0526) AGGCGCCTTTGCTTTGCCCAT 0.488000 0 SO:0001583 missense ENST00000358007.3 0 1 hg19 CCDS8655.1 . . . . . . . . . . G 26.1 4.703195 0.88924 . . ENSG00000213782 ENST00000352940;ENST00000358007 T;T 0.44083 0.93;2.57 5.6 4.71 0.59529 DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.53077 0.1774 L 0.49571 1.57 0.80722 D 1 B;B;B;B 0.30634 0.134;0.098;0.08;0.288 P;B;B;P 0.49387 0.609;0.326;0.34;0.475 T 0.48980 -0.8986 10 0.25106 T 0.35 -9.5993 14.6773 0.68989 0.0699:0.0:0.93:0.0 . 79;79;79;79 B4DYP6;Q9H4E3;G5E955;Q9H0S4 .;.;.;DDX47_HUMAN S 79 ENSP00000319578:A79S;ENSP00000350698:A79S ENSP00000319578:A79S A + 1 0 DDX47 12865462 1.000000 0.71417 0.992000 0.48379 0.993000 0.82548 9.201000 0.95017 1.370000 0.46153 0.555000 0.69702 GCT TCGA-S4-A8RM-01A-11D-A377-08 DDX47-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400674.1 0 0 0 10 1049 0 150 0 3.313435e-01 1 114 0 150 2 0 0 0 0 0 2 1 0.996661 9 1036 0 148 2 0 0 0 0 150 2 -2.878864 1 1 0 0 1 1 2 3 2.030759 0 0.640000 1.980000 0.641148 0.020000 0 0.060000 0.040000 0.031808 0.020000 0 1.000000e-02 0.050000 LRMP 4033 broad.mit.edu 37 12 25232195 25232195 + Silent SNP C C T rs114104872 by1000genomes TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:25232195C>T ENST00000354454.3 + 6 871 c.42C>T c.(40-42)cgC>cgT p.R14R LRMP_ENST00000547044.1_Silent_p.R14R|LRMP_ENST00000548766.1_Silent_p.R14R NM_006152.3 NP_006143.2 Q12912 LRMP_HUMAN lymphoid-restricted membrane protein 19 Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11) GTGTTGAACGCGTGTGTCCTG 0.373000 0 SO:0001819 synonymous_variant ENST00000354454.3 1 1 hg19 CCDS8701.1 TCGA-S4-A8RM-01A-11D-A377-08 LRMP-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407870.1 1 0 1 220 564 0 152 1 9.999242e-01 15 23 0 152 2 0 0 0 0 0 2 1 1.000000 217 556 0 150 2 0 0 0 0 152 2 -20.000000 1 1 121412 40 49 1 1 2 3 2.030759 0 0.640000 1.980000 0.641148 0.870000 7.700000e-01 0.980000 0.880000 0.880645 0.870000 1 8.200000e-01 0.930000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b 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-S4-A8RM-01A-11D-A377-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 82 228 0 51 1 9.999627e-01 27 18 0 51 2 1 1 111 310 0 247 2 1 1.000000 82 225 0 51 2 1 1 2492 5524 0 51 2 -20.000000 1 1 0 0 1 1 2 3 2.030759 0 0.640000 1.980000 0.641148 0.820000 6.700000e-01 0.990000 0.830000 0.831894 0.820000 0 7.400000e-01 0.910000 STAT6 6778 broad.mit.edu 37 12 57492807 57492807 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:57492807G>A ENST00000300134.3 - 17 2271 c.1946C>T c.(1945-1947)aCc>aTc p.T649I STAT6_ENST00000556155.1_Missense_Mutation_p.T649I|STAT6_ENST00000538913.2_Missense_Mutation_p.T539I|STAT6_ENST00000537215.2_Missense_Mutation_p.T539I|STAT6_ENST00000454075.3_Missense_Mutation_p.T649I|STAT6_ENST00000543873.2_Missense_Mutation_p.T649I NM_001178078.1|NM_003153.4 NP_001171549.1|NP_003144.3 P42226 STAT6_HUMAN signal transducer and activator of transcription 6, interleukin-4 induced 28 CCTTTCCACGGTCATCTTGAT 0.532000 0 SO:0001583 missense ENST00000300134.3 0 1 hg19 CCDS8931.1 . . . . . . . . . . G 15.64 2.894701 0.52121 . . ENSG00000166888 ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000555318;ENST00000542516 D;D;D;D;D;D;T 0.92048 -2.72;-2.96;-2.72;-2.72;-2.96;-2.72;-1.17 5.77 4.87 0.63330 SH2 motif (1); 0.344421 0.30473 N 0.009541 D 0.86535 0.5956 N 0.19112 0.55 0.36500 D 0.868949 P;P 0.48694 0.914;0.844 B;B 0.43623 0.425;0.313 D 0.89133 0.3511 10 0.51188 T 0.08 -11.3662 12.7493 0.57300 0.0:0.1647:0.8353:0.0 . 649;649 A8K4S9;P42226 .;STAT6_HUMAN I 649;539;539;649;649;539;649;539;77;649 ENSP00000300134:T649I;ENSP00000445409:T539I;ENSP00000438451:T649I;ENSP00000451742:T649I;ENSP00000444530:T539I;ENSP00000401486:T649I;ENSP00000450428:T77I ENSP00000300134:T649I T - 2 0 STAT6 55779074 0.998000 0.40836 0.998000 0.56505 0.954000 0.61252 3.174000 0.50847 1.417000 0.47077 0.561000 0.74099 ACC TCGA-S4-A8RM-01A-11D-A377-08 STAT6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412248.3 0 0 0 5 620 0 105 0 9.377629e-01 0 624 0 105 2 0 0 0 0 0 2 1 0.935358 5 611 0 104 2 0 0 0 0 105 2 -2.897311 1 1 0 0 1 0 0 0 1.993499 0 0.640000 1.980000 0.637681 0.020000 0 0.060000 0.020000 0.028882 0.020000 0 0 0.040000 B4GALNT1 2583 broad.mit.edu 37 12 58021575 58021575 + Missense_Mutation SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:58021575G>T ENST00000341156.4 - 10 1794 c.1210C>A c.(1210-1212)Ccc>Acc p.P404T B4GALNT1_ENST00000418555.2_Missense_Mutation_p.P349T NM_001478.3 NP_001469.1 Q00973 B4GN1_HUMAN beta-1,4-N-acetyl-galactosaminyl transferase 1 20 Melanoma(17;0.122) BRCA - Breast invasive adenocarcinoma(9;0.109) GGGGCGCCGGGCTCCACGCTC 0.706000 0 SO:0001583 missense ENST00000341156.4 1 1 hg19 CCDS8950.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 10.01|10.01 1.234514|1.234514 0.22626|0.22626 .|. .|. ENSG00000135454|ENSG00000135454 ENST00000341156;ENST00000418555|ENST00000547741 T;T|. 0.18338|. 2.22;2.26|. 4.5|4.5 2.54|2.54 0.30619|0.30619 Glycosyl transferase, family 2 (1);|. 0.499457|. 0.21274|. N|. 0.077269|. T|T 0.49474|0.49474 0.1559|0.1559 L|L 0.33753|0.33753 1.03|1.03 0.80722|0.80722 D|D 1|1 B;B|. 0.29805|. 0.126;0.257|. B;B|. 0.28916|. 0.096;0.082|. T|T 0.36114|0.36114 -0.9761|-0.9761 10|5 0.12430|. T|. 0.62|. -7.0386|-7.0386 8.8722|8.8722 0.35323|0.35323 0.0874:0.1505:0.7621:0.0|0.0874:0.1505:0.7621:0.0 .|. 349;404|. B4DE26;Q00973|. .;B4GN1_HUMAN|. T|R 404;349|86 ENSP00000341562:P404T;ENSP00000401601:P349T|. ENSP00000341562:P404T|. P|S -|- 1|3 0|2 B4GALNT1|B4GALNT1 56307842|56307842 0.097000|0.097000 0.21791|0.21791 0.942000|0.942000 0.38095|0.38095 0.968000|0.968000 0.65278|0.65278 0.656000|0.656000 0.24948|0.24948 1.063000|1.063000 0.40649|0.40649 0.462000|0.462000 0.41574|0.41574 CCC|AGC TCGA-S4-A8RM-01A-11D-A377-08 B4GALNT1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407853.1 1 0 0 20 53 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.999998 20 51 0 11 2 0 0 0 0 12 2 -20.000000 1 1 0 0 1 0 0 0 1.993499 0 0.640000 1.980000 0.637681 0.840000 5.600000e-01 1.000000 1.000000 0.844342 0.840000 0 6.900000e-01 1.000000 TPI1 7167 broad.mit.edu 37 12 6979268 6979268 + Missense_Mutation SNP C C T rs139532537 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:6979268C>T ENST00000229270.4 + 6 1047 c.710C>T c.(709-711)gCg>gTg p.A237V TPI1_ENST00000396705.5_Missense_Mutation_p.A200V|TPI1_ENST00000535434.1_Missense_Mutation_p.A118V|TPI1_ENST00000488464.2_Missense_Mutation_p.A118V NM_001159287.1 NP_001152759.1 P60174 TPIS_HUMAN triosephosphate isomerase 1 19 GTCTCTGATGCGGTGGCTCAG 0.552000 OREG0021638 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000229270.4 0 1 hg19 CCDS53740.1 . . . . . . . . . . C 13.87 2.366735 0.41902 0.0 1.16E-4 ENSG00000111669 ENST00000229270;ENST00000396705;ENST00000535434 D;D;D 0.94330 -3.4;-3.4;-3.4 5.44 3.57 0.40892 Aldolase-type TIM barrel (1); 0.213213 0.38837 U 0.001559 D 0.90748 0.7096 M 0.67569 2.06 0.18873 N 0.999984 B 0.17667 0.023 B 0.12156 0.007 T 0.83227 -0.0065 10 0.56958 D 0.05 . 8.4396 0.32808 0.4046:0.4513:0.144:0.0 . 237 P60174 TPIS_HUMAN V 237;200;118 ENSP00000229270:A237V;ENSP00000379933:A200V;ENSP00000443599:A118V ENSP00000229270:A237V A + 2 0 TPI1 6849529 0.989000 0.36119 0.048000 0.18961 0.889000 0.51656 2.951000 0.49089 0.626000 0.30322 0.462000 0.41574 GCG TCGA-S4-A8RM-01A-11D-A377-08 TPI1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000258252.1 0 0 0 5 577 0 76 0 9.940087e-01 1 1199 0 76 2 0 0 0 0 0 2 1 0.934302 5 565 0 75 2 0 0 0 0 76 2 -1.931661 0 1 121412 4 39 1 1 2 3 2.031110 0 0.640000 1.980000 0.641148 0.020000 0 0.070000 0.020000 0.031381 0.020000 0 1.000000e-02 0.050000 GDF3 9573 broad.mit.edu 37 12 7843026 7843026 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:7843026G>A ENST00000329913.3 - 2 590 c.543C>T c.(541-543)ttC>ttT p.F181F NM_020634.1 NP_065685.1 Q9NR23 GDF3_HUMAN growth differentiation factor 3 28 CCAGCAGGTTGAAGTGAACAG 0.507000 0 SO:0001819 synonymous_variant ENST00000329913.3 1 1 hg19 CCDS8581.1 TCGA-S4-A8RM-01A-11D-A377-08 GDF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399717.1 1 0 0 137 367 0 79 0 4.137300e-01 0 5 0 79 2 0 0 0 0 0 2 1 1.000000 135 360 0 79 2 0 0 0 0 79 2 -20.000000 1 1 0 0 1 1 2 3 2.031110 0 0.640000 1.980000 0.641148 0.840000 7.200000e-01 0.980000 0.850000 0.853793 0.840000 0 7.800000e-01 0.920000 NAV3 89795 broad.mit.edu 37 12 78604240 78604240 + Silent SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:78604240C>T ENST00000397909.2 + 40 7274 c.7101C>T c.(7099-7101)agC>agT p.S2367S NAV3_ENST00000536525.2_Silent_p.S2345S|NAV3_ENST00000228327.6_Silent_p.S2345S|NAV3_ENST00000266692.7_Silent_p.S2168S|NAV3_ENST00000541270.1_Silent_p.S197S Q8IVL0 NAV3_HUMAN neuron navigator 3 236 GCTGCGACAGCGAAAGCACCA 0.393000 HNSCC(70;0.22) 0 SO:0001819 synonymous_variant ENST00000397909.2 1 1 hg19 . . . . . . . . . . C 0.332 -0.955497 0.02267 . . ENSG00000067798 ENST00000552895;ENST00000551162 . . . 5.35 -5.24 0.02789 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -5.8606 16.3886 0.83524 0.0:0.3108:0.0:0.6892 . . . . X 1240;235 . . R + 1 2 NAV3 77128371 0.488000 0.25996 0.415000 0.26534 0.199000 0.23934 -0.262000 0.08682 -0.911000 0.03843 -0.768000 0.03414 CGA TCGA-S4-A8RM-01A-11D-A377-08 NAV3-001 KNOWN basic protein_coding protein_coding OTTHUMT00000406812.1 1 0 1 110 266 0 62 0 5.646561e-01 1 5 0 62 2 0 0 0 0 0 2 1 1.000000 108 262 0 61 2 0 0 0 0 62 2 -8.416818 1 1 120858 5 39 1 0 0 0 1.993499 0 0.640000 1.980000 0.637681 0.900000 7.600000e-01 1.000000 1.000000 0.906308 0.900000 1 8.300000e-01 0.980000 NDUFA12 55967 broad.mit.edu 37 12 95397439 95397439 + Silent SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:95397439G>T ENST00000327772.2 - 1 107 c.18C>A c.(16-18)gtC>gtA p.V6V NDUFA12_ENST00000547986.1_Silent_p.V6V|NDUFA12_ENST00000547157.1_Silent_p.V6V NM_018838.4 NP_061326.1 Q9UI09 NDUAC_HUMAN NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 6 CGCGTTTCAGGACCTGCACTA 0.647000 0 SO:0001819 synonymous_variant ENST00000327772.2 0 1 hg19 CCDS9050.1 TCGA-S4-A8RM-01A-11D-A377-08 NDUFA12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407245.2 0 0 0 14 489 0 51 1 9.852838e-01 12 233 0 51 2 0 0 0 0 0 2 1 0.999735 14 482 0 51 2 0 0 0 0 51 2 -3.579756 1 1 0 0 1 0 0 0 1.993499 0 0.640000 1.980000 0.637681 0.080000 4.000000e-02 0.140000 0.080000 0.092124 0.080000 0 6.000000e-02 0.120000 CCDC38 120935 broad.mit.edu 37 12 96292480 96292480 + Silent SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr12:96292480G>T ENST00000344280.3 - 6 956 c.399C>A c.(397-399)atC>atA p.I133I SNRPF_ENST00000552085.1_Intron NM_182496.2 NP_872302.2 Q502W7 CCD38_HUMAN coiled-coil domain containing 38 18 CAAACTTTTTGATTGTGTTTC 0.373000 0 SO:0001819 synonymous_variant ENST00000344280.3 1 1 hg19 CCDS9056.1 TCGA-S4-A8RM-01A-11D-A377-08 CCDC38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408634.1 1 0 1 89 222 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 1.000000 85 217 0 75 2 0 0 0 0 76 2 -20.000000 1 1 121412 1 33 1 0 0 0 1.993499 0 0.640000 1.980000 0.637681 0.880000 7.300000e-01 1.000000 1.000000 0.887777 0.880000 1 8.000000e-01 0.970000 EIF5 1983 broad.mit.edu 37 14 103805083 103805083 + Missense_Mutation SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr14:103805083G>T ENST00000216554.3 + 8 1273 c.597G>T c.(595-597)gaG>gaT p.E199D EIF5_ENST00000558506.1_Missense_Mutation_p.E199D|SNORA28_ENST00000606769.1_RNA|EIF5_ENST00000392715.2_Missense_Mutation_p.E199D NM_001969.4 NP_001960.2 P55010 IF5_HUMAN eukaryotic translation initiation factor 5 18 Melanoma(154;0.155) Epithelial(46;0.182) AAGAAGAGGAGGATGATGACT 0.413000 0 SO:0001583 missense ENST00000216554.3 1 1 hg19 CCDS9980.1 . . . . . . . . . . . 1.304 -0.604076 0.03717 . . ENSG00000100664 ENST00000216554;ENST00000392715 D;D 0.82433 -1.61;-1.61 5.37 0.862 0.19056 . 0.138874 0.64402 N 0.000008 T 0.57475 0.2056 N 0.16903 0.455 0.38094 D 0.937046 B 0.02656 0.0 B 0.01281 0.0 T 0.49570 -0.8926 10 0.02654 T 1 -4.7689 0.5359 0.00636 0.3386:0.1608:0.2956:0.2049 . 199 P55010 IF5_HUMAN D 199 ENSP00000216554:E199D;ENSP00000376477:E199D ENSP00000216554:E199D E + 3 2 EIF5 102874836 0.291000 0.24352 0.996000 0.52242 0.657000 0.38888 -0.406000 0.07187 -0.043000 0.13513 -0.259000 0.10710 GAG TCGA-S4-A8RM-01A-11D-A377-08 EIF5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415329.2 1 0 1 113 258 0 65 1 1 107 171 0 65 2 0 0 0 0 0 2 1 1.000000 102 270 0 65 2 0 0 0 0 65 2 -20.000000 1 0 0 0 1 0 0 0 1.995992 0 0.640000 1.980000 0.637681 0.940000 7.900000e-01 1.000000 1.000000 0.936814 0.940000 1 8.600000e-01 1.000000 OR4N2 390429 broad.mit.edu 37 14 20295937 20295937 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr14:20295937G>A ENST00000315947.1 + 1 330 c.330G>A c.(328-330)ggG>ggA p.G110G OR4N2_ENST00000568211.1_Silent_p.G110G NM_001004723.1 NP_001004723.1 Q8NGD1 OR4N2_HUMAN olfactory receptor, family 4, subfamily N, member 2 52 all_cancers(95;0.00108) Epithelial(56;9.96e-07)|all cancers(55;2.95e-06) TTGGAGGAGGGGAGGGATTAC 0.522000 0 SO:0001819 synonymous_variant ENST00000315947.1 0 1 hg19 CCDS32022.1 TCGA-S4-A8RM-01A-11D-A377-08 OR4N2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409821.2 0 0 0 22 866 1 206 0 0 0 1 206 2 0 0 0 0 0 2 1 0.922100 19 786 1 237 13 0 0 0 1 206 2 -2.093702 0 1 121412 2 39 1 0 2 2 1.914286 1 0.640000 1.980000 0.640000 0.080000 4.000000e-02 1.000000 0.080000 0.302127 0.080000 0 6.000000e-02 1.000000 PRMT5 10419 broad.mit.edu 37 14 23391693 23391693 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr14:23391693G>A ENST00000324366.8 - 15 1878 c.1655C>T c.(1654-1656)gCc>gTc p.A552V PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000538452.1_Missense_Mutation_p.A446V|PRMT5_ENST00000553897.1_Missense_Mutation_p.A508V|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000397440.4_Missense_Mutation_p.A381V|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000216350.8_Missense_Mutation_p.A491V|PRMT5_ENST00000397441.2_Missense_Mutation_p.A535V|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5-AS1_ENST00000609885.1_RNA NM_006109.3 NP_006100.2 O14744 ANM5_HUMAN protein arginine methyltransferase 5 25 all_cancers(95;2.76e-05) AAAGTAGCCGGCAAAGCCATG 0.463000 0 SO:0001583 missense ENST00000324366.8 0 1 hg19 CCDS9579.1 . . . . . . . . . . G 24.3 4.518793 0.85495 . . ENSG00000100462 ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000555454;ENST00000538452;ENST00000553897 T;T;T;T;T;T;T 0.21191 2.02;2.02;2.02;2.02;2.02;2.02;2.02 5.79 5.79 0.91817 . 0.046588 0.85682 D 0.000000 T 0.44286 0.1286 M 0.87547 2.89 0.80722 D 1 P;B;P;P;P 0.46142 0.694;0.416;0.792;0.832;0.873 B;B;P;B;P 0.48952 0.328;0.285;0.596;0.389;0.457 T 0.49542 -0.8929 10 0.66056 D 0.02 -12.7059 18.796 0.91994 0.0:0.0:1.0:0.0 . 508;491;381;552;535 G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91 .;.;.;ANM5_HUMAN;. V 552;535;381;491;151;446;508 ENSP00000319169:A552V;ENSP00000380583:A535V;ENSP00000380582:A381V;ENSP00000216350:A491V;ENSP00000451245:A151V;ENSP00000444915:A446V;ENSP00000452555:A508V ENSP00000216350:A491V A - 2 0 PRMT5 22461533 1.000000 0.71417 0.999000 0.59377 0.995000 0.86356 8.655000 0.91098 2.750000 0.94351 0.561000 0.74099 GCC TCGA-S4-A8RM-01A-11D-A377-08 PRMT5-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071674.3 0 0 0 9 934 0 160 0 3.208989e-01 0 110 0 160 2 0 0 0 0 0 2 1 0.993996 8 928 0 155 2 0 0 0 0 160 2 -2.094841 0 1 0 0 1 0 0 0 1.995992 0 0.640000 1.980000 0.637681 0.020000 0 0.060000 0.040000 0.032226 0.020000 0 1.000000e-02 0.050000 NID2 22795 broad.mit.edu 37 14 52505475 52505475 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr14:52505475G>A ENST00000216286.5 - 9 2246 c.2247C>T c.(2245-2247)ggC>ggT p.G749G NID2_ENST00000541773.1_Silent_p.G696G NM_007361.3 NP_031387.3 Q14112 NID2_HUMAN nidogen 2 (osteonidogen) 87 Breast(41;0.0639)|all_epithelial(31;0.123) CTTTGACCGGGCCAATTTGAT 0.438000 0 SO:0001819 synonymous_variant ENST00000216286.5 0 1 hg19 CCDS9706.1 . . . . . . . . . . G 0.970 -0.700373 0.03279 . . ENSG00000087303 ENST00000556572 . . . 6.17 4.27 0.50696 . . . . . T 0.55577 0.1929 . . . 0.80722 D 1 . . . . . . T 0.53690 -0.8403 4 . . . . 6.2489 0.20835 0.0705:0.2083:0.6002:0.1209 . . . . S 66 . . P - 1 0 NID2 51575225 0.998000 0.40836 1.000000 0.80357 0.083000 0.17756 0.369000 0.20416 1.636000 0.50526 -0.136000 0.14681 CCC TCGA-S4-A8RM-01A-11D-A377-08 NID2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276888.1 0 0 0 4 246 0 45 0 3.911369e-02 0 15 0 45 2 0 0 0 0 0 2 1 0.888247 4 243 0 45 2 0 0 0 0 45 2 -2.981512 1 1 0 0 1 0 0 0 1.995992 0 0.640000 1.980000 0.637681 0.050000 0 0.120000 0.050000 0.061362 0.050000 0 2.000000e-02 0.090000 PAPLN 89932 broad.mit.edu 37 14 73733472 73733472 + Missense_Mutation SNP C C G TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr14:73733472C>G ENST00000554301.1 + 24 3596 c.3433C>G c.(3433-3435)Cca>Gca p.P1145A PAPLN_ENST00000340738.5_Missense_Mutation_p.P1118A|PAPLN_ENST00000555445.1_Missense_Mutation_p.P1129A|PAPLN_ENST00000427855.1_Missense_Mutation_p.P1145A|PAPLN_ENST00000381166.3_Intron O95428 PPN_HUMAN papilin, proteoglycan-like sulfated glycoprotein 42 TGTGACAGTGCCAGAGGGTGA 0.547000 0 SO:0001583 missense ENST00000554301.1 1 1 hg19 . . . . . . . . . . C 0.066 -1.213152 0.01555 . . ENSG00000100767 ENST00000340738;ENST00000427855;ENST00000554301;ENST00000555445 T;T;T;T 0.65178 -0.14;-0.14;-0.14;-0.14 5.07 2.17 0.27698 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.35393 0.0930 N 0.05031 -0.125 0.53005 D 0.999961 B;B;B;B 0.19073 0.001;0.001;0.033;0.002 B;B;B;B 0.19946 0.004;0.008;0.027;0.007 T 0.04065 -1.0980 9 0.30854 T 0.27 . 5.6369 0.17542 0.1071:0.5598:0.2118:0.1213 . 1129;1145;344;1118 O95428-5;O95428;O95428-2;O95428-6 .;PPN_HUMAN;.;. A 1118;1145;1145;1129 ENSP00000345395:P1118A;ENSP00000403403:P1145A;ENSP00000451803:P1145A;ENSP00000451729:P1129A ENSP00000345395:P1118A P + 1 0 PAPLN 72803225 0.370000 0.25047 0.171000 0.22900 0.001000 0.01503 -0.021000 0.12504 0.030000 0.15379 -1.268000 0.01426 CCA TCGA-S4-A8RM-01A-11D-A377-08 PAPLN-002 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000413182.1 1 0 1 34 77 0 23 0 9.623422e-01 0 15 0 23 2 0 0 0 0 0 2 1 1.000000 31 76 0 23 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 0 0 0 1.995992 0 0.640000 1.980000 0.637681 0.940000 6.900000e-01 1.000000 1.000000 0.921762 0.940000 1 8.100000e-01 1.000000 EML5 161436 broad.mit.edu 37 14 89181392 89181392 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr14:89181392G>A ENST00000380664.5 - 9 1334 c.1335C>T c.(1333-1335)ggC>ggT p.G445G EML5_ENST00000352093.5_Silent_p.G445G|EML5_ENST00000554922.1_Silent_p.G445G Q05BV3 EMAL5_HUMAN echinoderm microtubule associated protein like 5 50 CCAAACACTCGCCAACTTTTT 0.383000 0 SO:0001819 synonymous_variant ENST00000380664.5 1 1 hg19 CCDS45148.1 TCGA-S4-A8RM-01A-11D-A377-08 EML5-010 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000410491.1 1 0 1 72 143 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 72 142 0 51 2 0 0 0 0 51 2 -20.000000 1 1 0 0 1 0 0 0 1.995992 0 0.640000 1.980000 0.637681 0.990000 8.400000e-01 1.000000 1.000000 0.978016 0.990000 1 9.300000e-01 1.000000 OCA2 4948 broad.mit.edu 37 15 28263652 28263652 + Missense_Mutation SNP G G T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr15:28263652G>T ENST00000354638.3 - 7 853 c.698C>A c.(697-699)gCa>gAa p.A233E OCA2_ENST00000382996.2_Missense_Mutation_p.A233E|OCA2_ENST00000353809.5_Missense_Mutation_p.A233E NM_000275.2 NP_000266.2 Q04671 P_HUMAN oculocutaneous albinism II 85 all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234) TAGGGCCCCTGCCAGGTCCAC 0.647000 Oculocutaneous Albinism 0 SO:0001583 missense Familial Cancer Database ENST00000354638.3 1 1 hg19 CCDS10020.1 . . . . . . . . . . G 11.17 1.558383 0.27827 . . ENSG00000104044 ENST00000354638;ENST00000353809;ENST00000382996;ENST00000431101 T;T;T;T 0.64618 -0.11;-0.11;-0.11;-0.11 5.54 2.47 0.30058 . 0.354079 0.28130 N 0.016485 T 0.47746 0.1462 M 0.61703 1.905 0.24313 N 0.99508 P;B 0.35944 0.529;0.36 B;B 0.36567 0.228;0.09 T 0.41520 -0.9504 10 0.02654 T 1 -4.3929 3.9439 0.09339 0.1888:0.0:0.5739:0.2373 . 233;233 Q04671-2;Q04671 .;P_HUMAN E 233 ENSP00000346659:A233E;ENSP00000261276:A233E;ENSP00000372457:A233E;ENSP00000415431:A233E ENSP00000261276:A233E A - 2 0 OCA2 25937247 0.795000 0.28851 0.641000 0.29422 0.139000 0.21198 0.946000 0.29069 0.565000 0.29255 -0.136000 0.14681 GCA TCGA-S4-A8RM-01A-11D-A377-08 OCA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250823.1 1 0 1 41 90 0 20 0 1.013354e-01 0 2 0 20 2 0 0 0 0 0 2 1 1.000000 41 90 0 19 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 1 2 3 2.043679 0 0.640000 1.980000 0.642289 0.980000 7.400000e-01 1.000000 1.000000 0.944432 0.980000 1 8.500000e-01 1.000000 ACAN 176 broad.mit.edu 37 15 89382106 89382106 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr15:89382106C>T ENST00000561243.1 + 2 283 c.283C>T c.(283-285)Cgg>Tgg p.R95W ACAN_ENST00000559004.1_Missense_Mutation_p.R95W|ACAN_ENST00000558207.1_Missense_Mutation_p.R95W|ACAN_ENST00000352105.7_Missense_Mutation_p.R95W|ACAN_ENST00000439576.2_Missense_Mutation_p.R95W P16112 PGCA_HUMAN aggrecan 93 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) AGGGCGCGTGCGGGTCAACAG 0.622000 0 SO:0001583 missense ENST00000561243.1 0 1 hg19 CCDS53970.1 . . . . . . . . . . C 14.01 2.407857 0.42715 . . ENSG00000157766 ENST00000439576;ENST00000352105;ENST00000268134 T;T 0.66815 -0.23;-0.23 5.36 1.15 0.20763 . . . . . T 0.81074 0.4747 M 0.79011 2.435 0.36546 D 0.871562 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.79784 0.987;0.987;0.993 D 0.84991 0.0894 9 0.87932 D 0 -12.5802 16.4177 0.83748 0.4344:0.5656:0.0:0.0 . 95;95;95 E7ENV9;E7EX88;Q6PID9 .;.;. W 95 ENSP00000387356:R95W;ENSP00000341615:R95W ENSP00000268134:R95W R + 1 2 ACAN 87183110 0.998000 0.40836 0.860000 0.33809 0.768000 0.43524 0.886000 0.28241 -0.170000 0.10816 -1.378000 0.01179 CGG TCGA-S4-A8RM-01A-11D-A377-08 ACAN-006 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416267.2 0 0 0 7 614 0 103 0 0 0 1 0 103 2 0 0 0 0 0 2 1 0.980125 7 609 0 103 2 0 0 0 0 103 2 -1.916548 0 1 121178 2 36 1 1 2 3 2.042131 0 0.640000 1.980000 0.642289 0.030000 0 0.080000 0.040000 0.049595 0.030000 0 1.000000e-02 0.060000 GP2 2813 broad.mit.edu 37 16 20329591 20329591 + Missense_Mutation SNP C C T rs145287300 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr16:20329591C>T ENST00000381362.4 - 8 1254 c.1178G>A c.(1177-1179)cGg>cAg p.R393Q GP2_ENST00000302555.5_Missense_Mutation_p.R390Q|GP2_ENST00000573897.1_5'Flank|GP2_ENST00000381360.5_Missense_Mutation_p.R246Q|GP2_ENST00000341642.5_Missense_Mutation_p.R243Q NM_001007240.1|NM_001502.2 NP_001007241.2|NP_001493.2 P55259 GP2_HUMAN glycoprotein 2 (zymogen granule membrane) 48 CAGGTTAAACCGGGAGGTGTC 0.498000 0 SO:0001583 missense ENST00000381362.4 1 1 hg19 CCDS42128.1 . . . . . . . . . . C 9.634 1.137313 0.21123 . . ENSG00000169347 ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520 D;D;D;D 0.82344 -1.6;-1.6;-1.6;-1.6 5.8 -0.158 0.13383 Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3); . . . . T 0.64560 0.2609 L 0.28192 0.835 0.09310 N 1 B;B;B;B 0.26147 0.012;0.122;0.135;0.143 B;B;B;B 0.23419 0.006;0.044;0.01;0.046 T 0.47433 -0.9118 9 0.11794 T 0.64 -6.5112 1.9729 0.03409 0.1244:0.4067:0.1377:0.3312 . 243;371;390;393 P55259-4;B7Z1G2;P55259-3;P55259 .;.;.;GP2_HUMAN Q 390;393;246;243;371 ENSP00000304044:R390Q;ENSP00000370767:R393Q;ENSP00000370765:R246Q;ENSP00000343861:R243Q ENSP00000304044:R390Q R - 2 0 GP2 20237092 0.033000 0.19621 0.017000 0.16124 0.778000 0.44026 0.163000 0.16520 0.089000 0.17243 -0.143000 0.13931 CGG TCGA-S4-A8RM-01A-11D-A377-08 GP2-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000436920.1 1 0 1 150 329 0 110 1 1 326 463 0 110 2 0 0 0 0 0 2 1 1.000000 150 327 0 110 2 0 0 0 0 110 2 -11.609830 1 1 121412 6 43 1 1 2 3 2.025948 0 0.640000 1.980000 0.641148 0.970000 8.400000e-01 1.000000 1.000000 0.963986 0.970000 1 9.100000e-01 1.000000 SLC47A1 55244 broad.mit.edu 37 17 19480756 19480756 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:19480756G>A ENST00000270570.4 + 17 1689 c.1603G>A c.(1603-1605)Gct>Act p.A535T SLC47A1_ENST00000395585.1_Missense_Mutation_p.A535T|RP11-1113L8.1_ENST00000574267.1_RNA|AC025627.7_ENST00000420951.1_RNA|SLC47A1_ENST00000457293.1_Missense_Mutation_p.A535T|SLC47A1_ENST00000575023.1_Missense_Mutation_p.A233T|SLC47A1_ENST00000436810.2_3'UTR|SLC47A1_ENST00000571335.1_Missense_Mutation_p.A281T NM_018242.2 NP_060712.2 Q96FL8 S47A1_HUMAN solute carrier family 47 (multidrug and toxin extrusion), member 1 23 all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345) Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877) ACAGGACGGCGCTAAATTGTC 0.512000 0 SO:0001583 missense ENST00000270570.4 0 1 hg19 CCDS11209.1 . . . . . . . . . . G 6.205 0.406028 0.11754 . . ENSG00000142494 ENST00000270570;ENST00000457293;ENST00000395585;ENST00000455670;ENST00000424755 T;T;T 0.32023 1.49;1.47;1.47 5.16 -10.3 0.00346 . 2.640820 0.01350 N 0.011864 T 0.15219 0.0367 N 0.21448 0.665 0.09310 N 1 B;B;B;B 0.12013 0.0;0.0;0.001;0.005 B;B;B;B 0.09377 0.0;0.0;0.001;0.004 T 0.08597 -1.0714 10 0.15066 T 0.55 -11.0131 6.0981 0.20031 0.1985:0.1763:0.5331:0.0921 . 210;210;535;535 E7ENC3;B4DDH5;Q96FL8;Q96FL8-3 .;.;S47A1_HUMAN;. T 535;535;535;210;247 ENSP00000270570:A535T;ENSP00000415586:A535T;ENSP00000378951:A535T ENSP00000270570:A535T A + 1 0 SLC47A1 19421348 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -2.188000 0.01249 -3.020000 0.00270 -0.672000 0.03802 GCT TCGA-S4-A8RM-01A-11D-A377-08 SLC47A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132250.1 0 0 0 5 523 0 98 0 0 0 1 0 98 2 0 0 0 0 0 2 1 0.935280 5 516 0 96 2 0 0 0 0 98 2 -1.916061 0 1 121412 4 42 1 0 1 1 1.453406 1 0.640000 1.980000 0.473068 0.010000 0 0.050000 0.020000 0.024022 0.010000 0 0 0.030000 P2RX1 5023 broad.mit.edu 37 17 3807664 3807664 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:3807664G>A ENST00000225538.3 - 4 661 c.387C>T c.(385-387)gaC>gaT p.D129D NM_002558.2 NP_002549.1 P51575 P2RX1_HUMAN purinergic receptor P2X, ligand-gated ion channel, 1 13 TACAGCCACTGTCTTCCTTGC 0.657000 0 SO:0001819 synonymous_variant ENST00000225538.3 1 1 hg19 CCDS11040.1 TCGA-S4-A8RM-01A-11D-A377-08 P2RX1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438391.1 1 0 0 9 194 0 48 0 2.604783e-03 0 2 0 48 2 0 0 0 0 0 2 1 0.993869 9 189 0 48 2 0 0 0 0 48 2 -11.617700 1 1 0 0 1 0 1 1 1.433139 1 0.640000 1.980000 0.473068 0.090000 4.000000e-02 0.170000 0.090000 0.103575 0.090000 0 6.000000e-02 0.130000 MAPT 4137 broad.mit.edu 37 17 44073913 44073913 + Silent SNP G G A rs115142761 by1000genomes TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:44073913G>A ENST00000571987.1 + 9 1656 c.1656G>A c.(1654-1656)tcG>tcA p.S552S MAPT_ENST00000431008.3_Silent_p.S235S|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000334239.8_Silent_p.S177S|MAPT_ENST00000351559.5_Silent_p.S235S|MAPT_ENST00000535772.1_Silent_p.S235S|MAPT_ENST00000344290.5_Silent_p.S570S|MAPT_ENST00000574436.1_Silent_p.S235S|MAPT_ENST00000446361.3_Silent_p.S177S|MAPT_ENST00000347967.5_Silent_p.S141S|MAPT_ENST00000340799.5_Silent_p.S206S|MAPT_ENST00000576518.1_Silent_p.S166S|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000420682.2_Silent_p.S206S|MAPT_ENST00000262410.5_Silent_p.S552S|MAPT_ENST00000415613.2_Silent_p.S570S P10636 TAU_HUMAN microtubule-associated protein tau 38 Melanoma(429;0.216) Docetaxel(DB01248)|Paclitaxel(DB01229) CACCCAAGTCGCCGTCTTCCG 0.662000 0 SO:0001819 synonymous_variant ENST00000571987.1 0 1 hg19 CCDS11501.1 TCGA-S4-A8RM-01A-11D-A377-08 MAPT-008 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000440133.1 1 0 0 8 142 0 20 0 3.869969e-03 0 2 0 20 2 0 0 0 0 0 2 1 0.988809 8 138 0 20 2 0 0 0 0 20 2 -11.449430 1 1 121388 5 37 1 1 2 3 2.070324 0 0.640000 1.980000 0.645669 0.170000 8.000000e-02 1.000000 0.170000 0.218171 0.170000 0 1.200000e-01 0.260000 RNF43 54894 broad.mit.edu 37 17 56440757 56440757 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:56440757G>A ENST00000584437.1 - 4 2416 c.461C>T c.(460-462)cCg>cTg p.P154L RNF43_ENST00000407977.2_Missense_Mutation_p.P154L|RNF43_ENST00000583753.1_Missense_Mutation_p.P113L|RNF43_ENST00000500597.2_Missense_Mutation_p.P113L|RNF43_ENST00000581868.1_Missense_Mutation_p.P27L|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.P154L|RNF43_ENST00000577625.1_Missense_Mutation_p.P27L Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) CAGCCCCAGCGGCTGCTGCAG 0.577000 0 SO:0001583 missense ENST00000584437.1 1 1 hg19 CCDS11607.1 . . . . . . . . . . G 35 5.475540 0.96291 . . ENSG00000108375 ENST00000407977;ENST00000500597 T;T 0.27104 1.69;3.06 5.68 5.68 0.88126 . 0.187766 0.47093 D 0.000257 T 0.30103 0.0754 N 0.19112 0.55 0.80722 D 1 D;D;D 0.69078 0.995;0.993;0.997 P;P;P 0.54140 0.743;0.721;0.551 T 0.01725 -1.1287 10 0.34782 T 0.22 -8.5077 18.7682 0.91881 0.0:0.0:1.0:0.0 . 113;154;154 Q68DV7-2;Q68DV7-4;Q68DV7 .;.;RNF43_HUMAN L 154;113 ENSP00000385328:P154L;ENSP00000441969:P113L ENSP00000385328:P154L P - 2 0 RNF43 53795756 1.000000 0.71417 1.000000 0.80357 0.963000 0.63663 8.661000 0.91125 2.684000 0.91462 0.591000 0.81541 CCG TCGA-S4-A8RM-01A-11D-A377-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 151 353 0 76 1 9.998374e-01 8 25 0 76 2 1 1 274 609 0 497 2 1 1.000000 150 347 0 76 2 0 0 0 0 76 2 -10.307860 1 1 121412 1 37 1 1 2 3 2.070324 0 0.640000 1.980000 0.645669 0.950000 8.200000e-01 1.000000 1.000000 0.945798 0.950000 1 8.800000e-01 1.000000 RNF157 114804 broad.mit.edu 37 17 74148532 74148532 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:74148532C>T ENST00000269391.6 - 18 1957 c.1825G>A c.(1825-1827)Gca>Aca p.A609T RNF157-AS1_ENST00000592748.1_RNA|RNF157_ENST00000319945.6_Missense_Mutation_p.A587T|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586661.1_RNA|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000585542.1_RNA NM_052916.2 NP_443148.1 Q96PX1 RN157_HUMAN ring finger protein 157 25 LUSC - Lung squamous cell carcinoma(166;0.187) CCTAGAAATGCGCACGTCCTC 0.458000 GBM(186;507 2120 27388 27773 52994) 0 SO:0001583 missense ENST00000269391.6 0 1 hg19 CCDS32740.1 . . . . . . . . . . C 18.55 3.649353 0.67358 . . ENSG00000141576 ENST00000269391;ENST00000319945 T;T 0.36699 1.7;1.24 5.71 4.68 0.58851 . 0.088535 0.49305 D 0.000154 T 0.35335 0.0928 L 0.54323 1.7 0.80722 D 1 P;P 0.52170 0.951;0.84 B;B 0.41946 0.371;0.089 T 0.24835 -1.0149 10 0.52906 T 0.07 -1.2912 13.8657 0.63588 0.1522:0.8478:0.0:0.0 . 587;609 Q96PX1-2;Q96PX1 .;RN157_HUMAN T 609;587 ENSP00000269391:A609T;ENSP00000321837:A587T ENSP00000269391:A609T A - 1 0 RNF157 71660127 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.443000 0.44881 2.684000 0.91462 0.655000 0.94253 GCA TCGA-S4-A8RM-01A-11D-A377-08 RNF157-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255874.2 0 0 0 6 398 0 67 0 1.001739e-03 0 3 0 67 2 0 0 0 0 0 2 1 0.964435 6 395 0 65 2 0 0 0 0 67 2 -2.576342 1 1 121412 7 43 1 1 2 3 2.070324 0 0.640000 1.980000 0.645669 0.040000 1.000000e-02 1.000000 0.050000 0.090569 0.040000 0 2.000000e-02 0.080000 CHD3 1107 broad.mit.edu 37 17 7807208 7807208 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:7807208G>A ENST00000330494.7 + 24 3943 c.3793G>A c.(3793-3795)Gac>Aac p.D1265N SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.D1265N|CHD3_ENST00000380358.4_Missense_Mutation_p.D1324N NM_001005273.2 NP_001005273.1 Q12873 CHD3_HUMAN chromodomain helicase DNA binding protein 3 65 Prostate(122;0.202) TCGGCTGTTGGACCGGAACCA 0.517000 0 SO:0001583 missense ENST00000330494.7 1 1 hg19 CCDS32554.1 . . . . . . . . . . G 26.3 4.723272 0.89298 . . ENSG00000170004 ENST00000380358;ENST00000358181;ENST00000330494 D;D;D 0.91631 -2.88;-2.81;-2.81 5.12 5.12 0.69794 . 0.000000 0.49305 D 0.000159 D 0.95242 0.8457 L 0.60957 1.885 0.80722 D 1 D;D;D 0.71674 0.998;0.997;0.997 D;D;D 0.81914 0.995;0.989;0.989 D 0.95103 0.8232 10 0.62326 D 0.03 -30.8593 19.1045 0.93287 0.0:0.0:1.0:0.0 . 1265;1265;1324 Q12873-2;Q12873;E9PG89 .;CHD3_HUMAN;. N 1324;1265;1265 ENSP00000369716:D1324N;ENSP00000350907:D1265N;ENSP00000332628:D1265N ENSP00000332628:D1265N D + 1 0 CHD3 7747933 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.203000 0.95033 2.811000 0.96726 0.655000 0.94253 GAC TCGA-S4-A8RM-01A-11D-A377-08 CHD3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318050.1 1 0 1 106 109 0 39 1 1 124 46 0 39 2 0 0 0 0 0 2 1 1.000000 105 106 0 39 2 0 0 0 0 39 2 -20.000000 1 1 0 0 1 0 1 1 1.433139 1 0.640000 1.980000 0.473068 0.970000 8.700000e-01 1.000000 1.000000 0.966016 0.970000 1 9.200000e-01 1.000000 RNF213 57674 broad.mit.edu 37 17 78321225 78321225 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr17:78321225G>A ENST00000582970.1 + 29 9233 c.9090G>A c.(9088-9090)ccG>ccA p.P3030P RNF213_ENST00000508628.2_Silent_p.P3079P|RNF213_ENST00000336301.6_Silent_p.P1103P NM_001256071.1 NP_001243000.1 Q63HN8 RN213_HUMAN ring finger protein 213 130 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) AGAAGGTGCCGGGTGGAGAGC 0.547000 0 SO:0001819 synonymous_variant ENST00000582970.1 1 1 hg19 CCDS58606.1 TCGA-S4-A8RM-01A-11D-A377-08 RNF213-020 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000443298.1 1 0 1 74 180 0 42 1 9.998978e-01 12 25 0 42 2 1 1 133 254 0 274 2 1 1.000000 74 179 0 42 2 0 0 0 0 42 2 -6.107752 1 1 121412 5 37 1 1 2 3 2.070324 0 0.640000 1.980000 0.645669 0.920000 7.500000e-01 1.000000 1.000000 0.920008 0.920000 1 8.300000e-01 1.000000 ZNF407 55628 broad.mit.edu 37 18 72347373 72347373 + Silent SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr18:72347373C>T ENST00000299687.5 + 1 4398 c.4398C>T c.(4396-4398)gcC>gcT p.A1466A ZNF407_ENST00000309902.6_Silent_p.A1466A|ZNF407_ENST00000582337.1_Silent_p.A1466A|ZNF407_ENST00000577538.1_Silent_p.A1466A NM_017757.2 NP_060227.2 Q9C0G0 ZN407_HUMAN zinc finger protein 407 67 Esophageal squamous(42;0.131)|Prostate(75;0.173) TGGCTAGTGCCGGCCACATGA 0.498000 0 SO:0001819 synonymous_variant ENST00000299687.5 1 1 hg19 CCDS45885.1 TCGA-S4-A8RM-01A-11D-A377-08 ZNF407-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444903.1 1 0 0 5 94 0 31 0 2.201027e-02 0 4 0 31 2 0 0 0 0 0 2 1 0.937535 5 93 0 31 2 0 0 0 0 31 2 -4.411144 1 1 120840 6 38 1 0 1 1 1.440698 1 0.640000 1.980000 0.473068 0.110000 4.000000e-02 0.230000 0.110000 0.125417 0.110000 0 7.000000e-02 0.170000 TRPM4 54795 broad.mit.edu 37 19 49684660 49684660 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr19:49684660C>T ENST00000252826.5 + 10 1331 c.1205C>T c.(1204-1206)gCt>gTt p.A402V TRPM4_ENST00000427978.2_Missense_Mutation_p.A402V|TRPM4_ENST00000355712.5_Intron|TRPM4_ENST00000601347.1_Intron NM_017636.3 NP_060106.2 Q8TD43 TRPM4_HUMAN transient receptor potential cation channel, subfamily M, member 4 49 all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15) TTGGCTGTGGCTTGGAACCGC 0.617000 0 SO:0001583 missense ENST00000252826.5 1 1 hg19 CCDS33073.1 . . . . . . . . . . C 18.38 3.611107 0.66558 . . ENSG00000130529 ENST00000252826;ENST00000427978 T;T 0.67865 -0.29;-0.29 3.92 3.92 0.45320 . 0.070546 0.64402 D 0.000018 T 0.81621 0.4861 M 0.84948 2.725 0.80722 D 1 D;D;D 0.71674 0.987;0.994;0.998 P;D;P 0.64144 0.807;0.922;0.887 D 0.85892 0.1429 10 0.87932 D 0 -11.7547 15.0744 0.72066 0.0:1.0:0.0:0.0 . 228;402;402 Q8TD43-2;Q8TD43-3;Q8TD43 .;.;TRPM4_HUMAN V 402 ENSP00000252826:A402V;ENSP00000407492:A402V ENSP00000252826:A402V A + 2 0 TRPM4 54376472 1.000000 0.71417 1.000000 0.80357 0.233000 0.25261 6.665000 0.74442 1.899000 0.54978 0.455000 0.32223 GCT TCGA-S4-A8RM-01A-11D-A377-08 TRPM4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000465543.2 1 0 1 93 247 0 34 1 1 83 141 0 34 2 0 0 0 0 0 2 1 1.000000 93 242 0 32 2 0 0 0 0 34 2 -5.227186 1 1 0 0 1 1 2 3 2.032905 0 0.640000 1.980000 0.641148 0.850000 7.100000e-01 1.000000 0.850000 0.859105 0.850000 1 7.700000e-01 0.940000 TNFSF9 8744 broad.mit.edu 37 19 6534843 6534843 + Silent SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr19:6534843C>T ENST00000245817.3 + 3 569 c.531C>T c.(529-531)gcC>gcT p.A177A NM_003811.3 NP_003802.1 P41273 TNFL9_HUMAN tumor necrosis factor (ligand) superfamily, member 9 5 CTGGGGCCGCCGCCCTGGCTT 0.692000 0 SO:0001819 synonymous_variant ENST00000245817.3 1 1 hg19 CCDS12169.1 TCGA-S4-A8RM-01A-11D-A377-08 TNFSF9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457856.1 1 0 0 30 65 0 20 0 3.833312e-01 0 4 0 20 2 0 0 0 0 0 2 1 1.000000 29 64 0 20 2 0 0 0 0 20 2 -20.000000 1 1 120038 1 29 1 1 2 3 2.087110 0 0.640000 1.980000 0.646782 0.990000 7.200000e-01 1.000000 1.000000 0.948828 0.990000 1 8.600000e-01 1.000000 SMG7 9887 broad.mit.edu 37 1 183515464 183515464 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr1:183515464C>T ENST00000347615.2 + 17 2853 c.2734C>T c.(2734-2736)Ccg>Tcg p.P912S SMG7_ENST00000508461.1_Missense_Mutation_p.P870S|SMG7_ENST00000507469.1_Missense_Mutation_p.P866S|SMG7_ENST00000515829.2_Missense_Mutation_p.P866S|SMG7_ENST00000367537.3_Missense_Mutation_p.P895S|SMG7_ENST00000456731.2_Missense_Mutation_p.P824S NM_173156.2 NP_775179.1 Q92540 SMG7_HUMAN SMG7 nonsense mediated mRNA decay factor 46 ACCCAGAATGCCGTTTGAGGT 0.458000 0 SO:0001583 missense ENST00000347615.2 0 1 hg19 CCDS1355.1 . . . . . . . . . . C 14.54 2.565506 0.45694 . . ENSG00000116698 ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829 T;T;T;T;T;T 0.44482 0.92;0.92;0.92;0.92;0.92;0.92 5.61 5.61 0.85477 . 0.492382 0.20703 N 0.087223 T 0.29556 0.0737 N 0.24115 0.695 0.46458 D 0.99905 B;B;B;B;B;B 0.28713 0.22;0.19;0.084;0.137;0.191;0.19 B;B;B;B;B;B 0.29942 0.054;0.034;0.051;0.109;0.073;0.081 T 0.08722 -1.0708 10 0.27082 T 0.32 -9.5004 11.4831 0.50337 0.1457:0.7286:0.1256:0.0 . 870;895;824;866;912;866 E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2 .;.;.;.;SMG7_HUMAN;. S 824;895;870;912;866;866 ENSP00000407629:P824S;ENSP00000356507:P895S;ENSP00000426915:P870S;ENSP00000340766:P912S;ENSP00000425133:P866S;ENSP00000421358:P866S ENSP00000340766:P912S P + 1 0 SMG7 181782087 1.000000 0.71417 1.000000 0.80357 0.951000 0.60555 2.030000 0.41108 2.620000 0.88729 0.655000 0.94253 CCG TCGA-S4-A8RM-01A-11D-A377-08 SMG7-002 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000085432.1 0 0 0 6 428 0 50 0 5.031734e-01 0 110 0 50 2 0 0 0 0 0 2 1 0.964463 6 425 0 50 2 0 0 0 0 50 2 -2.742843 1 1 121406 8 39 1 1 2 3 2.680464 1 0.640000 1.980000 0.727273 0.050000 1.000000e-02 0.120000 0.060000 0.065936 0.050000 0 3.000000e-02 0.090000 OBSCN 84033 broad.mit.edu 37 1 228506686 228506686 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr1:228506686C>T ENST00000422127.1 + 54 14277 c.14233C>T c.(14233-14235)Cgg>Tgg p.R4745W OBSCN_ENST00000284548.11_Missense_Mutation_p.R4745W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R2379W|OBSCN_ENST00000570156.2_Missense_Mutation_p.R5702W|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1864W NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) GGCCCTGGCTCGGAAACGTCG 0.687000 0 SO:0001583 missense ENST00000422127.1 0 1 hg19 CCDS58065.1 . . . . . . . . . . C 17.75 3.466374 0.63625 . . ENSG00000154358 ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709 T;T;T;T 0.65364 0.26;-0.15;-0.09;0.41 4.03 1.89 0.25635 . 0.207897 0.29139 N 0.013029 T 0.61702 0.2368 N 0.24115 0.695 0.31729 N 0.637237 D;D 0.76494 0.999;0.999 P;D 0.65140 0.857;0.932 T 0.66520 -0.5903 10 0.62326 D 0.03 . 10.3422 0.43884 0.6289:0.3711:0.0:0.0 . 4745;4745 Q5VST9;Q5VST9-3 OBSCN_HUMAN;. W 4745;4745;2379;1864 ENSP00000284548:R4745W;ENSP00000409493:R4745W;ENSP00000355668:R2379W;ENSP00000355670:R1864W ENSP00000284548:R4745W R + 1 2 OBSCN 226573309 1.000000 0.71417 0.998000 0.56505 0.428000 0.31595 5.230000 0.65321 0.882000 0.36016 0.313000 0.20887 CGG TCGA-S4-A8RM-01A-11D-A377-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 1 0 0 9 46 0 9 0 3.534299e-01 1 6 0 9 2 0 0 0 0 0 2 1 0.995547 8 47 0 9 2 0 0 0 0 9 2 -17.537120 1 1 120636 3 24 1 1 2 3 2.685707 1 0.640000 1.980000 0.727273 0.690000 3.500000e-01 1.000000 1.000000 0.707775 0.690000 0 5.000000e-01 0.910000 OR2AK2 391191 broad.mit.edu 37 1 248129097 248129097 + Missense_Mutation SNP T T G TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr1:248129097T>G ENST00000366480.3 + 1 563 c.464T>G c.(463-465)aTc>aGc p.I155S OR2L13_ENST00000366478.2_Intron NM_001004491.1 NP_001004491.1 Q8NG84 O2AK2_HUMAN olfactory receptor, family 2, subfamily AK, member 2 36 all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0152) AGCAAGAAGATCTGCTGCCTC 0.438000 Melanoma(45;390 1181 23848 28461 41504) 0 SO:0001583 missense ENST00000366480.3 0 1 hg19 CCDS31102.1 . . . . . . . . . . . 12.99 2.103841 0.37145 . . ENSG00000187080 ENST00000366480 T 0.00164 8.64 3.03 -3.31 0.04988 GPCR, rhodopsin-like superfamily (1); . . . . T 0.00210 0.0006 L 0.33485 1.01 0.09310 N 1 D 0.56746 0.977 P 0.60541 0.876 T 0.46303 -0.9201 9 0.87932 D 0 . 4.6463 0.12574 0.1485:0.3771:0.0:0.4744 . 155 Q8NG84 O2AK2_HUMAN S 155 ENSP00000355436:I155S ENSP00000355436:I155S I + 2 0 OR2AK2 246195720 0.001000 0.12720 0.000000 0.03702 0.024000 0.10985 0.382000 0.20635 -0.847000 0.04168 -0.475000 0.04921 ATC TCGA-S4-A8RM-01A-11D-A377-08 OR2AK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096858.2 0 0 0 9 1127 0 187 0 0 0 0 187 2 0 0 0 0 0 2 1 0.993972 9 1117 0 185 2 0 0 0 0 187 2 -5.786677 1 1 0 0 1 1 2 3 2.685707 1 0.640000 1.980000 0.727273 0.020000 0 0.070000 0.030000 0.033467 0.020000 0 1.000000e-02 0.050000 HCRTR1 3061 broad.mit.edu 37 1 32087188 32087188 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr1:32087188C>T ENST00000373706.5 + 4 886 c.733C>T c.(733-735)Cgc>Tgc p.R245C HCRTR1_ENST00000403528.2_Missense_Mutation_p.R245C|HCRTR1_ENST00000468521.1_3'UTR|HCRTR1_ENST00000373705.1_Missense_Mutation_p.R245C O43613 OX1R_HUMAN hypocretin (orexin) receptor 1 7 Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116) GCTCTGGGGCCGCCAGGTGAG 0.597000 0 SO:0001583 missense ENST00000373706.5 0 1 hg19 CCDS344.1 . . . . . . . . . . c 29.2 4.987869 0.93106 . . ENSG00000121764 ENST00000403528;ENST00000373706;ENST00000373705 T;T;T 0.38887 1.11;1.11;1.11 5.25 5.25 0.73442 GPCR, rhodopsin-like superfamily (1); 0.129259 0.56097 D 0.000036 T 0.63674 0.2531 M 0.73430 2.235 0.80722 D 1 D;D 0.76494 0.994;0.999 P;D 0.63703 0.846;0.917 T 0.66622 -0.5877 10 0.87932 D 0 . 17.1746 0.86838 0.0:1.0:0.0:0.0 . 245;245 A6NMV7;O43613 .;OX1R_HUMAN C 245 ENSP00000384387:R245C;ENSP00000362810:R245C;ENSP00000362809:R245C ENSP00000362809:R245C R + 1 0 HCRTR1 31859775 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 4.354000 0.59417 2.836000 0.97738 0.651000 0.88453 CGC TCGA-S4-A8RM-01A-11D-A377-08 HCRTR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000011042.1 0 0 0 7 252 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 0.979916 7 248 0 47 2 0 0 0 0 48 2 -7.979174 1 1 0 0 1 0 1 1 1.449678 1 0.640000 1.980000 0.475524 0.050000 2.000000e-02 0.110000 0.060000 0.065468 0.050000 0 3.000000e-02 0.090000 BARHL2 343472 broad.mit.edu 37 1 91180182 91180182 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr1:91180182G>A ENST00000370445.4 - 2 798 c.757C>T c.(757-759)Cgg>Tgg p.R253W NM_020063.1 NP_064447.1 Q9NY43 BARH2_HUMAN BarH-like homeobox 2 24 all_lung(203;0.0263)|Lung SC(238;0.128) TACTTCTGCCGCTCAAAGCTA 0.567000 GBM(199;3561 4100 22440) 0 SO:0001583 missense ENST00000370445.4 0 1 hg19 CCDS730.1 . . . . . . . . . . G 17.81 3.481732 0.63849 . . ENSG00000143032 ENST00000370445 D 0.96427 -4.01 5.48 4.55 0.56014 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.088225 0.53938 D 0.000059 D 0.97763 0.9266 M 0.85299 2.745 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.98465 1.0598 10 0.72032 D 0.01 . 14.0787 0.64907 0.0:0.0:0.848:0.1519 . 253 Q9NY43 BARH2_HUMAN W 253 ENSP00000359474:R253W ENSP00000359474:R253W R - 1 2 BARHL2 90952770 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 1.479000 0.35453 1.243000 0.43853 0.655000 0.94253 CGG TCGA-S4-A8RM-01A-11D-A377-08 BARHL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000027728.2 0 0 0 6 532 0 111 0 0 0 0 111 2 0 0 0 0 0 2 1 0.963704 6 526 0 110 2 0 0 0 0 111 2 -2.204897 0 1 0 0 1 0 1 1 1.449678 1 0.640000 1.980000 0.475524 0.020000 0 0.050000 0.020000 0.027753 0.020000 0 1.000000e-02 0.040000 ZSWIM3 140831 broad.mit.edu 37 20 44506675 44506675 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr20:44506675G>A ENST00000255152.2 + 2 1687 c.1478G>A c.(1477-1479)gGc>gAc p.G493D ZSWIM3_ENST00000454862.2_Missense_Mutation_p.G487D NM_080752.3 NP_542790.2 Q96MP5 ZSWM3_HUMAN zinc finger, SWIM-type containing 3 35 Myeloproliferative disorder(115;0.0122) TCGCAGGTTGGCATGCTGGAC 0.582000 0 SO:0001583 missense ENST00000255152.2 0 1 hg19 CCDS13381.1 . . . . . . . . . . G 0.793 -0.758013 0.03019 . . ENSG00000132801 ENST00000255152;ENST00000454862 T;T 0.25414 1.84;1.8 5.65 2.51 0.30379 . 0.603536 0.17459 N 0.173509 T 0.12092 0.0294 N 0.17082 0.46 0.27138 N 0.961732 B;B 0.11235 0.004;0.004 B;B 0.09377 0.004;0.004 T 0.29761 -1.0001 10 0.11794 T 0.64 -12.4254 6.0596 0.19830 0.2499:0.1427:0.6074:0.0 . 487;493 E7ETT6;Q96MP5 .;ZSWM3_HUMAN D 493;487 ENSP00000255152:G493D;ENSP00000406313:G487D ENSP00000255152:G493D G + 2 0 ZSWIM3 43940082 0.515000 0.26210 0.928000 0.36995 0.504000 0.33889 0.453000 0.21811 0.941000 0.37499 0.655000 0.94253 GGC TCGA-S4-A8RM-01A-11D-A377-08 ZSWIM3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079540.1 0 0 0 4 217 1 49 0 3.425885e-03 0 4 1 49 2 0 0 0 0 0 2 0 0.006899 4 212 1 49 15 0 0 0 1 49 2 -5.343423 1 1 0 0 1 0 0 0 2.000980 0 0.640000 1.980000 0.637681 0.050000 1.000000e-02 0.140000 0.060000 0.069377 0.050000 0 3.000000e-02 0.100000 DIDO1 11083 broad.mit.edu 37 20 61511162 61511162 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr20:61511162G>A ENST00000266070.4 - 16 6471 c.6146C>T c.(6145-6147)gCg>gTg p.A2049V DIDO1_ENST00000395343.1_Missense_Mutation_p.A2049V NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 99 Breast(26;5.68e-08) GGAGGAGAGCGCGGAGGGCGG 0.716000 Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095) 0 SO:0001583 missense ENST00000266070.4 1 1 hg19 CCDS33506.1 . . . . . . . . . . G 6.147 0.395336 0.11638 . . ENSG00000101191 ENST00000266070;ENST00000395343 T;T 0.09163 3.01;3.01 3.89 1.76 0.24704 . 1.633200 0.04269 U 0.341785 T 0.07999 0.0200 N 0.22421 0.69 0.09310 N 0.999999 B 0.30211 0.273 B 0.15484 0.013 T 0.34576 -0.9823 10 0.56958 D 0.05 0.4278 6.5979 0.22685 0.088:0.0:0.5951:0.3169 . 2049 Q9BTC0 DIDO1_HUMAN V 2049 ENSP00000266070:A2049V;ENSP00000378752:A2049V ENSP00000266070:A2049V A - 2 0 DIDO1 60981607 0.027000 0.19231 0.002000 0.10522 0.013000 0.08279 2.240000 0.43088 0.084000 0.17077 0.563000 0.77884 GCG TCGA-S4-A8RM-01A-11D-A377-08 DIDO1-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080091.2 1 0 0 177 419 0 109 1 9.999491e-01 18 19 0 109 2 0 0 0 0 0 2 1 1.000000 173 410 0 106 2 0 0 0 0 109 2 -20.000000 1 1 118202 4 39 1 0 0 0 2.000980 0 0.640000 1.980000 0.637681 0.910000 8.000000e-01 1.000000 1.000000 0.920609 0.910000 1 8.500000e-01 0.980000 COL20A1 57642 broad.mit.edu 37 20 61950533 61950533 + Silent SNP C C A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr20:61950533C>A ENST00000358894.6 + 22 2887 c.2787C>A c.(2785-2787)ctC>ctA p.L929L COL20A1_ENST00000422202.1_Silent_p.L936L|COL20A1_ENST00000435874.1_Silent_p.L936L|COL20A1_ENST00000326996.6_Silent_p.L929L NM_020882.2 NP_065933.2 Q9P218 COKA1_HUMAN collagen, type XX, alpha 1 36 all_cancers(38;1.39e-10) TCCAGCCCCTCCTTGGGGTTC 0.667000 0 SO:0001819 synonymous_variant ENST00000358894.6 1 1 hg19 CCDS46628.1 TCGA-S4-A8RM-01A-11D-A377-08 COL20A1-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000144595.2 1 0 1 38 106 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 1.000000 38 104 0 10 2 0 0 0 0 12 2 -20.000000 1 1 0 0 1 0 0 0 2.000980 0 0.640000 1.980000 0.637681 0.810000 6.000000e-01 1.000000 1.000000 0.822544 0.810000 0 7.000000e-01 0.930000 IL1RL1 9173 broad.mit.edu 37 2 102957161 102957161 + Silent SNP G G A rs142878092 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:102957161G>A ENST00000233954.1 + 5 754 c.483G>A c.(481-483)gcG>gcA p.A161A IL1RL1_ENST00000404917.2_Silent_p.A44A|IL1RL1_ENST00000393393.3_Silent_p.A161A|IL1RL1_ENST00000311734.2_Silent_p.A161A|IL1RL1_ENST00000409584.1_Silent_p.A161A NM_016232.4 NP_057316.3 Q01638 ILRL1_HUMAN interleukin 1 receptor-like 1 16 GGTACAGGGCGCACAAGTCAT 0.358000 0 SO:0001819 synonymous_variant ENST00000233954.1 0 1 hg19 CCDS2057.1 TCGA-S4-A8RM-01A-11D-A377-08 IL1RL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253296.1 0 0 0 6 590 0 112 0 4.627791e-04 1 2 0 112 2 0 0 0 0 0 2 1 0.964195 6 585 0 111 2 0 0 0 0 112 2 -2.056157 0 1 121410 8 44 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.030000 0 0.070000 0.040000 0.035947 0.030000 0 1.000000e-02 0.050000 LRP1B 53353 broad.mit.edu 37 2 141571360 141571360 + Missense_Mutation SNP T T C TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:141571360T>C ENST00000389484.3 - 32 6196 c.5225A>G c.(5224-5226)tAt>tGt p.Y1742C NM_018557.2 NP_061027.2 Q9NZR2 LRP1B_HUMAN low density lipoprotein receptor-related protein 1B 606 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) GTTTTCCACATAGTCTATCGA 0.348000 TSP Lung(27;0.18) Colon(99;50 2074 2507 20106) 0 SO:0001583 missense ENST00000389484.3 0 1 hg19 CCDS2182.1 . . . . . . . . . . T 17.43 3.388112 0.61956 . . ENSG00000168702 ENST00000389484;ENST00000544579 D 0.91295 -2.82 5.71 5.71 0.89125 Six-bladed beta-propeller, TolB-like (1); 0.164731 0.41938 D 0.000793 D 0.94686 0.8286 M 0.85099 2.735 0.41501 D 0.988284 D 0.69078 0.997 P 0.57283 0.817 D 0.95215 0.8329 10 0.56958 D 0.05 . 15.9781 0.80086 0.0:0.0:0.0:1.0 . 1742 Q9NZR2 LRP1B_HUMAN C 1742;1680 ENSP00000374135:Y1742C ENSP00000374135:Y1742C Y - 2 0 LRP1B 141287830 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.982000 0.56909 2.171000 0.68590 0.533000 0.62120 TAT TCGA-S4-A8RM-01A-11D-A377-08 LRP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254736.2 0 0 0 4 296 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 0.889445 4 294 0 61 2 0 0 0 0 62 2 -3.038080 1 1 0 0 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.040000 0 0.100000 0.040000 0.051410 0.040000 0 2.000000e-02 0.070000 SCN9A 6335 broad.mit.edu 37 2 167133600 167133600 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:167133600C>T ENST00000409435.1 - 15 2766 c.2767G>A c.(2767-2769)Gtg>Atg p.V923M AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Missense_Mutation_p.V912M|SCN9A_ENST00000303354.6_Missense_Mutation_p.V924M|SCN9A_ENST00000375387.4_Missense_Mutation_p.V924M Q15858 SCN9A_HUMAN sodium channel, voltage-gated, type IX, alpha subunit 108 Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909) CCACACAGCACGCGGAACACA 0.478000 0 SO:0001583 missense ENST00000409435.1 1 1 hg19 CCDS46441.1 . . . . . . . . . . C 26.1 4.703467 0.88924 . . ENSG00000169432 ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435 D;D;D;D 0.98602 -5.02;-5.02;-5.02;-5.02 5.65 5.65 0.86999 . 0.000000 0.64402 D 0.000013 D 0.98620 0.9538 L 0.55834 1.745 0.58432 D 0.999994 D 0.89917 1.0 D 0.81914 0.995 D 0.99865 1.1088 10 0.87932 D 0 . 20.096 0.97843 0.0:1.0:0.0:0.0 . 912 E7EUN6 . M 912;924;924;923 ENSP00000386306:V912M;ENSP00000364536:V924M;ENSP00000304748:V924M;ENSP00000386330:V923M ENSP00000304748:V924M V - 1 0 SCN9A 166841846 1.000000 0.71417 0.968000 0.41197 0.996000 0.88848 7.715000 0.84713 2.819000 0.97034 0.650000 0.86243 GTG TCGA-S4-A8RM-01A-11D-A377-08 SCN9A-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000333639.1 1 0 0 43 688 0 130 0 8.013086e-02 1 7 0 130 2 0 0 0 0 0 2 1 1.000000 41 669 0 152 2 0 0 0 0 130 2 -7.602644 1 1 121406 3 39 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.180000 1.200000e-01 0.240000 0.180000 0.187425 0.180000 0 1.500000e-01 0.210000 COL5A2 1290 broad.mit.edu 37 2 189904090 189904090 + Missense_Mutation SNP T T G TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 T G T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:189904090T>G ENST00000374866.3 - 51 4107 c.3833A>C c.(3832-3834)cAg>cCg p.Q1278P NM_000393.3 NP_000384.2 P05997 CO5A2_HUMAN collagen, type V, alpha 2 95 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127) GGTTTCAATCTGACTACTGAG 0.522000 0 SO:0001583 missense ENST00000374866.3 1 1 hg19 CCDS33350.1 . . . . . . . . . . T 19.38 3.817476 0.70912 . . ENSG00000204262 ENST00000374866;ENST00000452536 D 0.83914 -1.78 5.28 5.28 0.74379 Fibrillar collagen, C-terminal (2); 0.000000 0.43747 D 0.000537 D 0.91781 0.7400 M 0.90369 3.11 0.80722 D 1 D;D 0.61697 0.99;0.99 D;D 0.70487 0.969;0.969 D 0.91360 0.5111 10 0.27082 T 0.32 . 15.1969 0.73100 0.0:0.0:0.0:1.0 . 918;1278 Q5PR22;P05997 .;CO5A2_HUMAN P 1278;918 ENSP00000364000:Q1278P ENSP00000364000:Q1278P Q - 2 0 COL5A2 189612335 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.977000 0.88081 1.983000 0.57843 0.533000 0.62120 CAG TCGA-S4-A8RM-01A-11D-A377-08 COL5A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313523.1 1 0 1 111 248 0 52 0 1 0 139 0 52 2 0 0 0 0 0 2 1 1.000000 109 246 0 51 2 0 0 0 0 52 2 -20.000000 1 1 0 0 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.960000 8.100000e-01 1.000000 1.000000 0.950781 0.960000 1 8.800000e-01 1.000000 HDAC4 9759 broad.mit.edu 37 2 239975284 239975284 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:239975284G>A ENST00000345617.3 - 26 3878 c.3087C>T c.(3085-3087)cgC>cgT p.R1029R HDAC4_ENST00000543185.1_Silent_p.R613R NM_006037.3 NP_006028.2 P56524 HDAC4_HUMAN histone deacetylase 4 62 all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159) GCTGCAGGCAGCGCCAGTACT 0.627000 0 SO:0001819 synonymous_variant ENST00000345617.3 1 1 hg19 CCDS2529.1 . . . . . . . . . . G 7.965 0.747822 0.15710 . . ENSG00000068024 ENST00000430200 . . . 4.38 2.12 0.27331 . . . . . T 0.53190 0.1781 . . . 0.80722 D 1 . . . . . . T 0.46105 -0.9215 4 . . . . 6.304 0.21129 0.3473:0.0:0.6527:0.0 . . . . V 120 . . A - 2 0 HDAC4 239640221 1.000000 0.71417 1.000000 0.80357 0.767000 0.43475 1.786000 0.38694 0.972000 0.38314 -0.142000 0.14014 GCT TCGA-S4-A8RM-01A-11D-A377-08 HDAC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257174.2 1 0 1 26 79 0 20 0 4.687787e-01 1 5 0 20 2 0 0 0 0 0 2 1 1.000000 26 79 0 20 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.770000 5.300000e-01 1.000000 1.000000 0.780974 0.770000 0 6.400000e-01 0.910000 NRXN1 9378 broad.mit.edu 37 2 51254893 51254893 + Silent SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:51254893C>T ENST00000406316.2 - 2 1995 c.519G>A c.(517-519)tcG>tcA p.S173S NRXN1_ENST00000405581.1_Silent_p.S173S|NRXN1_ENST00000406859.3_Silent_p.S173S|NRXN1_ENST00000404971.1_Silent_p.S173S|NRXN1_ENST00000401669.2_Silent_p.S173S|NRXN1_ENST00000402717.3_Silent_p.S173S|NRXN1_ENST00000405472.3_Silent_p.S173S NM_004801.4 NP_004792.1 Q9ULB1 NRX1A_HUMAN neurexin 1 58 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192) Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116) GCTCCCTCACCGAGGCCAGGG 0.672000 0 SO:0001819 synonymous_variant ENST00000406316.2 1 1 hg19 CCDS54360.1 TCGA-S4-A8RM-01A-11D-A377-08 NRXN1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000325291.2 1 0 0 35 69 0 19 0 0 0 1 0 19 2 0 0 0 0 0 2 1 1.000000 33 67 0 18 2 0 0 0 0 19 2 -20.000000 1 1 0 0 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.990000 7.800000e-01 1.000000 1.000000 0.967091 0.990000 1 9.000000e-01 1.000000 INPP4A 3631 broad.mit.edu 37 2 99163080 99163080 + Silent SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr2:99163080G>A ENST00000523221.1 + 11 1086 c.1086G>A c.(1084-1086)gcG>gcA p.A362A INPP4A_ENST00000545415.1_Silent_p.A362A|INPP4A_ENST00000409851.3_Silent_p.A362A|INPP4A_ENST00000409540.3_Silent_p.A362A|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Silent_p.A362A|INPP4A_ENST00000074304.5_Silent_p.A362A Q96PE3 INP4A_HUMAN inositol polyphosphate-4-phosphatase, type I, 107kDa 43 CCATTGGGGCGCCAGCAGCAC 0.493000 0 SO:0001819 synonymous_variant ENST00000523221.1 0 1 hg19 CCDS46369.1 TCGA-S4-A8RM-01A-11D-A377-08 INPP4A-009 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000376095.1 0 0 0 4 236 0 26 0 3.212255e-02 0 12 0 26 2 0 0 0 0 0 2 1 0.886131 4 232 0 26 2 0 0 0 0 26 2 -2.894204 1 1 120882 7 37 1 0 0 0 2.007309 0 0.640000 1.980000 0.640000 0.050000 1.000000e-02 0.130000 0.060000 0.064301 0.050000 0 3.000000e-02 0.090000 CD86 942 broad.mit.edu 37 3 121822548 121822548 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr3:121822548G>A ENST00000330540.2 + 3 370 c.254G>A c.(253-255)cGc>cAc p.R85H CD86_ENST00000264468.5_Intron|CD86_ENST00000493101.1_Intron|CD86_ENST00000469710.1_Missense_Mutation_p.R3H|CD86_ENST00000393627.2_Missense_Mutation_p.R79H NM_175862.4 NP_787058 P42081 CD86_HUMAN CD86 molecule 23 Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681) TATATGGGCCGCACAAGTTTT 0.423000 GBM(67;1379 1389 36064 39806) 0 SO:0001583 missense ENST00000330540.2 0 1 hg19 CCDS3009.1 . . . . . . . . . . G 25.3 4.619268 0.87460 . . ENSG00000114013 ENST00000469710;ENST00000330540;ENST00000482356;ENST00000393627 T;T;T;T 0.72505 1.2;-0.66;-0.66;-0.66 5.54 5.54 0.83059 Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1); 0.000000 0.64402 D 0.000016 D 0.87414 0.6171 M 0.93106 3.38 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.89572 0.3814 10 0.87932 D 0 -18.8448 14.8575 0.70351 0.0:0.0:1.0:0.0 . 85 P42081 CD86_HUMAN H 3;85;79;79 ENSP00000418988:R3H;ENSP00000332049:R85H;ENSP00000419116:R79H;ENSP00000377248:R79H ENSP00000332049:R85H R + 2 0 CD86 123305238 0.999000 0.42202 0.958000 0.39756 0.915000 0.54546 4.887000 0.63156 2.884000 0.98904 0.655000 0.94253 CGC TCGA-S4-A8RM-01A-11D-A377-08 CD86-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000355671.1 0 0 0 6 766 1 152 0 1.003833e-02 0 16 1 152 2 0 7.103134e-01 0 1338 1 710 9 0 0.009939 7 756 1 152 18 0 0 0 1 152 2 -1.804410 0 1 0 0 1 0 0 0 2.015211 0 0.640000 1.980000 0.640000 0.020000 0 0.050000 0.020000 0.027051 0.020000 0 0 0.040000 SIAH2 6478 broad.mit.edu 37 3 150460176 150460176 + Missense_Mutation SNP G G C TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr3:150460176G>C ENST00000312960.3 - 2 1254 c.727C>G c.(727-729)Cag>Gag p.Q243E NM_005067.5 NP_005058.3 O43255 SIAH2_HUMAN siah E3 ubiquitin protein ligase 2 16 LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066) AAAAACTGCTGGTGGCCTTCG 0.527000 0 SO:0001583 missense ENST00000312960.3 1 1 hg19 CCDS3152.1 . . . . . . . . . . G 23.1 4.372610 0.82573 . . ENSG00000181788 ENST00000312960 T 0.25749 1.78 5.67 4.79 0.61399 TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1); 0.000000 0.85682 D 0.000000 T 0.36799 0.0980 M 0.83603 2.65 0.54753 D 0.999986 B 0.27450 0.179 B 0.32805 0.153 T 0.19418 -1.0306 10 0.25106 T 0.35 . 15.8794 0.79193 0.0:0.0:0.8633:0.1367 . 243 O43255 SIAH2_HUMAN E 243 ENSP00000322457:Q243E ENSP00000322457:Q243E Q - 1 0 SIAH2 151942866 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.848000 0.99507 1.349000 0.45751 0.591000 0.81541 CAG TCGA-S4-A8RM-01A-11D-A377-08 SIAH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357697.1 1 0 1 103 200 0 57 1 1 37 38 0 57 2 0 0 0 0 0 2 1 1.000000 103 198 0 57 2 0 0 0 0 57 2 -11.521760 1 1 0 0 1 0 0 0 2.015211 0 0.640000 1.980000 0.640000 0.990000 8.900000e-01 1.000000 1.000000 0.989100 0.990000 1 9.700000e-01 1.000000 PCDHB7 56129 broad.mit.edu 37 5 140553506 140553506 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr5:140553506G>A ENST00000231137.3 + 1 1264 c.1090G>A c.(1090-1092)Gtc>Atc p.V364I NM_018940.2 NP_061763.1 Q9Y5E2 PCDB7_HUMAN protocadherin beta 7 119 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) ACCCGAGACAGTCGTGGCTGT 0.473000 0 SO:0001583 missense ENST00000231137.3 1 1 hg19 CCDS4249.1 . . . . . . . . . . G 11.86 1.765245 0.31228 . . ENSG00000113212 ENST00000231137;ENST00000543636 T 0.51817 0.69 4.61 3.73 0.42828 Cadherin (3);Cadherin-like (1); . . . . T 0.40979 0.1139 L 0.60845 1.875 0.09310 N 1 B 0.17038 0.02 B 0.20384 0.029 T 0.35475 -0.9787 9 0.41790 T 0.15 . 4.5756 0.12232 0.0834:0.1519:0.6079:0.1567 . 364 Q9Y5E2 PCDB7_HUMAN I 364;147 ENSP00000231137:V364I ENSP00000231137:V364I V + 1 0 PCDHB7 140533690 0.027000 0.19231 0.079000 0.20413 0.449000 0.32228 1.974000 0.40559 1.038000 0.40049 0.650000 0.86243 GTC TCGA-S4-A8RM-01A-11D-A377-08 PCDHB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251803.2 1 0 1 82 150 0 54 0 5.788988e-01 0 5 0 54 2 0 0 0 0 0 2 1 1.000000 81 145 0 52 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.024827 0 0.640000 1.980000 0.641148 0.990000 9.100000e-01 1.000000 1.000000 0.993822 0.990000 1 9.900000e-01 1.000000 FAM153B 202134 broad.mit.edu 37 5 175528575 175528575 + Missense_Mutation SNP C C G TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr5:175528575C>G ENST00000253490.4 + 12 712 c.655C>G c.(655-657)Ctg>Gtg p.L219V FAM153B_ENST00000515817.1_Missense_Mutation_p.L142V|FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000510151.1_Missense_Mutation_p.L142V P0C7A2 F153B_HUMAN family with sequence similarity 153, member B 16 all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164) Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183) CCCAGACACACTGGCCGAACG 0.453000 0 SO:0001583 missense ENST00000253490.4 1 1 hg19 . . . . . . . . . . C 6.823 0.520995 0.13005 . . ENSG00000182230 ENST00000515817;ENST00000253490 . . . 0.607 -1.05 0.10036 . . . . . T 0.20333 0.0489 N 0.19112 0.55 0.09310 N 1 P 0.45594 0.862 P 0.46110 0.504 T 0.13361 -1.0512 7 0.46703 T 0.11 . . . . . 219 P0C7A2 F153B_HUMAN V 142;219 . ENSP00000253490:L219V L + 1 2 FAM153B 175461181 0.007000 0.16637 0.000000 0.03702 0.008000 0.06430 -0.346000 0.07760 -0.368000 0.08040 0.173000 0.16961 CTG TCGA-S4-A8RM-01A-11D-A377-08 FAM153B-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 1 0 1 92 256 0 61 1 9.999978e-01 15 41 0 61 2 0 0 0 0 0 2 1 1.000000 90 254 0 61 2 0 0 0 0 61 2 -20.000000 1 0 0 0 1 1 2 3 2.024827 0 0.640000 1.980000 0.641148 0.820000 6.800000e-01 0.980000 0.830000 0.831287 0.820000 0 7.500000e-01 0.910000 MAK 4117 broad.mit.edu 37 6 10802169 10802169 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr6:10802169C>T ENST00000313243.2 - 8 1169 c.787G>A c.(787-789)Gaa>Aaa p.E263K MAK_ENST00000538030.1_Missense_Mutation_p.E263K|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000536370.1_Missense_Mutation_p.E263K|MAK_ENST00000474039.1_Missense_Mutation_p.E263K|MAK_ENST00000354489.2_Missense_Mutation_p.E263K|RP11-637O19.3_ENST00000480294.1_Intron P20794 MAK_HUMAN male germ cell-associated kinase 22 Breast(50;0.107)|Ovarian(93;0.107) all_hematologic(90;0.117) TTCAACATTTCGGTCATGAGC 0.408000 OREG0017187 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000313243.2 1 1 hg19 CCDS4516.1 . . . . . . . . . . C 26.2 4.710536 0.89112 2.27E-4 4.65E-4 ENSG00000111837 ENST00000313243;ENST00000354489;ENST00000538030;ENST00000536370 T;T;T;T 0.63580 -0.05;-0.05;-0.05;-0.05 5.42 5.42 0.78866 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.146778 0.64402 D 0.000016 T 0.18923 0.0454 N 0.00399 -1.545 0.80722 D 1 B 0.20368 0.044 B 0.23419 0.046 T 0.19386 -1.0307 10 0.29301 T 0.29 . 19.6002 0.95559 0.0:1.0:0.0:0.0 . 263 P20794 MAK_HUMAN K 263 ENSP00000313021:E263K;ENSP00000346484:E263K;ENSP00000442250:E263K;ENSP00000442221:E263K ENSP00000313021:E263K E - 1 0 MAK 10910155 1.000000 0.71417 0.927000 0.36925 0.966000 0.64601 4.566000 0.60843 2.691000 0.91804 0.655000 0.94253 GAA TCGA-S4-A8RM-01A-11D-A377-08 MAK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039841.1 0 0 0 10 328 1 97 0 3.329006e-03 0 3 1 97 2 0 0 0 0 0 2 0 0.328179 10 326 1 97 13 0 0 0 1 97 2 -2.817017 1 1 121412 26 46 1 0 1 1 1.396540 1 0.640000 1.980000 0.480370 0.060000 2.000000e-02 0.110000 0.060000 0.069816 0.060000 0 4.000000e-02 0.090000 RPS6KA2 6196 broad.mit.edu 37 6 166844030 166844030 + Missense_Mutation SNP T T G TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr6:166844030T>G ENST00000265678.4 - 16 1715 c.1492A>C c.(1492-1494)Atc>Ctc p.I498L RPS6KA2_ENST00000481261.2_Missense_Mutation_p.I409L|RPS6KA2_ENST00000405189.3_Missense_Mutation_p.I409L|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.I506L|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.I523L NM_021135.4 NP_066958.2 Q15349 KS6A2_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 2 45 Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105) TGCCGGAGGATGCGGTCCAGG 0.587000 0 SO:0001583 missense ENST00000265678.4 1 1 hg19 CCDS5294.1 . . . . . . . . . . T 14.06 2.422481 0.43020 . . ENSG00000071242 ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189 T;T;T;T;T 0.62788 0.0;0.0;0.0;0.0;0.0 3.63 3.63 0.41609 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.128885 0.50627 D 0.000112 T 0.53818 0.1820 N 0.25031 0.7 0.80722 D 1 B;B;B 0.31989 0.052;0.042;0.35 B;B;P 0.55545 0.413;0.166;0.778 T 0.58657 -0.7598 10 0.33940 T 0.23 . 11.8701 0.52515 0.0:0.0:0.0:1.0 . 523;506;498 F2Z2J1;Q15349-3;Q15349 .;.;KS6A2_HUMAN L 498;523;506;409;409 ENSP00000265678:I498L;ENSP00000422435:I523L;ENSP00000427015:I506L;ENSP00000422484:I409L;ENSP00000386050:I409L ENSP00000265678:I498L I - 1 0 RPS6KA2 166764020 1.000000 0.71417 0.998000 0.56505 0.526000 0.34562 7.272000 0.78516 1.661000 0.50771 0.402000 0.26972 ATC TCGA-S4-A8RM-01A-11D-A377-08 RPS6KA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043075.3 1 0 0 11 174 0 40 0 5.099499e-01 0 27 0 40 2 0 0 0 0 0 2 1 0.998395 10 173 0 40 2 0 0 0 0 40 2 -14.966800 1 1 0 0 1 0 1 1 1.429478 1 0.640000 1.980000 0.480370 0.120000 6.000000e-02 0.220000 0.130000 0.138123 0.120000 0 9.000000e-02 0.170000 SLC17A3 10786 broad.mit.edu 37 6 25845701 25845701 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr6:25845701G>A ENST00000360657.3 - 11 1457 c.1172C>T c.(1171-1173)gCc>gTc p.A391V SLC17A3_ENST00000397060.4_Missense_Mutation_p.A469V|SLC17A3_ENST00000361703.6_Missense_Mutation_p.A391V O00476 NPT4_HUMAN solute carrier family 17 (organic anion transporter), member 3 20 CAGGTTAACGGCAAACAGCAA 0.413000 0 SO:0001583 missense ENST00000360657.3 0 1 hg19 CCDS4566.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 17.73|17.73 3.460762|3.460762 0.63513|0.63513 .|. .|. ENSG00000124564|ENSG00000124564 ENST00000505420;ENST00000397060;ENST00000360657;ENST00000361703|ENST00000481949 T;T;T;T|. 0.58940|. 0.38;0.3;0.3;0.3|. 4.78|4.78 3.91|3.91 0.45181|0.45181 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|. 0.141196|. 0.32533|. N|. 0.005969|. T|T 0.36880|0.36880 0.0983|0.0983 L|L 0.46741|0.46741 1.465|1.465 0.36016|0.36016 D|D 0.838379|0.838379 B;P|. 0.43973|. 0.165;0.823|. B;P|. 0.48089|. 0.081;0.566|. T|T 0.24119|0.24119 -1.0169|-1.0169 10|5 0.48119|. T|. 0.1|. .|. 9.3173|9.3173 0.37941|0.37941 0.1012:0.0:0.8988:0.0|0.1012:0.0:0.8988:0.0 .|. 469;391|. B7Z511;O00476|. .;NPT4_HUMAN|. V|S 22;469;391;391|70 ENSP00000424027:A22V;ENSP00000380250:A469V;ENSP00000353873:A391V;ENSP00000355307:A391V|. ENSP00000353873:A391V|. A|P -|- 2|1 0|0 SLC17A3|SLC17A3 25953680|25953680 0.135000|0.135000 0.22499|0.22499 0.305000|0.305000 0.25099|0.25099 0.036000|0.036000 0.12997|0.12997 1.724000|1.724000 0.38064|0.38064 1.130000|1.130000 0.42092|0.42092 0.591000|0.591000 0.81541|0.81541 GCC|CCG TCGA-S4-A8RM-01A-11D-A377-08 SLC17A3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000040070.2 0 0 0 6 405 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 0.963896 6 400 0 65 2 0 0 0 0 66 2 -2.430920 0 1 0 0 1 0 0 0 1.994505 0 0.640000 1.980000 0.637681 0.040000 1.000000e-02 0.100000 0.040000 0.052561 0.040000 0 2.000000e-02 0.070000 SLC44A4 80736 broad.mit.edu 37 6 31832445 31832445 + Silent SNP C C T rs146889731 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr6:31832445C>T ENST00000229729.6 - 20 2015 c.1995G>A c.(1993-1995)acG>acA p.T665T SLC44A4_ENST00000544672.1_Silent_p.T589T|NEU1_ENST00000375631.4_5'Flank|SLC44A4_ENST00000375562.4_Silent_p.T623T NM_025257.2 NP_079533.2 Q53GD3 CTL4_HUMAN solute carrier family 44, member 4 35 Choline(DB00122) AGAGGAAGAGCGTGTCCACAC 0.522000 0 SO:0001819 synonymous_variant ENST00000229729.6 1 1 hg19 CCDS4724.2 TCGA-S4-A8RM-01A-11D-A377-08 SLC44A4-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076234.3 1 0 1 93 305 0 69 1 1 687 818 0 69 2 0 0 0 0 0 2 1 1.000000 92 300 0 68 2 0 0 0 0 69 2 -20.000000 1 1 121408 1 35 1 0 0 0 1.994505 0 0.640000 1.980000 0.637681 0.720000 5.900000e-01 0.850000 0.720000 0.728635 0.720000 0 6.500000e-01 0.790000 CYP21A2 1589 broad.mit.edu 37 6 32008351 32008351 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr6:32008351C>T ENST00000418967.2 + 8 1266 c.1108C>T c.(1108-1110)Cgg>Tgg p.R370W CYP21A2_ENST00000435122.2_Missense_Mutation_p.R340W NM_000500.7 NP_000491.4 P08686 CP21A_HUMAN cytochrome P450, family 21, subfamily A, polypeptide 2 11 Ketoconazole(DB01026) CCGCACCACACGGCCCAGCAG 0.667000 Melanoma(174;1669 1998 3915 34700 46447) 0 SO:0001583 missense ENST00000418967.2 1 1 hg19 CCDS4735.1 . . . . . . . . . . c 15.70 2.911619 0.52439 . . ENSG00000231852 ENST00000418967;ENST00000435122 T;T 0.80123 -1.34;-1.34 4.75 2.87 0.33458 . 0.508711 0.16495 N 0.211913 D 0.83940 0.5363 M 0.80847 2.515 0.09310 N 0.999998 D;D 0.89917 1.0;1.0 D;D 0.83275 0.986;0.996 T 0.75297 -0.3367 10 0.66056 D 0.02 . 9.7965 0.40737 0.3896:0.6104:0.0:0.0 . 340;370 Q5ST44;Q16874 .;. W 370;340 ENSP00000408860:R370W;ENSP00000415043:R340W ENSP00000408860:R370W R + 1 2 CYP21A2 32116330 0.000000 0.05858 0.073000 0.20177 0.715000 0.41141 0.215000 0.17562 0.656000 0.30886 0.651000 0.88453 CGG TCGA-S4-A8RM-01A-11D-A377-08 CYP21A2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268768.2 0 0 0 37 255 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 36 218 0 50 2 0 0 0 0 44 2 -16.178910 1 1 121070 2 34 1 1 2 3 2.578348 1 0.640000 1.980000 0.719801 0.510000 3.700000e-01 1.000000 0.510000 0.561059 0.510000 0 4.300000e-01 0.630000 SLC35A1 10559 broad.mit.edu 37 6 88216129 88216129 + Silent SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr6:88216129C>T ENST00000369552.4 + 5 564 c.537C>T c.(535-537)ggC>ggT p.G179G SLC35A1_ENST00000369556.3_Silent_p.G179G|SLC35A1_ENST00000544441.1_Silent_p.G45G|C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000464978.1_Intron|SLC35A1_ENST00000369557.5_Intron NM_006416.4 NP_006407.1 P78382 S35A1_HUMAN solute carrier family 35 (CMP-sialic acid transporter), member A1 9 all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575) TAGGGTTTGGCGCTATAGCTA 0.313000 NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932) 0 SO:0001819 synonymous_variant ENST00000369552.4 0 1 hg19 CCDS5010.1 TCGA-S4-A8RM-01A-11D-A377-08 SLC35A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041446.1 0 0 0 5 359 0 89 0 4.128829e-01 0 89 0 89 2 0 0 0 0 0 2 1 0.937048 5 357 0 89 2 0 0 0 0 89 2 -2.180427 0 1 0 0 1 0 1 1 1.396305 1 0.640000 1.980000 0.473068 0.020000 0 0.070000 0.030000 0.034891 0.020000 0 1.000000e-02 0.050000 TMEM176A 55365 broad.mit.edu 37 7 150498695 150498695 + Silent SNP C C A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr7:150498695C>A ENST00000484928.1 + 2 638 c.57C>A c.(55-57)atC>atA p.I19I TMEM176B_ENST00000492607.1_5'Flank|TMEM176A_ENST00000004103.3_Silent_p.I19I|TMEM176B_ENST00000450753.2_5'Flank|TMEM176B_ENST00000326442.5_5'Flank|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000434545.1_5'Flank|TMEM176A_ENST00000461345.1_Intron Q96HP8 T176A_HUMAN transmembrane protein 176A 12 OV - Ovarian serous cystadenocarcinoma(82;0.0121) ACACCCACATCGATGTGCACA 0.657000 0 SO:0001819 synonymous_variant ENST00000484928.1 1 1 hg19 CCDS5909.1 TCGA-S4-A8RM-01A-11D-A377-08 TMEM176A-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350222.1 1 0 1 57 260 0 31 1 1 253 1218 0 31 2 0 0 0 0 0 2 1 1.000000 57 254 0 30 2 0 0 0 0 31 2 -3.414216 1 1 0 0 1 1 2 3 2.628128 1 0.640000 1.980000 0.725944 0.730000 5.700000e-01 0.950000 0.740000 0.747855 0.730000 0 6.500000e-01 0.840000 PTPRN2 5799 broad.mit.edu 37 7 157929382 157929382 + Missense_Mutation SNP C C T rs144837405 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr7:157929382C>T ENST00000389418.4 - 8 1147 c.1138G>A c.(1138-1140)Gga>Aga p.G380R PTPRN2_ENST00000389413.3_Missense_Mutation_p.G380R|PTPRN2_ENST00000409483.1_Missense_Mutation_p.G342R|PTPRN2_ENST00000404321.2_Missense_Mutation_p.G403R|PTPRN2_ENST00000389416.4_Missense_Mutation_p.G363R 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) TCCTGCACTCCGTCATCTGTA 0.448000 0 SO:0001583 missense ENST00000389418.4 1 1 hg19 CCDS5947.1 . . . . . . . . . . C 5.514 0.279739 0.10458 0.0 2.33E-4 ENSG00000155093 ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321 T;T;T;T;T 0.02656 4.21;4.22;4.24;4.23;4.23 4.54 -4.67 0.03319 . . . . . T 0.01156 0.0038 N 0.03608 -0.345 0.09310 N 1 B;B;B;B;B 0.06786 0.001;0.0;0.0;0.0;0.0 B;B;B;B;B 0.04013 0.001;0.0;0.001;0.0;0.0 T 0.49428 -0.8941 9 0.12430 T 0.62 . 6.5936 0.22659 0.0:0.4711:0.1567:0.3722 . 403;342;380;363;380 Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932 .;.;.;.;PTPR2_HUMAN R 342;380;363;380;403 ENSP00000387114:G342R;ENSP00000374064:G380R;ENSP00000374067:G363R;ENSP00000374069:G380R;ENSP00000385464:G403R ENSP00000374064:G380R G - 1 0 PTPRN2 157622143 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -1.284000 0.02793 -0.743000 0.04784 -1.056000 0.02311 GGA TCGA-S4-A8RM-01A-11D-A377-08 PTPRN2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000353214.1 1 0 1 80 524 0 83 1 9.999986e-01 24 101 0 83 2 0 0 0 0 0 2 1 1.000000 80 514 0 83 2 0 0 0 0 83 2 -2.443736 0 1 121412 6 39 1 1 2 3 2.628128 1 0.640000 1.980000 0.725944 0.540000 4.300000e-01 0.680000 0.540000 0.552771 0.540000 0 4.800000e-01 0.610000 PURB 5814 broad.mit.edu 37 7 44924053 44924053 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr7:44924053C>T ENST00000395699.2 - 1 907 c.895G>A c.(895-897)Ggc>Agc p.G299S MIR4657_ENST00000578157.1_RNA|RP4-673M15.1_ENST00000608450.1_RNA NM_033224.3 NP_150093.1 Q96QR8 PURB_HUMAN purine-rich element binding protein B 7 TCGCCGCCGCCGCTGCCCCCA 0.587000 0 SO:0001583 missense ENST00000395699.2 0 1 hg19 CCDS5499.1 . . . . . . . . . . C 15.74 2.923148 0.52653 . . ENSG00000146676 ENST00000395699 T 0.29655 1.56 3.06 3.06 0.35304 . 0.137657 0.27549 U 0.018864 T 0.31104 0.0786 N 0.14661 0.345 0.35690 D 0.81476 D 0.89917 1.0 D 0.65684 0.937 T 0.19063 -1.0317 10 0.16896 T 0.51 . 12.3432 0.55105 0.0:1.0:0.0:0.0 . 299 Q96QR8 PURB_HUMAN S 299 ENSP00000379051:G299S ENSP00000379051:G299S G - 1 0 PURB 44890578 0.980000 0.34600 0.998000 0.56505 0.984000 0.73092 3.212000 0.51145 1.998000 0.58463 0.591000 0.81541 GGC TCGA-S4-A8RM-01A-11D-A377-08 PURB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251332.2 0 0 0 5 704 0 84 1 8.693792e-02 2 54 0 84 2 0 0 0 0 0 2 1 0.937268 5 702 0 83 2 0 0 0 0 84 2 -1.955223 0 0 0 0 1 1 2 3 2.612313 1 0.640000 1.980000 0.724602 0.020000 0 1.000000 0.030000 0.062338 0.020000 0 1.000000e-02 0.050000 SEMA3E 9723 broad.mit.edu 37 7 83014659 83014659 + Missense_Mutation SNP G G A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr7:83014659G>A ENST00000307792.3 - 16 2293 c.1826C>T c.(1825-1827)gCg>gTg p.A609V SEMA3E_ENST00000427262.1_Missense_Mutation_p.A549V NM_012431.2 NP_036563.1 O15041 SEM3E_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E 51 Medulloblastoma(109;0.109) GATAACTTTCGCTTGTAAAGA 0.398000 0 SO:0001583 missense ENST00000307792.3 0 1 hg19 CCDS34674.1 . . . . . . . . . . G 35 5.430525 0.96150 . . ENSG00000170381 ENST00000307792;ENST00000427262;ENST00000541514 T;T 0.19394 2.15;2.15 5.54 5.54 0.83059 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.49440 0.1557 M 0.76838 2.35 0.80722 D 1 D 0.76494 0.999 D 0.68039 0.955 T 0.49854 -0.8895 10 0.59425 D 0.04 . 19.4854 0.95027 0.0:0.0:1.0:0.0 . 609 O15041 SEM3E_HUMAN V 609;549;609 ENSP00000303212:A609V;ENSP00000405052:A549V ENSP00000303212:A609V A - 2 0 SEMA3E 82852595 1.000000 0.71417 0.998000 0.56505 0.994000 0.84299 9.255000 0.95524 2.597000 0.87782 0.650000 0.86243 GCG TCGA-S4-A8RM-01A-11D-A377-08 SEMA3E-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336606.1 0 0 0 8 803 0 111 0 2.407403e-02 1 20 0 111 2 0 0 0 0 0 2 1 0.988671 8 791 0 110 2 0 0 0 0 111 2 -2.488768 0 1 121410 2 37 1 1 2 3 2.612313 1 0.640000 1.980000 0.724602 0.030000 0 1.000000 0.030000 0.070787 0.030000 0 1.000000e-02 0.070000 CYP3A43 64816 broad.mit.edu 37 7 99454485 99454485 + Silent SNP C C A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr7:99454485C>A ENST00000354829.2 + 9 931 c.828C>A c.(826-828)atC>atA p.I276I CYP3A43_ENST00000222382.5_Silent_p.I276I|CYP3A43_ENST00000417625.1_Silent_p.I166I|CYP3A43_ENST00000342499.4_Silent_p.I136I|CYP3A43_ENST00000415413.1_Silent_p.I65I|CYP3A43_ENST00000312017.5_Silent_p.I276I|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000444905.1_Silent_p.I23I NM_022820.3|NM_057095.1 NP_073731.1|NP_476436.1 Q9HB55 CP343_HUMAN cytochrome P450, family 3, subfamily A, polypeptide 43 19 Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323) Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943) AACAGATGATCGACTCCCAGA 0.433000 0 SO:0001819 synonymous_variant ENST00000354829.2 1 1 hg19 CCDS5676.1 TCGA-S4-A8RM-01A-11D-A377-08 CYP3A43-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000344379.1 1 0 0 50 1068 0 147 0 0 0 1 0 147 2 0 0 0 0 0 2 1 1.000000 50 1061 0 147 2 0 0 0 0 147 2 -4.878029 1 1 0 0 1 1 2 3 2.612313 1 0.640000 1.980000 0.724602 0.180000 1.200000e-01 1.000000 0.180000 0.209381 0.180000 0 1.500000e-01 0.220000 VPS13B 157680 broad.mit.edu 37 8 100493941 100493941 + Missense_Mutation SNP C C A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr8:100493941C>A ENST00000358544.2 + 25 3892 c.3781C>A c.(3781-3783)Cct>Act p.P1261T VPS13B_ENST00000357162.2_Missense_Mutation_p.P1261T|VPS13B_ENST00000395996.1_Missense_Mutation_p.P1261T NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) AGGGCCTGTTCCTACTTCTCC 0.468000 Colon(161;2205 2542 7338 31318) 0 SO:0001583 missense ENST00000358544.2 1 1 hg19 CCDS6280.1 . . . . . . . . . . C 18.16 3.562912 0.65538 . . ENSG00000132549 ENST00000357162;ENST00000358544;ENST00000395996 T;T;T 0.64260 -0.09;-0.09;-0.09 5.08 5.08 0.68730 . 0.060752 0.64402 D 0.000004 T 0.77054 0.4074 M 0.63843 1.955 0.54753 D 0.999983 D;D;D;P 0.76494 0.994;0.999;0.998;0.669 D;D;P;B 0.83275 0.991;0.996;0.863;0.264 T 0.75001 -0.3471 10 0.33940 T 0.23 . 18.4942 0.90858 0.0:1.0:0.0:0.0 . 1260;1261;1261;1261 Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3 .;.;VP13B_HUMAN;. T 1261 ENSP00000349685:P1261T;ENSP00000351346:P1261T;ENSP00000379318:P1261T ENSP00000349685:P1261T P + 1 0 VPS13B 100563117 1.000000 0.71417 0.778000 0.31720 0.391000 0.30476 6.906000 0.75719 2.365000 0.80145 0.655000 0.94253 CCT TCGA-S4-A8RM-01A-11D-A377-08 VPS13B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000277138.1 0 0 0 15 462 0 79 0 6.097650e-02 0 12 0 79 2 0 0 0 0 0 2 1 0.999869 15 459 0 79 2 0 0 0 0 79 2 -3.582072 1 1 0 0 1 2 2 4 2.124784 0 0.640000 1.980000 0.659607 0.100000 5.000000e-02 1.000000 0.110000 0.174982 0.100000 0 7.000000e-02 0.150000 CSMD3 114788 broad.mit.edu 37 8 113277800 113277800 + Silent SNP T T A TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr8:113277800T>A ENST00000297405.5 - 60 9772 c.9528A>T c.(9526-9528)ccA>ccT p.P3176P CSMD3_ENST00000352409.3_Silent_p.P3106P|CSMD3_ENST00000455883.2_Silent_p.P3007P|CSMD3_ENST00000343508.3_Silent_p.P3136P NM_198123.1 NP_937756.1 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 646 CTGGTATACCTGGGTCTCCAC 0.418000 HNSCC(6;0.00088)|TCGA Ovarian(7;0.080) 0 SO:0001819 synonymous_variant ENST00000297405.5 1 1 hg19 CCDS6315.1 TCGA-S4-A8RM-01A-11D-A377-08 CSMD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347141.1 1 0 1 133 371 0 83 0 0 0 1 0 83 2 0 0 0 0 0 2 1 1.000000 133 367 0 82 2 0 0 0 0 83 2 -20.000000 1 1 0 0 1 2 2 4 2.124784 0 0.640000 1.980000 0.659607 0.870000 7.400000e-01 1.000000 0.870000 0.882745 0.870000 1 8.000000e-01 0.960000 SCARA5 286133 broad.mit.edu 37 8 27824044 27824044 + Missense_Mutation SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr8:27824044C>T ENST00000354914.3 - 3 613 c.128G>A c.(127-129)cGg>cAg p.R43Q SCARA5_ENST00000524352.1_Missense_Mutation_p.R43Q|SCARA5_ENST00000380385.2_Missense_Mutation_p.R43Q|SCARA5_ENST00000518030.1_Intron|SCARA5_ENST00000301906.4_Intron NM_173833.5 NP_776194.2 Q6ZMJ2 SCAR5_HUMAN scavenger receptor class A, member 5 18 Ovarian(32;0.0218) GCTTGCCCGCCGTTTGTGACA 0.522000 0 SO:0001583 missense ENST00000354914.3 0 1 hg19 CCDS6064.1 . . . . . . . . . . C 18.12 3.554049 0.65425 . . ENSG00000168079 ENST00000354914;ENST00000380385;ENST00000524352 D;D;D 0.92299 -2.56;-2.5;-3.01 5.93 5.93 0.95920 . 0.128700 0.49305 D 0.000152 D 0.91043 0.7182 M 0.62723 1.935 0.80722 D 1 P;D;P 0.61697 0.927;0.99;0.949 P;P;B 0.44359 0.447;0.447;0.261 D 0.89580 0.3820 10 0.30078 T 0.28 . 15.8364 0.78801 0.0:1.0:0.0:0.0 . 43;43;43 Q6ZMJ2-4;Q6ZMJ2-2;Q6ZMJ2 .;.;SCAR5_HUMAN Q 43 ENSP00000346990:R43Q;ENSP00000369746:R43Q;ENSP00000428663:R43Q ENSP00000346990:R43Q R - 2 0 SCARA5 27879963 0.312000 0.24545 0.847000 0.33407 0.982000 0.71751 1.699000 0.37804 2.814000 0.96858 0.563000 0.77884 CGG TCGA-S4-A8RM-01A-11D-A377-08 SCARA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255223.2 0 0 0 5 582 0 86 0 1.176250e-03 0 5 0 86 2 0 0 0 0 0 2 1 0.934033 6 568 0 81 2 0 0 0 0 86 2 -2.302391 0 1 121412 3 41 1 2 2 4 2.124784 0 0.640000 1.980000 0.659607 0.020000 0 1.000000 0.020000 0.103069 0.020000 0 1.000000e-02 0.060000 ADAMTSL1 92949 broad.mit.edu 37 9 18706844 18706844 + Silent SNP C C T TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chr9:18706844C>T ENST00000380548.4 + 14 2013 c.1674C>T c.(1672-1674)tcC>tcT p.S558S ADAMTSL1_ENST00000276935.6_Silent_p.S558S NM_001040272.5 NP_001035362.3 Q8N6G6 ATL1_HUMAN ADAMTS-like 1 42 TCTCTCAGTCCGTGGCTGACC 0.602000 0 SO:0001819 synonymous_variant ENST00000380548.4 1 1 hg19 CCDS47954.1 TCGA-S4-A8RM-01A-11D-A377-08 ADAMTSL1-012 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401206.1 1 0 1 34 77 0 17 0 2.304935e-01 0 3 0 17 2 0 0 0 0 0 2 1 1.000000 35 76 0 16 2 0 0 0 0 17 2 -20.000000 1 1 121408 2 34 1 0 1 1 2.001361 1 0.640000 1.980000 0.470588 0.640000 4.700000e-01 0.820000 0.640000 0.651522 0.640000 0 5.500000e-01 0.740000 FOXR2 139628 broad.mit.edu 37 X 55650498 55650498 + Silent SNP A A G TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chrX:55650498A>G ENST00000339140.3 + 1 666 c.354A>G c.(352-354)gaA>gaG p.E118E NM_198451.3 NP_940853.1 Q6PJQ5 FOXR2_HUMAN forkhead box R2 19 AAAAAGACGAAGGGTCTAACT 0.527000 0 SO:0001819 synonymous_variant ENST00000339140.3 1 1 hg19 CCDS35308.1 TCGA-S4-A8RM-01A-11D-A377-08 FOXR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056877.2 1 0 1 92 60 0 27 0 0 0 0 27 2 0 0 0 0 0 2 1 1.000000 91 60 0 27 2 0 0 0 0 27 2 -20.000000 1 1 0 0 1 0 1 1 0.640000 1.980000 0.640000 0.920000 8.000000e-01 1.000000 0.940000 0.923310 0.920000 1 8.600000e-01 0.970000 KLHL4 56062 broad.mit.edu 37 X 86887279 86887279 + Missense_Mutation SNP G G A rs146910003 TCGA-S4-A8RM-01A-11D-A377-08 TCGA-S4-A8RM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a f9ea46fe-0a5b-46ab-a347-8fa786bdea4b g.chrX:86887279G>A ENST00000373119.4 + 7 1539 c.1394G>A c.(1393-1395)cGt>cAt p.R465H KLHL4_ENST00000373114.4_Missense_Mutation_p.R465H NM_019117.4 NP_061990.2 Q9C0H6 KLHL4_HUMAN kelch-like family member 4 p.R465H(1) 67 ATGAATGGCCGTAGGCTTCAA 0.388000 1 Substitution - Missense(1) SO:0001583 missense ENST00000373119.4 1 1 hg19 CCDS14457.1 . . . . . . . . . . G 21.5 4.165472 0.78339 2.61E-4 0.0 ENSG00000102271 ENST00000373119;ENST00000373114 T;T 0.66815 -0.23;-0.23 5.32 3.55 0.40652 Galactose oxidase, beta-propeller (1); 0.059533 0.64402 N 0.000005 T 0.65365 0.2684 M 0.69358 2.11 0.58432 D 0.999997 P;D 0.55605 0.692;0.972 B;P 0.44860 0.344;0.462 T 0.66396 -0.5934 10 0.87932 D 0 . 10.0307 0.42099 0.1676:0.0:0.8324:0.0 . 465;465 Q9C0H6;Q9C0H6-2 KLHL4_HUMAN;. H 465 ENSP00000362211:R465H;ENSP00000362206:R465H ENSP00000362206:R465H R + 2 0 KLHL4 86773935 1.000000 0.71417 0.760000 0.31359 0.976000 0.68499 6.184000 0.72008 0.448000 0.26722 0.506000 0.49869 CGT TCGA-S4-A8RM-01A-11D-A377-08 KLHL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057413.1 1 0 1 108 73 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 1.000000 108 72 0 30 2 0 0 0 0 31 2 -20.000000 1 1 121404 3 40 1 0 1 1 0.640000 1.980000 0.640000 0.910000 8.000000e-01 1.000000 0.930000 0.917623 0.910000 1 8.600000e-01 0.970000