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 PRC1 9055 broad.mit.edu 37 15 91527307 91527308 + Frame_Shift_Ins INS - - T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 - T - - Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr15:91527307_91527308insT ENST00000361188.5 - 3 1418_1419 c.207_208insA c.(205-210)atatccfs p.S70fs PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000394249.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000361919.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000442656.2_Intron|PRC1_ENST00000556129.1_5'UTR protein regulator of cytokinesis 1 25 Lung NSC(78;0.0987)|all_lung(78;0.175) TGACAGACGGATATGCTTTTGA 0.490000 0 SO:0001589 frameshift_variant ENST00000361188.5 0 1 hg19 CCDS45352.1 TCGA-IB-A7LX-01A-12D-A36O-08 PRC1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414760.1 1 0 0 397 1227 0 362 0 9.992689e-01 0 35 0 362 2 0 0 0 0 0 0 1 1.000000 404 1221 0 354 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 2 4 6 2.035251 1 0.550000 3.150000 0.667160 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 BDP1 55814 broad.mit.edu 37 5 70751780 70751798 + Frame_Shift_Del DEL AATCCCCAGCGTGGACGGG AATCCCCAGCGTGGACGGG - rs3748042 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:70751780_70751798delAATCCCCAGCGTGGACGGG ENST00000358731.4 + 1 339_357 c.76_94delAATCCCCAGCGTGGACGGG c.(76-96)aatccccagcgtggacgggagfs p.NPQRGRE26fs BDP1_ENST00000380675.2_5'UTR NM_018429.2 NP_060899.2 A6H8Y1 BDP1_HUMAN B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 72 Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198) CACAGCTTCCAATCCCCAGCGTGGACGGGAGTCTCCCAG 0.680000 0 SO:0001589 frameshift_variant ENST00000358731.4 0 1 hg19 CCDS43328.1 TCGA-IB-A7LX-01A-12D-A36O-08 BDP1-016 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000374681.2 1 0 0 14 104 0 32 0 4.498035e-02 0 3 0 32 2 0 0 0 0 0 0 1 0.699014 17 107 1 33 13 0 0 0 0 0 0 -19.996320 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.560000 0.320000 0.870000 0.550000 0.575410 0.560000 0 4.300000e-01 7.100000e-01 HIF1AN 55662 broad.mit.edu 37 10 102296374 102296374 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr10:102296374C>A ENST00000299163.6 + 2 484 c.384C>A c.(382-384)ttC>ttA p.F128L HIF1AN_ENST00000528044.1_3'UTR NM_017902.2 NP_060372.2 Q9NWT6 HIF1N_HUMAN hypoxia inducible factor 1, alpha subunit inhibitor 10 Colorectal(252;0.234) TTCATGAGTTCGTTGAGAAAC 0.418000 0 SO:0001583 missense ENST00000299163.6 1 0 hg19 CCDS7498.1 . . . . . . . . . . C 24.1 4.497411 0.85069 . . ENSG00000166135 ENST00000533589;ENST00000299163;ENST00000442724 T;T 0.75589 -0.95;-0.95 5.6 -3.81 0.04294 . 3.236230 0.00682 N 0.000698 D 0.83348 0.5235 L 0.57130 1.785 0.58432 D 0.999997 D 0.89917 1.0 D 0.91635 0.999 T 0.72711 -0.4211 10 0.42905 T 0.14 -26.9035 12.1375 0.53979 0.0:0.3619:0.0:0.6381 . 128 Q9NWT6 HIF1N_HUMAN L 21;128;161 ENSP00000433360:F21L;ENSP00000299163:F128L ENSP00000299163:F128L F + 3 2 HIF1AN 102286364 1.000000 0.71417 0.931000 0.37212 0.916000 0.54674 1.676000 0.37565 -0.977000 0.03537 -1.154000 0.01816 TTC TCGA-IB-A7LX-01A-12D-A36O-08 HIF1AN-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049865.5 1 0 0 13 375 0 98 0 5.557056e-01 0 53 0 98 2 0 0 0 0 0 2 1 0.999477 13 366 0 97 2 0 0 0 0 98 2 -3.023347 1 1 0 0 1 2 2 4 2.372051 1 0.550000 3.150000 0.709677 0.190000 0.090000 0.310000 0.200000 0.202123 0.190000 0 1.400000e-01 2.500000e-01 DHX32 55760 broad.mit.edu 37 10 127569154 127569154 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr10:127569154G>T ENST00000284690.3 - 1 730 c.240C>A c.(238-240)atC>atA p.I80I DHX32_ENST00000284688.6_Silent_p.I80I NM_018180.2 NP_060650.2 Q7L7V1 DHX32_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 32 29 all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936) AAACAATCACGATTTGATTTT 0.318000 0 SO:0001819 synonymous_variant ENST00000284690.3 1 0 hg19 CCDS7652.1 TCGA-IB-A7LX-01A-12D-A36O-08 DHX32-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050945.2 1 0 0 13 325 0 84 0 8.589719e-01 0 90 0 84 2 0 0 0 0 0 2 1 0.999502 13 319 0 83 2 0 0 0 0 84 2 -3.805459 1 1 0 0 1 2 2 4 2.357296 1 0.550000 3.150000 0.709677 0.220000 0.110000 0.360000 0.210000 0.231810 0.220000 0 1.600000e-01 2.900000e-01 GPR158 57512 broad.mit.edu 37 10 25701403 25701403 + Splice_Site SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr10:25701403G>T ENST00000376351.3 + 4 1694 c.e4+1 NM_020752.2 NP_065803.2 Q5T848 GP158_HUMAN G protein-coupled receptor 158 119 CAAAGCAAAGGTAAACCCAGG 0.433000 0 SO:0001630 splice_region_variant ENST00000376351.3 1 1 hg19 CCDS31166.1 . . . . . . . . . . G 29.4 4.999869 0.93227 . . ENSG00000151025 ENST00000376351 . . . 6.16 6.16 0.99307 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.8598 0.99761 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . GPR158 25741409 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.252000 0.95491 2.937000 0.99478 0.650000 0.86243 . TCGA-IB-A7LX-01A-12D-A36O-08 GPR158-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047248.2 1 0 0 46 312 0 123 0 0 0 0 123 2 0 0 0 0 0 2 1 1.000000 44 299 0 122 2 0 0 0 0 123 2 -20.000000 1 1 0 0 1 1 2 3 1.868416 1 0.550000 3.150000 0.647059 0.590000 0.440000 0.760000 0.600000 0.604385 0.590000 0 5.100000e-01 6.800000e-01 WAC 51322 broad.mit.edu 37 10 28878735 28878735 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr10:28878735G>T ENST00000354911.4 + 5 613 c.452G>T c.(451-453)cGa>cTa p.R151L WAC_ENST00000347934.4_Missense_Mutation_p.R151L|WAC_ENST00000375664.4_Missense_Mutation_p.R106L|WAC_ENST00000375646.1_Missense_Mutation_p.R106L|WAC_ENST00000428935.1_Missense_Mutation_p.R106L NM_016628.4 NP_057712.2 Q9BTA9 WAC_HUMAN WW domain containing adaptor with coiled-coil 32 TACAATTGTCGAACAGAAGTT 0.318000 0 SO:0001583 missense ENST00000354911.4 1 0 hg19 CCDS7159.1 . . . . . . . . . . G 31 5.081695 0.94050 . . ENSG00000095787 ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911;ENST00000428935;ENST00000420266;ENST00000424454;ENST00000538000;ENST00000442148;ENST00000414108 D;D;D;D;D;D;D;D 0.82255 -1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59 5.24 4.33 0.51752 WW/Rsp5/WWP (6); 0.000000 0.85682 D 0.000000 T 0.79009 0.4374 N 0.20304 0.555 0.80722 D 1 P;B;P 0.49447 0.811;0.447;0.924 P;B;P 0.49085 0.464;0.245;0.6 T 0.81284 -0.1002 10 0.52906 T 0.07 -5.4856 16.1738 0.81836 0.0:0.1336:0.8664:0.0 . 106;151;151 Q9BTA9-2;Q9BTA9-5;Q9BTA9 .;.;WAC_HUMAN L 106;106;151;151;106;106;106;106;106;106 ENSP00000364816:R106L;ENSP00000364797:R106L;ENSP00000311106:R151L;ENSP00000346986:R151L;ENSP00000399706:R106L;ENSP00000404758:R106L;ENSP00000400848:R106L;ENSP00000415645:R106L ENSP00000311106:R151L R + 2 0 WAC 28918741 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.567000 0.98161 1.315000 0.45114 0.563000 0.77884 CGA TCGA-IB-A7LX-01A-12D-A36O-08 WAC-017 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000047371.1 1 0 0 20 437 0 142 0 9.847569e-01 0 148 0 142 2 0 0 0 0 0 2 1 0.999994 20 426 0 138 2 0 0 0 0 142 2 -3.100219 1 1 0 0 1 1 2 3 1.868416 1 0.550000 3.150000 0.647059 0.200000 0.120000 0.300000 0.210000 0.211863 0.200000 0 1.600000e-01 2.600000e-01 RHOBTB1 9886 broad.mit.edu 37 10 62648097 62648097 + Missense_Mutation SNP G G T rs151278163 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr10:62648097G>T ENST00000337910.5 - 6 1666 c.1329C>A c.(1327-1329)ttC>ttA p.F443L RHOBTB1_ENST00000357917.4_Missense_Mutation_p.F443L NM_001242359.1|NM_014836.4 NP_001229288.1|NP_055651.1 O94844 RHBT1_HUMAN Rho-related BTB domain containing 1 23 Prostate(12;0.0112) TCCTCAAATCGAACATCTCGA 0.463000 0 SO:0001583 missense ENST00000337910.5 1 0 hg19 CCDS7261.1 . . . . . . . . . . G 6.234 0.411291 0.11812 . . ENSG00000072422 ENST00000357917;ENST00000337910 T;T 0.66460 -0.21;-0.21 5.71 2.11 0.27256 BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2); 0.000000 0.85682 D 0.000000 T 0.73505 0.3595 M 0.64567 1.98 0.58432 D 0.999993 D 0.89917 1.0 D 0.97110 1.0 T 0.67639 -0.5619 10 0.16896 T 0.51 . 8.601 0.33745 0.7158:0.0:0.2842:0.0 . 443 O94844 RHBT1_HUMAN L 443 ENSP00000350595:F443L;ENSP00000338671:F443L ENSP00000338671:F443L F - 3 2 RHOBTB1 62318103 1.000000 0.71417 0.993000 0.49108 0.846000 0.48090 2.104000 0.41815 0.115000 0.18071 -0.793000 0.03317 TTC TCGA-IB-A7LX-01A-12D-A36O-08 RHOBTB1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048220.1 1 0 0 18 330 0 80 0 3.159376e-01 0 21 0 80 2 0 0 0 0 0 2 1 0.999982 17 327 0 79 2 0 0 0 0 80 2 -2.919542 1 1 0 0 1 2 2 4 2.372051 1 0.550000 3.150000 0.709677 0.290000 0.170000 0.440000 0.280000 0.305621 0.290000 0 2.300000e-01 3.700000e-01 FAS 355 broad.mit.edu 37 10 90773947 90773947 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr10:90773947C>A ENST00000355740.2 + 9 968 c.748C>A c.(748-750)Cga>Aga p.R250R FAS_ENST00000355279.2_3'UTR|FAS_ENST00000352159.4_3'UTR|FAS_ENST00000357339.2_Silent_p.R229R|RP11-399O19.9_ENST00000562983.1_RNA NM_000043.4|NM_152871.2|NM_152872.2 NP_000034.1|NP_690610.1|NP_690611.1 P49327 FAS_HUMAN Fas cell surface death receptor 18 Colorectal(252;0.0161) Cerulenin(DB01034)|Orlistat(DB01083) AGGCTTTGTTCGAAAGAATGG 0.353000 0 GRCh37 CM961371 FAS M SO:0001819 synonymous_variant ENST00000355740.2 1 0 hg19 CCDS7393.1 TCGA-IB-A7LX-01A-12D-A36O-08 FAS-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049274.3 1 0 0 27 596 0 129 0 6.293041e-01 1 47 0 129 2 0 0 0 0 0 2 1 1.000000 26 592 0 129 2 0 0 0 0 129 2 -3.186713 1 1 121412 1 31 1 2 2 4 2.372051 1 0.550000 3.150000 0.709677 0.240000 0.150000 0.350000 0.240000 0.252349 0.240000 0 1.900000e-01 3.000000e-01 TRIM29 23650 broad.mit.edu 37 11 119993732 119993732 + Silent SNP C C A rs137882673 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:119993732C>A ENST00000341846.5 - 5 1786 c.1365G>T c.(1363-1365)acG>acT p.T455T TRIM29_ENST00000528870.1_5'UTR|TRIM29_ENST00000524816.3_Silent_p.T21T|TRIM29_ENST00000541857.1_Silent_p.T188T|TRIM29_ENST00000529044.1_Silent_p.T194T|TRIM29_ENST00000525887.1_5'Flank NM_012101.3 NP_036233.2 Q14134 TRI29_HUMAN tripartite motif containing 29 30 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) CGAAGCTGTTCGTGTAGTTGT 0.577000 0 SO:0001819 synonymous_variant ENST00000341846.5 1 0 hg19 CCDS8428.1 . . . . . . . . . . C 4.375 0.069135 0.08436 . . ENSG00000137699 ENST00000525327 . . . 4.12 -8.25 0.01025 . . . . . . . . . . . 0.18873 N 0.999985 . . . . . . . . . . . . . . 6.2926 0.21069 0.0942:0.2723:0.4906:0.1429 . . . . X 48 . . E - 1 0 TRIM29 119498942 0.000000 0.05858 0.001000 0.08648 0.690000 0.40134 -3.482000 0.00456 -4.073000 0.00076 -1.707000 0.00718 GAA TCGA-IB-A7LX-01A-12D-A36O-08 TRIM29-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277108.2 1 0 0 14 340 0 123 0 9.999955e-01 0 572 0 123 2 0 0 0 0 0 2 1 0.999743 15 334 0 121 2 0 0 0 0 123 2 -2.740996 1 1 0 0 1 0 2 2 1.608709 1 0.550000 3.150000 0.550000 0.140000 0.070000 0.230000 0.140000 0.152847 0.140000 0 1.000000e-01 1.900000e-01 RPS13 6207 broad.mit.edu 37 11 17097027 17097027 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:17097027G>T ENST00000525634.1 - 4 440 c.295C>A c.(295-297)Cga>Aga p.R99R PIK3C2A_ENST00000531428.1_5'Flank|AC116533.1_ENST00000408395.1_RNA|SNORD14B_ENST00000364533.1_RNA|RPS13_ENST00000526895.1_5'UTR|SNORD14A_ENST00000606526.1_RNA|RPS13_ENST00000228140.2_Silent_p.R99R P62277 RS13_HUMAN ribosomal protein S13 p.R99*(1)|p.R99G(1) 5 AGATGCTTTCGAACAGCAACT 0.353000 2 Substitution - Missense(1)|Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000525634.1 1 0 hg19 CCDS7823.1 TCGA-IB-A7LX-01A-12D-A36O-08 RPS13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387320.2 1 0 0 13 276 0 55 1 1 2 5206 0 55 2 0 0 0 0 0 2 1 0.999545 13 274 0 54 2 0 0 0 0 55 2 -2.993735 1 1 0 0 1 2 5 7 2.287299 1 0.550000 3.150000 0.701740 0.270000 0.140000 1.000000 0.250000 0.429577 0.270000 0 1.900000e-01 1 RAPSN 5913 broad.mit.edu 37 11 47469684 47469684 + Missense_Mutation SNP C C A rs150051760 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:47469684C>A ENST00000298854.2 - 2 424 c.211G>T c.(211-213)Gac>Tac p.D71Y RAPSN_ENST00000352508.3_Missense_Mutation_p.D71Y|RAPSN_ENST00000529341.1_Missense_Mutation_p.D71Y|RAPSN_ENST00000524487.1_Missense_Mutation_p.D71Y NM_005055.4 NP_005046.2 Q13702 RAPSN_HUMAN receptor-associated protein of the synapse 12 CGGGCCGTGTCGATCTGGACC 0.622000 0 SO:0001583 missense ENST00000298854.2 1 0 hg19 CCDS7936.1 . . . . . . . . . . C 17.65 3.442798 0.63067 . . ENSG00000165917 ENST00000298854;ENST00000352508;ENST00000524487;ENST00000529341 D;D;D;D 0.81739 -1.53;-1.53;-1.53;-1.53 4.72 4.72 0.59763 Tetratricopeptide-like helical (1);Rapsyn, myristoylation/linker region, N-terminal (1); 0.047920 0.85682 D 0.000000 D 0.86772 0.6013 L 0.47716 1.5 0.58432 D 0.99999 P;D;D 0.89917 0.468;0.996;1.0 B;D;D 0.75484 0.339;0.92;0.986 D 0.87824 0.2640 10 0.59425 D 0.04 -53.4394 18.0701 0.89403 0.0:1.0:0.0:0.0 . 71;71;71 E9PK11;Q13702-2;Q13702 .;.;RAPSN_HUMAN Y 71 ENSP00000298854:D71Y;ENSP00000298853:D71Y;ENSP00000435551:D71Y;ENSP00000431732:D71Y ENSP00000298854:D71Y D - 1 0 RAPSN 47426260 1.000000 0.71417 0.998000 0.56505 0.691000 0.40173 5.569000 0.67391 2.334000 0.79466 0.557000 0.71058 GAC TCGA-IB-A7LX-01A-12D-A36O-08 RAPSN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391726.1 1 0 0 7 129 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 0.979399 7 125 0 44 2 0 0 0 0 44 2 -10.377630 1 0 0 0 1 2 6 8 2.128606 1 0.550000 3.150000 0.681416 0.300000 0.120000 1.000000 0.270000 0.422891 0.300000 0 2.000000e-01 1 OR4C15 81309 broad.mit.edu 37 11 55322649 55322649 + Silent SNP T T A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:55322649T>A ENST00000314644.2 + 1 867 c.867T>A c.(865-867)gcT>gcA p.A289A NM_001001920.1 NP_001001920.1 Q8NGM1 OR4CF_HUMAN olfactory receptor, family 4, subfamily C, member 15 56 GCTGGAAAGCTCTCTCCACCT 0.438000 HNSCC(20;0.049) 0 SO:0001819 synonymous_variant ENST00000314644.2 1 1 hg19 CCDS31501.1 TCGA-IB-A7LX-01A-12D-A36O-08 OR4C15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391164.1 1 0 1 202 276 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 204 273 0 146 2 0 0 0 0 147 2 -20.000000 1 0 0 0 1 0.550000 3.150000 0 0 OR4C15 81309 broad.mit.edu 37 11 55322650 55322650 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:55322650C>A ENST00000314644.2 + 1 868 c.868C>A c.(868-870)Ctc>Atc p.L290I NM_001001920.1 NP_001001920.1 Q8NGM1 OR4CF_HUMAN olfactory receptor, family 4, subfamily C, member 15 56 CTGGAAAGCTCTCTCCACCTG 0.433000 HNSCC(20;0.049) 0 SO:0001583 missense ENST00000314644.2 1 1 hg19 CCDS31501.1 . . . . . . . . . . C 13.12 2.141818 0.37825 . . ENSG00000181939 ENST00000314644 T 0.00137 8.68 5.02 5.02 0.67125 GPCR, rhodopsin-like superfamily (1); . . . . T 0.00300 0.0009 M 0.81682 2.555 0.25891 N 0.983471 P 0.44195 0.828 P 0.48524 0.58 T 0.42965 -0.9420 9 0.87932 D 0 . 9.2831 0.37740 0.0:0.9041:0.0:0.0959 . 236 Q8NGM1 OR4CF_HUMAN I 290 ENSP00000324958:L290I ENSP00000324958:L290I L + 1 0 OR4C15 55079226 0.000000 0.05858 0.971000 0.41717 0.282000 0.26991 -0.491000 0.06474 2.608000 0.88229 0.385000 0.25706 CTC TCGA-IB-A7LX-01A-12D-A36O-08 OR4C15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391164.1 1 0 1 203 276 0 149 0 0 0 0 149 2 0 0 0 0 0 2 1 1.000000 205 272 0 148 2 0 0 0 0 149 2 -20.000000 1 1 0 0 1 0.550000 3.150000 0 0 OR8K3 219473 broad.mit.edu 37 11 56086466 56086466 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:56086466G>T ENST00000312711.1 + 1 684 c.684G>T c.(682-684)atG>atT p.M228I NM_001005202.1 NP_001005202.1 Q8NH51 OR8K3_HUMAN olfactory receptor, family 8, subfamily K, member 3 40 Esophageal squamous(21;0.00448) TTCTCAGGATGAATTCTGCTG 0.413000 0 SO:0001583 missense ENST00000312711.1 1 0 hg19 CCDS31527.1 . . . . . . . . . . G 0.620 -0.821600 0.02755 . . ENSG00000181689 ENST00000312711 T 0.00021 9.03 4.28 2.37 0.29283 GPCR, rhodopsin-like superfamily (1); 0.077917 0.56097 D 0.000035 T 0.00039 0.0001 N 0.02379 -0.575 0.09310 N 0.999998 B 0.19817 0.039 B 0.26969 0.075 T 0.02464 -1.1155 10 0.08599 T 0.76 . 9.6999 0.40180 0.1726:0.0:0.8274:0.0 . 228 Q8NH51 OR8K3_HUMAN I 228 ENSP00000323555:M228I ENSP00000323555:M228I M + 3 0 OR8K3 55843042 0.001000 0.12720 0.971000 0.41717 0.029000 0.11900 -0.140000 0.10342 0.542000 0.28846 0.471000 0.43371 ATG TCGA-IB-A7LX-01A-12D-A36O-08 OR8K3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391602.1 1 0 0 17 409 0 112 0 0 0 0 112 2 0 0 0 0 0 2 1 0.999963 17 404 0 111 2 0 0 0 0 112 2 -4.239183 1 1 0 0 1 2 5 7 2.095029 1 0.550000 3.150000 0.675090 0.210000 0.120000 1.000000 0.200000 0.364225 0.210000 0 1.600000e-01 1 EML3 256364 broad.mit.edu 37 11 62370095 62370095 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:62370095G>A ENST00000394773.2 - 22 2850 c.2543C>T c.(2542-2544)aCg>aTg p.T848M EML3_ENST00000529309.1_Silent_p.H811H|EML3_ENST00000494176.2_Silent_p.H783H|MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000531557.1_Missense_Mutation_p.T631M|EML3_ENST00000278845.4_Missense_Mutation_p.T849M|MTA2_ENST00000527204.1_5'Flank NM_153265.2 NP_694997.2 Q32P44 EMAL3_HUMAN echinoderm microtubule associated protein like 3 26 GTCGTCGTGCGTGAATCGGAC 0.746000 0 SO:0001583 missense ENST00000394773.2 0 1 hg19 CCDS8023.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 21.3|21.3 4.126410|4.126410 0.77549|0.77549 .|. .|. ENSG00000149499|ENSG00000149499 ENST00000394776|ENST00000439994;ENST00000394773;ENST00000278845;ENST00000531557 .|T;T;T;T .|0.41400 .|2.28;1.52;1.0;1.0 4.96|4.96 4.96|4.96 0.65561|0.65561 .|WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1); .|0.511488 .|0.19627 .|N .|0.109775 T|T 0.54191|0.54191 0.1843|0.1843 L|L 0.39397|0.39397 1.21|1.21 0.80722|0.80722 D|D 1|1 .|D;P;D .|0.76494 .|0.995;0.882;0.999 .|P;B;D .|0.66351 .|0.832;0.325;0.943 T|T 0.50775|0.50775 -0.8788|-0.8788 5|10 .|0.42905 .|T .|0.14 -32.5046|-32.5046 16.0654|16.0654 0.80867|0.80867 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|848;631;849 .|Q32P44;G3V195;B7WPE2 .|EMAL3_HUMAN;.;. C|M 806|89;848;849;631 .|ENSP00000409611:T89M;ENSP00000378254:T848M;ENSP00000278845:T849M;ENSP00000433417:T631M .|ENSP00000278845:T849M R|T -|- 1|2 0|0 EML3|EML3 62126671|62126671 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.988000|0.988000 0.76386|0.76386 3.027000|3.027000 0.49697|0.49697 2.472000|2.472000 0.83506|0.83506 0.462000|0.462000 0.41574|0.41574 CGC|ACG TCGA-IB-A7LX-01A-12D-A36O-08 EML3-001 KNOWN NAGNAG_splice_site|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000313432.1 0 0 0 4 36 0 11 0 9.946877e-01 0 113 0 11 2 0 0 0 0 0 2 0 0.859457 1 34 0 10 2 0 0 0 0 11 2 -9.647493 1 0 0 0 1 2 5 7 2.095029 1 0.550000 3.150000 0.675090 0.630000 0.200000 1.000000 1.000000 0.663491 0.630000 0 3.700000e-01 1 DNHD1 144132 broad.mit.edu 37 11 6593035 6593035 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:6593035G>A ENST00000527990.2 + 41 14081 c.14081G>A c.(14080-14082)aGt>aAt p.S4694N DNHD1_ENST00000254579.6_Missense_Mutation_p.S4694N Q96M86 DNHD1_HUMAN dynein heavy chain domain 1 55 Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171) CCGGGCACCAGTGACCTGCCA 0.637000 0 SO:0001583 missense ENST00000527990.2 1 1 hg19 CCDS44532.1 . . . . . . . . . . G 1.262 -0.615437 0.03663 . . ENSG00000179532 ENST00000254579;ENST00000527990;ENST00000530197 T;T 0.26067 1.76;1.76 4.75 -5.17 0.02849 Dynein heavy chain (1); 1.578020 0.03032 N 0.152237 T 0.11922 0.0290 N 0.08118 0 0.09310 N 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.001;0.001;0.001 T 0.28490 -1.0042 10 0.12103 T 0.63 1.5404 9.9464 0.41611 0.1879:0.1309:0.6813:0.0 . 3782;747;4694 B0I1S4;Q9NSW8;Q96M86 .;.;DNHD1_HUMAN N 4694;4694;962 ENSP00000254579:S4694N;ENSP00000436180:S4694N ENSP00000254579:S4694N S + 2 0 DNHD1 6549611 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -1.007000 0.03667 -0.921000 0.03794 -0.165000 0.13383 AGT TCGA-IB-A7LX-01A-12D-A36O-08 DNHD1-007 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000384673.2 1 0 0 46 150 0 66 1 5.963972e-01 3 5 0 66 2 0 0 0 0 0 2 1 1.000000 45 145 0 65 2 0 0 0 0 66 2 -20.000000 1 1 0 0 1 2 5 7 2.287299 1 0.550000 3.150000 0.701740 0.990000 0.990000 1.000000 1.000000 0.998724 0.990000 1 9.900000e-01 1 KDM2A 22992 broad.mit.edu 37 11 67012810 67012810 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:67012810C>A ENST00000529006.2 + 14 2160 c.1714C>A c.(1714-1716)Cga>Aga p.R572R KDM2A_ENST00000308783.5_Silent_p.R30R|KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_Silent_p.R133R|KDM2A_ENST00000398645.2_Silent_p.R572R NM_012308.2 NP_036440.1 Q9Y2K7 KDM2A_HUMAN lysine (K)-specific demethylase 2A 36 AGTGCGATGTCGAAAATGCAA 0.552000 0 SO:0001819 synonymous_variant ENST00000529006.2 1 0 hg19 CCDS44657.1 TCGA-IB-A7LX-01A-12D-A36O-08 KDM2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393140.2 1 0 0 11 236 0 75 0 9.606481e-01 0 121 0 75 2 0 0 0 0 0 2 1 0.997992 11 225 0 74 2 0 0 0 0 75 2 -12.880610 1 1 0 0 1 2 5 7 2.095029 1 0.550000 3.150000 0.675090 0.250000 0.120000 1.000000 0.230000 0.388959 0.250000 0 1.700000e-01 1 C11orf30 56946 broad.mit.edu 37 11 76257216 76257216 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:76257216G>A ENST00000529032.1 + 19 3649 c.3649G>A c.(3649-3651)Gtt>Att p.V1217I C11orf30_ENST00000524767.1_Missense_Mutation_p.V1232I|C11orf30_ENST00000334736.3_Missense_Mutation_p.V1217I|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000525038.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000524490.1_Missense_Mutation_p.V1119I|C11orf30_ENST00000525919.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000533248.1_Missense_Mutation_p.V1126I Q7Z589 EMSY_HUMAN chromosome 11 open reading frame 30 60 TCCATCCACTGTTGGCTCTTC 0.512000 0 SO:0001583 missense ENST00000529032.1 1 1 hg19 CCDS8244.1 . . . . . . . . . . G 9.733 1.162780 0.21538 . . ENSG00000158636 ENST00000524490;ENST00000334736;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032 . . . 6.06 3.0 0.34707 . 0.499003 0.20569 N 0.089772 T 0.36166 0.0957 N 0.14661 0.345 0.80722 D 1 B;B;B;B;B;B 0.22346 0.068;0.0;0.0;0.0;0.0;0.0 B;B;B;B;B;B 0.20767 0.031;0.0;0.0;0.0;0.0;0.0 T 0.15150 -1.0447 9 0.27082 T 0.32 -1.8144 9.3812 0.38316 0.1312:0.119:0.7498:0.0 . 1126;1218;1232;1218;1119;1217 B7ZKT8;B7ZKU2;B7ZKU0;Q17RM7;E9PMC9;Q7Z589 .;.;.;.;.;EMSY_HUMAN I 1119;1217;899;1232;1126;1218;1218;1217 . ENSP00000334130:V1217I V + 1 0 C11orf30 75934864 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 2.038000 0.41184 1.580000 0.49851 0.650000 0.86243 GTT TCGA-IB-A7LX-01A-12D-A36O-08 C11orf30-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000383288.2 1 0 0 15 326 0 95 0 2.058821e-01 0 18 0 95 2 0 0 0 0 0 2 1 0.999866 14 322 0 95 2 0 0 0 0 95 2 -4.221989 1 1 0 0 1 2 5 7 2.111242 1 0.550000 3.150000 0.678284 0.240000 0.130000 1.000000 0.210000 0.387989 0.240000 0 1.800000e-01 1 NOX4 50507 broad.mit.edu 37 11 89133524 89133524 + Silent SNP A A G TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:89133524A>G ENST00000263317.4 - 10 1108 c.870T>C c.(868-870)ccT>ccC p.P290P NOX4_ENST00000535633.1_Silent_p.P266P|NOX4_ENST00000528341.1_Silent_p.P265P|NOX4_ENST00000542487.1_Silent_p.P266P|NOX4_ENST00000534731.1_Silent_p.P290P|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000532825.1_Silent_p.P266P|NOX4_ENST00000527626.1_Silent_p.P124P|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Silent_p.P266P|NOX4_ENST00000424319.1_Silent_p.P266P|NOX4_ENST00000413594.2_Silent_p.P311P|NOX4_ENST00000343727.5_Silent_p.P266P|NOX4_ENST00000375979.3_Intron Q9NPH5 NOX4_HUMAN NADPH oxidase 4 44 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011) ACAGGCACAAAGGTCCAGAAA 0.398000 0 SO:0001819 synonymous_variant ENST00000263317.4 1 1 hg19 CCDS8285.1 TCGA-IB-A7LX-01A-12D-A36O-08 NOX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394054.1 1 0 0 11 199 0 78 0 7.448056e-02 0 8 0 78 2 0 0 0 0 0 2 1 0.997876 10 188 0 82 2 0 0 0 0 78 2 -4.718546 1 1 0 0 1 0 2 2 1.592599 1 0.550000 3.150000 0.550000 0.190000 0.100000 0.320000 0.190000 0.205018 0.190000 0 1.400000e-01 2.600000e-01 TAF1D 79101 broad.mit.edu 37 11 93472407 93472407 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr11:93472407G>T ENST00000448108.2 - 2 714 c.64C>A c.(64-66)Cga>Aga p.R22R C11orf54_ENST00000354421.3_5'Flank|C11orf54_ENST00000528288.1_5'Flank|C11orf54_ENST00000528099.1_5'Flank|C11orf54_ENST00000540113.1_5'Flank|C11orf54_ENST00000331239.4_5'Flank NM_024116.3 NP_077021.1 Q9H5J8 TAF1D_HUMAN TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa 7 ACTCACCTTCGATTTGCAAGT 0.318000 0 SO:0001819 synonymous_variant ENST00000448108.2 1 0 hg19 CCDS8293.1 TCGA-IB-A7LX-01A-12D-A36O-08 TAF1D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394662.2 1 0 0 12 255 0 81 0 9.973335e-01 0 218 0 81 2 0 0 0 0 0 2 1 0.999053 12 249 0 80 2 0 0 0 0 81 2 -3.261399 1 1 0 0 1 0 2 2 1.608709 1 0.550000 3.150000 0.550000 0.160000 0.080000 0.270000 0.160000 0.175182 0.160000 0 1.200000e-01 2.200000e-01 UHRF1BP1L 23074 broad.mit.edu 37 12 100491190 100491190 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:100491190G>T ENST00000279907.7 - 6 834 c.622C>A c.(622-624)Cga>Aga p.R208R UHRF1BP1L_ENST00000356828.3_Silent_p.R208R NM_015054.1 NP_055869.1 A0JNW5 UH1BL_HUMAN UHRF1 binding protein 1-like p.R208*(2) 50 GTTATTAATCGAACAGGAGCA 0.343000 2 Substitution - Nonsense(2) SO:0001819 synonymous_variant ENST00000279907.7 1 0 hg19 CCDS31882.1 TCGA-IB-A7LX-01A-12D-A36O-08 UHRF1BP1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407875.1 1 0 0 10 200 0 62 0 6.368889e-02 0 8 0 62 2 0 0 0 0 0 2 1 0.996710 10 196 0 60 2 0 0 0 0 62 2 -3.207791 1 1 0 0 1 0 2 2 1.513293 1 0.550000 3.150000 0.550000 0.170000 0.080000 0.300000 0.180000 0.187931 0.170000 0 1.200000e-01 2.400000e-01 DRAM1 55332 broad.mit.edu 37 12 102295199 102295199 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:102295199C>A ENST00000258534.8 + 3 769 c.330C>A c.(328-330)gtC>gtA p.V110V DRAM1_ENST00000544152.1_Silent_p.V110V NM_018370.2 NP_060840.2 Q8N682 DRAM1_HUMAN DNA-damage regulated autophagy modulator 1 12 TGGGCATTGTCGCCAATTTTC 0.428000 0 SO:0001819 synonymous_variant ENST00000258534.8 1 0 hg19 CCDS41823.1 TCGA-IB-A7LX-01A-12D-A36O-08 DRAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409195.1 1 0 0 9 158 0 78 0 6.905539e-01 0 43 0 78 2 0 0 0 0 0 2 1 0.994147 9 156 0 77 2 0 0 0 0 78 2 -3.299010 1 1 0 0 1 0 2 2 1.513293 1 0.550000 3.150000 0.550000 0.200000 0.090000 0.350000 0.200000 0.214106 0.200000 0 1.400000e-01 2.800000e-01 UBE3B 89910 broad.mit.edu 37 12 109945463 109945463 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:109945463G>T ENST00000342494.3 + 15 2140 c.1545G>T c.(1543-1545)ctG>ctT p.L515L UBE3B_ENST00000535900.1_3'UTR|UBE3B_ENST00000280774.5_Silent_p.L515L|UBE3B_ENST00000434735.2_Silent_p.L515L NM_130466.3 NP_569733.2 Q7Z3V4 UBE3B_HUMAN ubiquitin protein ligase E3B 45 TGGAATGCCTGAACAATGACA 0.522000 0 SO:0001819 synonymous_variant ENST00000342494.3 1 0 hg19 CCDS9129.1 TCGA-IB-A7LX-01A-12D-A36O-08 UBE3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403119.1 1 0 0 20 474 0 152 0 2.081888e-01 0 20 0 152 2 0 0 0 0 0 2 1 0.999995 19 471 0 151 2 0 0 0 0 152 2 -3.064727 1 1 0 0 1 0 2 2 1.513293 1 0.550000 3.150000 0.550000 0.140000 0.080000 0.220000 0.140000 0.153688 0.140000 0 1.100000e-01 1.900000e-01 TBX5 6910 broad.mit.edu 37 12 114841631 114841631 + Missense_Mutation SNP C C A rs148195311 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:114841631C>A ENST00000310346.4 - 2 739 c.73G>T c.(73-75)Gat>Tat p.D25Y TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000405440.2_Missense_Mutation_p.D25Y|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000526441.1_Missense_Mutation_p.D25Y NM_000192.3 NP_000183.2 Q99593 TBX5_HUMAN T-box 5 56 Medulloblastoma(191;0.163)|all_neural(191;0.178) GGTTTCGAATCGCAGGGCAGG 0.706000 NSCLC(152;1358 1980 4050 23898 40356) 0 SO:0001583 missense ENST00000310346.4 1 0 hg19 CCDS9173.1 . . . . . . . . . . C 23.4 4.413796 0.83449 2.27E-4 0.0 ENSG00000089225 ENST00000310346;ENST00000405440;ENST00000526441 D;D;D 0.88201 -2.35;-2.35;-2.31 5.31 5.31 0.75309 . 0.307696 0.35615 N 0.003093 D 0.86764 0.6011 N 0.19112 0.55 0.46701 D 0.999163 P;P 0.49447 0.887;0.924 P;P 0.49012 0.598;0.594 D 0.88669 0.3194 10 0.62326 D 0.03 . 18.988 0.92780 0.0:1.0:0.0:0.0 . 25;25 Q99593-2;Q99593 .;TBX5_HUMAN Y 25 ENSP00000309913:D25Y;ENSP00000384152:D25Y;ENSP00000433292:D25Y ENSP00000309913:D25Y D - 1 0 TBX5 113326014 0.997000 0.39634 0.575000 0.28536 0.908000 0.53690 3.897000 0.56273 2.476000 0.83614 0.655000 0.94253 GAT TCGA-IB-A7LX-01A-12D-A36O-08 TBX5-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000388297.1 1 0 0 12 166 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 0.998929 12 157 0 44 2 0 0 0 0 45 2 -15.904110 1 1 121398 1 30 1 0 2 2 1.513293 1 0.550000 3.150000 0.550000 0.240000 0.130000 0.400000 0.240000 0.261411 0.240000 0 1.800000e-01 3.300000e-01 CLIP1 6249 broad.mit.edu 37 12 122839066 122839066 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:122839066C>A ENST00000540338.1 - 6 1282 c.1241G>T c.(1240-1242)cGa>cTa p.R414L CLIP1_ENST00000361654.4_Missense_Mutation_p.R414L|CLIP1_ENST00000545889.1_Missense_Mutation_p.R115L|CLIP1_ENST00000537178.1_Missense_Mutation_p.R414L|CLIP1_ENST00000302528.7_Missense_Mutation_p.R414L|CLIP1_ENST00000358808.2_Missense_Mutation_p.R414L P30622 CLIP1_HUMAN CAP-GLY domain containing linker protein 1 60 all_neural(191;0.0837)|Medulloblastoma(191;0.163) CACCATTGTTCGCAGCTGGTC 0.512000 0 SO:0001583 missense ENST00000540338.1 1 0 hg19 CCDS58285.1 . . . . . . . . . . C 31 5.083510 0.94050 . . ENSG00000130779 ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304;ENST00000537004 T;T;T;T;T;T;T 0.69040 2.38;0.45;0.45;0.44;0.48;-0.11;-0.37 5.84 5.84 0.93424 . 0.000000 0.85682 D 0.000000 T 0.82116 0.4967 M 0.72118 2.19 0.80722 D 1 D;D;D;D;D 0.89917 0.995;1.0;0.996;0.989;0.993 P;D;D;D;P 0.76071 0.878;0.987;0.935;0.935;0.862 T 0.81402 -0.0949 10 0.52906 T 0.07 -7.3582 20.1346 0.98019 0.0:1.0:0.0:0.0 . 348;115;414;414;414 F6VGP8;F5H0N7;P30622-2;P30622-1;P30622 .;.;.;.;CLIP1_HUMAN L 115;414;414;259;414;414;348;348 ENSP00000438743:R115L;ENSP00000303585:R414L;ENSP00000351665:R414L;ENSP00000445531:R414L;ENSP00000439093:R414L;ENSP00000437786:R348L;ENSP00000441409:R348L ENSP00000303585:R414L R - 2 0 CLIP1 121405019 1.000000 0.71417 0.925000 0.36789 0.973000 0.67179 7.818000 0.86416 2.765000 0.95021 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 CLIP1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000401625.1 1 0 0 11 271 0 71 0 6.345548e-01 1 52 0 71 2 0 0 0 0 0 2 1 0.998258 11 266 0 69 2 0 0 0 0 71 2 -3.002067 1 1 0 0 1 0 3 3 1.820111 1 0.550000 3.150000 0.641648 0.180000 0.090000 1.000000 0.180000 0.237578 0.180000 0 1.300000e-01 2.600000e-01 RILPL2 196383 broad.mit.edu 37 12 123907604 123907604 + Missense_Mutation SNP T T A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:123907604T>A ENST00000280571.8 - 3 888 c.592A>T c.(592-594)Atc>Ttc p.I198F NM_145058.1 NP_659495.1 Q969X0 RIPL2_HUMAN Rab interacting lysosomal protein-like 2 6 all_neural(191;0.101)|Medulloblastoma(191;0.163) TTTTTTATGATTGTCTTCTCC 0.507000 0 SO:0001583 missense ENST00000280571.8 0 1 hg19 CCDS9248.1 . . . . . . . . . . T 13.79 2.342477 0.41498 . . ENSG00000150977 ENST00000280571 T 0.45668 0.89 5.0 3.85 0.44370 . 0.229969 0.44688 D 0.000439 T 0.32224 0.0822 L 0.29908 0.895 0.38433 D 0.946505 P 0.49961 0.93 P 0.44860 0.462 T 0.14392 -1.0474 10 0.48119 T 0.1 . 8.3232 0.32140 0.0:0.0913:0.0:0.9087 . 198 Q969X0 RIPL2_HUMAN F 198 ENSP00000280571:I198F ENSP00000280571:I198F I - 1 0 RILPL2 122473557 0.981000 0.34729 0.610000 0.28997 0.063000 0.16089 1.962000 0.40442 0.858000 0.35431 0.533000 0.62120 ATC TCGA-IB-A7LX-01A-12D-A36O-08 RILPL2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 6 322 0 82 1 5.462801e-01 2 89 0 82 2 0 0 0 0 0 2 1 0.963650 6 317 0 82 2 0 0 0 0 82 2 -6.754241 1 0 0 0 1 0 3 3 1.820111 1 0.550000 3.150000 0.641648 0.090000 0.030000 1.000000 0.090000 0.147092 0.090000 0 5.000000e-02 1.400000e-01 PLEKHA5 54477 broad.mit.edu 37 12 19512436 19512436 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:19512436C>A ENST00000299275.6 + 22 2947 c.2941C>A c.(2941-2943)Caa>Aaa p.Q981K PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q970K|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q1147K|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q1044K|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q963K|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q739K|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q925K NM_019012.5 NP_061885.2 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A member 5 35 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AGAAATTGTTCAACTAAAAGA 0.383000 Pancreas(196;329 2193 11246 14234 19524) 0 SO:0001583 missense ENST00000299275.6 1 0 hg19 CCDS8682.1 . . . . . . . . . . C 12.07 1.828021 0.32329 . . ENSG00000052126 ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972 T;T;T;T;T;T;T;T;T;T;T 0.09073 3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02 4.75 4.75 0.60458 . 1.239000 0.05720 N 0.597588 T 0.07818 0.0196 N 0.24115 0.695 0.09310 N 1 B;B;B;B;B;B;B;B 0.22146 0.065;0.024;0.014;0.011;0.003;0.02;0.014;0.024 B;B;B;B;B;B;B;B 0.18561 0.022;0.018;0.008;0.008;0.006;0.008;0.008;0.018 T 0.11916 -1.0568 10 0.42905 T 0.14 3.8378 9.1527 0.36973 0.0:0.9019:0.0:0.0981 . 1044;963;970;1142;925;1147;981;1039 Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2 .;.;.;.;.;.;PKHA5_HUMAN;. K 1044;1039;925;1143;1147;981;739;1039;970;963;936;262 ENSP00000325155:Q1044K;ENSP00000347560:Q1039K;ENSP00000352104:Q925K;ENSP00000404296:Q1147K;ENSP00000299275:Q981K;ENSP00000440611:Q739K;ENSP00000439673:Q1039K;ENSP00000400411:Q970K;ENSP00000439837:Q963K;ENSP00000440371:Q936K;ENSP00000443553:Q262K ENSP00000299275:Q981K Q + 1 0 PLEKHA5 19403703 0.013000 0.17824 0.005000 0.12908 0.173000 0.22820 2.184000 0.42575 2.627000 0.88993 0.460000 0.39030 CAA TCGA-IB-A7LX-01A-12D-A36O-08 PLEKHA5-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000397013.1 1 0 0 17 401 0 63 0 9.999126e-01 0 370 0 63 2 0 0 0 0 0 2 1 0.999960 17 392 0 63 2 0 0 0 0 63 2 -3.260106 1 1 0 0 1 2 4 6 3.113844 1 0.550000 3.150000 0.779951 0.310000 0.170000 1.000000 0.290000 0.344369 0.310000 0 2.300000e-01 4.100000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D 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 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D 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-IB-A7LX-01A-12D-A36O-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 230 222 0 84 1 1 26 20 0 84 2 1 1 210 282 0 767 2 1 1.000000 225 214 0 82 2 1 1 4367 3666 0 84 2 -20.000000 1 1 121404 2 44 1 2 4 6 3.113844 1 0.550000 3.150000 0.779951 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 STK38L 23012 broad.mit.edu 37 12 27461299 27461299 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:27461299C>A ENST00000389032.3 + 4 383 c.214C>A c.(214-216)Cgc>Agc p.R72S STK38L_ENST00000539577.1_Intron NM_015000.3 NP_055815.1 serine/threonine kinase 38 like 12 Colorectal(261;0.0847) ACAACACGCTCGCAAAGAAAC 0.368000 0 SO:0001583 missense ENST00000389032.3 1 0 hg19 CCDS31761.1 . . . . . . . . . . C 17.50 3.405421 0.62288 . . ENSG00000211455 ENST00000541191;ENST00000389032;ENST00000540996;ENST00000543246;ENST00000544969 T;T;T;T;T 0.49720 0.99;0.77;0.99;0.99;0.99 4.54 4.54 0.55810 Protein kinase-like domain (1); 0.000000 0.85682 D 0.000000 T 0.46639 0.1403 L 0.56199 1.76 0.80722 D 1 B 0.10296 0.003 B 0.12837 0.008 T 0.46331 -0.9199 10 0.51188 T 0.08 . 17.29 0.87153 0.0:1.0:0.0:0.0 . 72 Q9Y2H1 ST38L_HUMAN S 72 ENSP00000437856:R72S;ENSP00000373684:R72S;ENSP00000443838:R72S;ENSP00000442253:R72S;ENSP00000440279:R72S ENSP00000373684:R72S R + 1 0 STK38L 27352566 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 4.515000 0.60489 2.257000 0.74773 0.460000 0.39030 CGC TCGA-IB-A7LX-01A-12D-A36O-08 STK38L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403297.1 1 0 0 36 770 0 144 0 9.916101e-01 0 159 0 144 2 0 0 0 0 0 2 1 1.000000 39 757 0 142 2 0 0 0 0 144 2 -2.488282 0 1 0 0 1 2 4 6 3.113844 1 0.550000 3.150000 0.779951 0.330000 0.220000 1.000000 0.340000 0.365460 0.330000 0 2.700000e-01 4.100000e-01 CNTN1 1272 broad.mit.edu 37 12 41414201 41414201 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:41414201C>A ENST00000551295.2 + 20 2599 c.2482C>A c.(2482-2484)Cat>Aat p.H828N CNTN1_ENST00000347616.1_Missense_Mutation_p.H828N|CNTN1_ENST00000348761.2_Missense_Mutation_p.H817N|CNTN1_ENST00000550305.1_3'UTR NM_001843.3 NP_001834.2 Q12860 CNTN1_HUMAN contactin 1 p.H828Y(1) 90 all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716) Lung NSC(34;0.0211)|all_lung(34;0.0294) GATATCTGTTCATTGGGAACA 0.294000 1 Substitution - Missense(1) SO:0001583 missense ENST00000551295.2 1 0 hg19 CCDS8737.1 . . . . . . . . . . C 11.19 1.566934 0.28003 . . ENSG00000018236 ENST00000551295;ENST00000347616;ENST00000348761 T;T;T 0.55760 0.5;0.5;0.5 5.75 3.58 0.41010 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.366663 0.30639 N 0.009186 T 0.26268 0.0641 N 0.08118 0 0.80722 D 1 B;B 0.09022 0.001;0.002 B;B 0.15870 0.008;0.014 T 0.09292 -1.0681 10 0.35671 T 0.21 . 3.1624 0.06524 0.0:0.4877:0.2254:0.2869 . 817;828 Q12860-2;Q12860 .;CNTN1_HUMAN N 828;828;817 ENSP00000447006:H828N;ENSP00000325660:H828N;ENSP00000261160:H817N ENSP00000325660:H828N H + 1 0 CNTN1 39700468 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 2.154000 0.42291 1.583000 0.49898 -0.140000 0.14226 CAT TCGA-IB-A7LX-01A-12D-A36O-08 CNTN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403692.2 1 0 0 17 386 0 86 0 1.883276e-02 0 5 0 86 2 0 0 0 0 0 2 1 0.999963 20 377 0 85 2 0 0 0 0 86 2 -3.010795 1 1 0 0 1 2 2 4 2.117339 1 0.550000 3.150000 0.677650 0.230000 0.120000 1.000000 0.210000 0.375333 0.230000 0 1.700000e-01 1 SOCS2 8835 broad.mit.edu 37 12 93968645 93968645 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr12:93968645G>T ENST00000340600.2 + 3 885 c.287G>T c.(286-288)cGa>cTa p.R96L SOCS2_ENST00000536696.2_Missense_Mutation_p.R96L|SOCS2_ENST00000548537.1_3'UTR|SOCS2_ENST00000549122.1_Missense_Mutation_p.R96L|SOCS2_ENST00000551556.1_Missense_Mutation_p.R96L|SOCS2_ENST00000549206.1_Missense_Mutation_p.R96L NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4 NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1 O14508 SOCS2_HUMAN suppressor of cytokine signaling 2 p.R96Q(1) 14 ACTAATCTTCGAATCGAATAC 0.378000 1 Substitution - Missense(1) SO:0001583 missense ENST00000340600.2 1 0 hg19 CCDS9047.1 . . . . . . . . . . G 18.78 3.696989 0.68386 . . ENSG00000120833 ENST00000340600;ENST00000549206;ENST00000536696;ENST00000539385;ENST00000548091;ENST00000549122;ENST00000549887;ENST00000551556 D;D;D;D;D;D;D 0.89485 -2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52 5.84 5.84 0.93424 SH2 motif (4); 0.055893 0.64402 D 0.000001 D 0.94830 0.8330 M 0.79343 2.45 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 D 0.94707 0.7888 10 0.87932 D 0 -0.8535 20.1346 0.98019 0.0:0.0:1.0:0.0 . 96 O14508 SOCS2_HUMAN L 96;96;96;44;96;96;96;96 ENSP00000339428:R96L;ENSP00000448815:R96L;ENSP00000442898:R96L;ENSP00000447902:R96L;ENSP00000447161:R96L;ENSP00000448611:R96L;ENSP00000449227:R96L ENSP00000339428:R96L R + 2 0 SOCS2 92492776 1.000000 0.71417 0.966000 0.40874 0.239000 0.25481 9.531000 0.98054 2.765000 0.95021 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 SOCS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407731.2 1 0 0 11 234 0 93 0 1.162609e-01 0 12 0 93 2 0 0 0 0 0 2 1 0.998211 11 228 0 93 2 0 0 0 0 93 2 -3.084451 1 1 0 0 1 0 2 2 1.513293 1 0.550000 3.150000 0.550000 0.160000 0.080000 0.280000 0.160000 0.176061 0.160000 0 1.200000e-01 2.200000e-01 CUL4A 8451 broad.mit.edu 37 13 113887578 113887578 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr13:113887578C>A ENST00000375440.4 + 6 684 c.600C>A c.(598-600)atC>atA p.I200I CUL4A_ENST00000451881.1_Silent_p.I100I|CUL4A_ENST00000326335.4_Silent_p.I100I|CUL4A_ENST00000375441.3_Silent_p.I100I NM_001008895.1 NP_001008895.1 Q13619 CUL4A_HUMAN cullin 4A 17 Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188) all cancers(43;0.112) TACTGCTGATCGAGCGCGAGA 0.512000 0 SO:0001819 synonymous_variant ENST00000375440.4 1 0 hg19 CCDS41908.1 TCGA-IB-A7LX-01A-12D-A36O-08 CUL4A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045888.3 1 0 0 13 370 0 83 0 9.257780e-01 0 130 0 83 2 0 0 0 0 0 2 1 0.999512 13 365 0 83 2 0 0 0 0 83 2 -3.216127 1 1 0 0 1 2 2 4 2.350227 1 0.550000 3.150000 0.709677 0.190000 0.100000 0.320000 0.200000 0.204745 0.190000 0 1.400000e-01 2.600000e-01 WASF3 10810 broad.mit.edu 37 13 27239254 27239254 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr13:27239254C>A ENST00000335327.5 + 4 401 c.223C>A c.(223-225)Cgc>Agc p.R75S WASF3_ENST00000361042.4_Missense_Mutation_p.R75S|WASF3_ENST00000496788.1_3'UTR NM_006646.5 NP_006637.2 Q9UPY6 WASF3_HUMAN WAS protein family, member 3 22 Colorectal(5;0.000247) Lung SC(185;0.0156)|Breast(139;0.147) CAGAATTGATCGCCTTGCTGT 0.413000 0 SO:0001583 missense ENST00000335327.5 1 0 hg19 CCDS9318.1 . . . . . . . . . . C 28.9 4.956245 0.92726 . . ENSG00000132970 ENST00000361042;ENST00000335327 T;T 0.67523 -0.27;-0.27 5.64 5.64 0.86602 . 0.052354 0.85682 D 0.000000 T 0.77343 0.4116 M 0.79805 2.47 0.80722 D 1 P;P 0.50156 0.932;0.498 P;B 0.49387 0.609;0.318 T 0.79259 -0.1877 10 0.51188 T 0.08 -23.1243 19.6999 0.96048 0.0:1.0:0.0:0.0 . 75;75 Q86VQ2;Q9UPY6 .;WASF3_HUMAN S 75 ENSP00000354325:R75S;ENSP00000335055:R75S ENSP00000335055:R75S R + 1 0 WASF3 26137254 1.000000 0.71417 1.000000 0.80357 0.923000 0.55619 7.320000 0.79064 2.659000 0.90383 0.650000 0.86243 CGC TCGA-IB-A7LX-01A-12D-A36O-08 WASF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044258.1 1 0 0 9 236 0 66 0 3.210462e-02 0 7 0 66 2 0 0 0 0 0 2 1 0.993916 9 231 0 65 2 0 0 0 0 66 2 -3.116152 1 1 0 0 1 2 2 4 2.350227 1 0.550000 3.150000 0.709677 0.210000 0.100000 0.370000 0.200000 0.227817 0.210000 0 1.500000e-01 3.000000e-01 FREM2 341640 broad.mit.edu 37 13 39452994 39452994 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr13:39452994G>T ENST00000280481.7 + 23 9102 c.8886G>T c.(8884-8886)gcG>gcT p.A2962A NM_207361.4 NP_997244.3 Q5SZK8 FREM2_HUMAN FRAS1 related extracellular matrix protein 2 148 Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114) AGACACAAGCGACCAGTTTTG 0.443000 0 SO:0001819 synonymous_variant ENST00000280481.7 1 0 hg19 CCDS31960.1 TCGA-IB-A7LX-01A-12D-A36O-08 FREM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044599.2 1 0 0 15 439 0 110 0 1.305232e-03 0 2 0 110 2 0 0 0 0 0 2 1 0.999856 15 430 0 110 2 0 0 0 0 110 2 -2.980733 1 1 0 0 1 2 2 4 2.350227 1 0.550000 3.150000 0.709677 0.180000 0.100000 0.300000 0.200000 0.197593 0.180000 0 1.400000e-01 2.500000e-01 NHLRC3 387921 broad.mit.edu 37 13 39616292 39616292 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr13:39616292C>A ENST00000379600.3 + 4 758 c.436C>A c.(436-438)Caa>Aaa p.Q146K NHLRC3_ENST00000470258.1_5'UTR|NHLRC3_ENST00000379599.2_Intron NM_001012754.3 NP_001012772.1 Q5JS37 NHLC3_HUMAN NHL repeat containing 3 11 Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114) TGATCTTGTTCAAGTCTTGGG 0.338000 0 SO:0001583 missense ENST00000379600.3 1 0 hg19 CCDS31961.1 . . . . . . . . . . C 9.802 1.180739 0.21787 . . ENSG00000188811 ENST00000379600 T 0.45276 0.9 5.3 5.3 0.74995 Six-bladed beta-propeller, TolB-like (1); 0.000000 0.85682 D 0.000000 T 0.48804 0.1520 L 0.42245 1.32 0.80722 D 1 P;D 0.56521 0.473;0.976 B;P 0.52343 0.056;0.696 T 0.36625 -0.9740 9 . . . -10.6501 17.9281 0.88989 0.0:1.0:0.0:0.0 . 146;146 Q5JS37;B4DRC8 NHLC3_HUMAN;. K 146 ENSP00000368920:Q146K . Q + 1 0 NHLRC3 38514292 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 3.945000 0.56637 2.457000 0.83068 0.467000 0.42956 CAA TCGA-IB-A7LX-01A-12D-A36O-08 NHLRC3-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044616.2 1 0 0 17 384 0 91 0 4.728714e-01 0 36 0 91 2 0 0 0 0 0 2 1 0.999960 15 377 0 90 2 0 0 0 0 91 2 -4.523921 1 1 0 0 1 2 2 4 2.350227 1 0.550000 3.150000 0.709677 0.240000 0.130000 0.370000 0.240000 0.251497 0.240000 0 1.800000e-01 3.100000e-01 PCDH17 27253 broad.mit.edu 37 13 58298909 58298909 + Silent SNP C C T rs138830034 byFrequency TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr13:58298909C>T ENST00000377918.3 + 4 2987 c.2961C>T c.(2959-2961)taC>taT p.Y987Y NM_001040429.2 NP_001035519.1 O14917 PCD17_HUMAN protocadherin 17 120 Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132) CTGAGACTTACGAAACTGTGA 0.413000 Melanoma(72;952 1291 1619 12849 33676) 0 SO:0001819 synonymous_variant ENST00000377918.3 1 1 hg19 CCDS31986.1 TCGA-IB-A7LX-01A-12D-A36O-08 PCDH17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045139.1 1 0 1 97 203 0 83 0 8.812058e-01 0 10 0 83 2 0 0 0 0 0 2 1 1.000000 96 201 0 83 2 0 0 0 0 83 2 -2.879461 1 1 121410 85 52 1 2 2 4 2.350227 1 0.550000 3.150000 0.709677 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 OR11H6 122748 broad.mit.edu 37 14 20692623 20692623 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr14:20692623G>T ENST00000315519.2 + 1 833 c.755G>T c.(754-756)cGa>cTa p.R252L NM_001004480.1 NP_001004480.1 Q8NGC7 O11H6_HUMAN olfactory receptor, family 11, subfamily H, member 6 29 all_cancers(95;0.00108) Epithelial(56;1.75e-06)|all cancers(55;1.22e-05) GGTGCTGGTCGAACTAAAGCT 0.483000 0 SO:0001583 missense ENST00000315519.2 1 0 hg19 CCDS32033.1 . . . . . . . . . . G 17.36 3.369552 0.61624 . . ENSG00000176219 ENST00000315519 T 0.00330 8.08 4.78 3.89 0.44902 GPCR, rhodopsin-like superfamily (1); 0.000000 0.41500 D 0.000870 T 0.00666 0.0022 M 0.85462 2.755 0.09310 N 1 P 0.51449 0.945 P 0.56127 0.792 T 0.27673 -1.0067 10 0.72032 D 0.01 . 10.7593 0.46256 0.0939:0.0:0.9061:0.0 . 252 Q8NGC7 O11H6_HUMAN L 252 ENSP00000319071:R252L ENSP00000319071:R252L R + 2 0 OR11H6 19762463 0.000000 0.05858 0.878000 0.34440 0.949000 0.60115 0.442000 0.21628 1.223000 0.43536 0.471000 0.43371 CGA TCGA-IB-A7LX-01A-12D-A36O-08 OR11H6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000410676.1 1 0 0 15 278 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 0.999866 15 273 0 71 2 0 0 0 0 71 2 -4.686283 1 1 0 0 1 2 2 4 2.243649 1 0.550000 3.150000 0.695637 0.290000 0.160000 1.000000 0.270000 0.365046 0.290000 0 2.100000e-01 4.100000e-01 TEP1 7011 broad.mit.edu 37 14 20841221 20841221 + Silent SNP T T C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr14:20841221T>C ENST00000262715.5 - 48 6940 c.6900A>G c.(6898-6900)caA>caG p.Q2300Q TEP1_ENST00000556935.1_Silent_p.Q2192Q|TEP1_ENST00000545983.1_Silent_p.Q638Q NM_007110.4 NP_009041.2 Q99973 TEP1_HUMAN telomerase-associated protein 1 96 all_cancers(95;0.00123) all_lung(585;0.235) Epithelial(56;7.42e-08)|all cancers(55;6.46e-07) GTTCCCCAGCTTGATTTCCAG 0.522000 0 SO:0001819 synonymous_variant ENST00000262715.5 1 1 hg19 CCDS9548.1 . . . . . . . . . . T 8.134 0.783739 0.16189 . . ENSG00000129566 ENST00000553984 . . . 5.77 0.76 0.18442 . . . . . T 0.32041 0.0816 . . . 0.21719 N 0.999572 . . . . . . T 0.26849 -1.0091 4 . . . -0.0235 7.2173 0.25967 0.0:0.4669:0.0:0.5331 . . . . G 7 . . S - 1 0 TEP1 19911061 0.053000 0.20554 0.110000 0.21437 0.973000 0.67179 0.124000 0.15728 0.135000 0.18707 0.533000 0.62120 AGC TCGA-IB-A7LX-01A-12D-A36O-08 TEP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000073563.2 1 0 1 91 178 0 69 1 9.999992e-01 21 24 0 69 2 0 0 0 0 0 2 1 1.000000 87 174 0 67 2 0 0 0 0 69 2 -20.000000 1 1 121412 1 34 1 2 2 4 2.243649 1 0.550000 3.150000 0.695637 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 AKAP6 9472 broad.mit.edu 37 14 33291486 33291486 + Silent SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr14:33291486C>T ENST00000280979.4 + 13 4637 c.4467C>T c.(4465-4467)agC>agT p.S1489S AKAP6_ENST00000557272.1_Intron NM_004274.4 NP_004265.3 Q13023 AKAP6_HUMAN A kinase (PRKA) anchor protein 6 122 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) AGTCACAAAGCGAAAAAGCGC 0.348000 Melanoma(49;821 1200 7288 13647 42351) 0 SO:0001819 synonymous_variant ENST00000280979.4 1 1 hg19 CCDS9644.1 TCGA-IB-A7LX-01A-12D-A36O-08 AKAP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276617.2 1 0 1 86 190 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 86 189 0 73 2 0 0 0 0 73 2 -20.000000 1 1 121390 7 38 1 2 2 4 2.243649 1 0.550000 3.150000 0.695637 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ARID4A 5926 broad.mit.edu 37 14 58785281 58785281 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr14:58785281G>T ENST00000355431.3 + 6 669 c.296G>T c.(295-297)cGa>cTa p.R99L ARID4A_ENST00000431317.2_Missense_Mutation_p.R99L|ARID4A_ENST00000348476.3_Missense_Mutation_p.R99L|ARID4A_ENST00000395168.3_Missense_Mutation_p.R99L NM_002892.3 NP_002883.3 P29374 ARI4A_HUMAN AT rich interactive domain 4A (RBP1-like) 60 GGTGATGAGCGAACATTGAGA 0.378000 0 SO:0001583 missense ENST00000355431.3 1 0 hg19 CCDS9732.1 . . . . . . . . . . G 25.2 4.610945 0.87258 . . ENSG00000032219 ENST00000355431;ENST00000348476;ENST00000395168;ENST00000445108;ENST00000431317 T;T;T;T;T 0.38887 1.11;1.11;1.11;1.11;1.11 5.78 5.78 0.91487 Tudor domain (1); 0.041251 0.85682 D 0.000000 T 0.59622 0.2207 L 0.43923 1.385 0.53688 D 0.999977 D;D;D 0.76494 0.999;0.997;0.998 D;D;D 0.70935 0.971;0.954;0.97 T 0.59883 -0.7370 10 0.87932 D 0 -25.8845 20.0079 0.97439 0.0:0.0:1.0:0.0 . 99;99;99 P29374-3;P29374;P29374-2 .;ARI4A_HUMAN;. L 99;99;99;62;99 ENSP00000347602:R99L;ENSP00000344556:R99L;ENSP00000378597:R99L;ENSP00000392567:R62L;ENSP00000397368:R99L ENSP00000344556:R99L R + 2 0 ARID4A 57855034 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 6.001000 0.70685 2.722000 0.93159 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 ARID4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276927.2 1 0 0 14 358 0 73 0 3.222530e-01 0 29 0 73 2 0 0 0 0 0 2 1 0.999733 12 353 0 71 2 0 0 0 0 73 2 -3.158608 1 1 0 0 1 2 2 4 2.243649 1 0.550000 3.150000 0.695637 0.210000 0.110000 1.000000 0.190000 0.297157 0.210000 0 1.500000e-01 3.100000e-01 MAP3K9 4293 broad.mit.edu 37 14 71216711 71216711 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr14:71216711C>A ENST00000554752.2 - 4 1088 c.1089G>T c.(1087-1089)atG>atT p.M363I MAP3K9_ENST00000553414.1_Missense_Mutation_p.M57I|MAP3K9_ENST00000554146.1_Missense_Mutation_p.M100I|MAP3K9_ENST00000381250.4_Missense_Mutation_p.M363I|MAP3K9_ENST00000555993.2_Missense_Mutation_p.M363I NM_001284230.1 NP_001271159.1 P80192 M3K9_HUMAN mitogen-activated protein kinase kinase kinase 9 46 CGAGTTTGTTCATGGCCACTC 0.507000 GBM(114;411 1587 13539 28235 50070) 0 SO:0001583 missense ENST00000554752.2 1 0 hg19 . . . . . . . . . . C 21.9 4.221675 0.79464 . . ENSG00000006432 ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284 D;D;D;D 0.88896 -2.44;-2.44;-2.44;-2.44 5.91 5.02 0.67125 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.81202 0.4773 N 0.05554 -0.025 0.50632 D 0.999885 B;B;B;B 0.29188 0.022;0.236;0.198;0.198 B;B;B;B 0.37989 0.032;0.262;0.113;0.171 T 0.78272 -0.2268 10 0.33141 T 0.24 . 14.5088 0.67769 0.0:0.9302:0.0:0.0698 . 100;363;363;57 G3V4P9;P80192;P80192-4;G3V347 .;M3K9_HUMAN;.;. I 363;363;57;363;100;91 ENSP00000451612:M363I;ENSP00000451038:M57I;ENSP00000370649:M363I;ENSP00000451921:M100I ENSP00000005198:M363I M - 3 0 MAP3K9 70286464 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 1.115000 0.31209 2.808000 0.96608 0.655000 0.94253 ATG TCGA-IB-A7LX-01A-12D-A36O-08 MAP3K9-001 KNOWN basic protein_coding protein_coding OTTHUMT00000412550.2 1 0 0 14 316 0 68 0 1.467250e-01 0 15 0 68 2 0 0 0 0 0 2 1 0.999714 13 308 0 68 2 0 0 0 0 68 2 -3.196010 1 1 0 0 1 2 2 4 2.243649 1 0.550000 3.150000 0.695637 0.240000 0.120000 1.000000 0.220000 0.321530 0.240000 0 1.700000e-01 3.500000e-01 BATF 10538 broad.mit.edu 37 14 75989073 75989073 + Silent SNP T T G TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr14:75989073T>G ENST00000286639.6 + 1 306 c.48T>G c.(46-48)ccT>ccG p.P16P BATF_ENST00000555795.1_Intron|BATF_ENST00000555504.1_Silent_p.P16P NM_006399.3 NP_006390.1 Q16520 BATF_HUMAN basic leucine zipper transcription factor, ATF-like 3 GCCGCTCTCCTCCCCCTGGCA 0.587000 0 SO:0001819 synonymous_variant ENST00000286639.6 1 1 hg19 CCDS9843.1 TCGA-IB-A7LX-01A-12D-A36O-08 BATF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413669.1 1 0 1 79 166 0 54 1 1 44 47 0 54 2 0 0 0 0 0 2 1 1.000000 77 164 0 54 2 0 0 0 0 54 2 -8.900294 1 1 0 0 1 2 2 4 2.243649 1 0.550000 3.150000 0.695637 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ADAMTSL3 57188 broad.mit.edu 37 15 84683327 84683327 + Missense_Mutation SNP G G C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr15:84683327G>C ENST00000286744.5 + 24 4231 c.4007G>C c.(4006-4008)aGa>aCa p.R1336T ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1336T NM_207517.2 NP_997400.2 P82987 ATL3_HUMAN ADAMTS-like 3 p.R1336I(1) 130 BRCA - Breast invasive adenocarcinoma(143;0.211) TGGTTGAAGAGAGGAGGATCT 0.428000 1 Substitution - Missense(1) SO:0001583 missense ENST00000286744.5 1 1 hg19 CCDS10326.1 . . . . . . . . . . G 10.69 1.420685 0.25639 . . ENSG00000156218 ENST00000286744 T 0.27402 1.67 4.7 1.68 0.24146 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.739929 0.11659 N 0.541996 T 0.15696 0.0378 N 0.17082 0.46 0.26572 N 0.973534 B;B 0.09022 0.001;0.002 B;B 0.12837 0.008;0.007 T 0.31280 -0.9949 10 0.22109 T 0.4 . 4.2489 0.10684 0.4199:0.1664:0.4137:0.0 . 1336;1336 P82987-2;P82987 .;ATL3_HUMAN T 1336 ENSP00000286744:R1336T ENSP00000286744:R1336T R + 2 0 ADAMTSL3 82474331 1.000000 0.71417 0.999000 0.59377 0.986000 0.74619 0.900000 0.28431 0.048000 0.15891 -0.266000 0.10368 AGA TCGA-IB-A7LX-01A-12D-A36O-08 ADAMTSL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000304007.2 1 0 0 35 593 0 182 0 4.274176e-02 0 6 0 182 2 0 0 0 0 0 2 1 1.000000 34 581 0 179 2 0 0 0 0 182 2 -5.808365 1 1 0 0 1 2 4 6 2.035251 1 0.550000 3.150000 0.667160 0.280000 0.190000 1.000000 0.270000 0.431600 0.280000 0 2.300000e-01 1 CPD 1362 broad.mit.edu 37 17 28747986 28747986 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:28747986C>A ENST00000225719.4 + 3 1198 c.1122C>A c.(1120-1122)atC>atA p.I374I CPD_ENST00000543464.2_Silent_p.I127I NM_001304.4 NP_001295.2 O75976 CBPD_HUMAN carboxypeptidase D 36 AGTCTTTGATCACATTGATTG 0.393000 0 SO:0001819 synonymous_variant ENST00000225719.4 1 0 hg19 CCDS11257.1 TCGA-IB-A7LX-01A-12D-A36O-08 CPD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256214.3 1 0 0 12 246 0 69 0 9.087127e-01 0 88 0 69 2 0 0 0 0 0 2 1 0.999118 12 243 0 67 2 0 0 0 0 69 2 -3.217508 1 1 0 0 1 2 2 4 2.274668 1 0.550000 3.150000 0.700100 0.260000 0.130000 1.000000 0.260000 0.325280 0.260000 0 1.900000e-01 3.700000e-01 CCL7 6354 broad.mit.edu 37 17 32597292 32597292 + Translation_Start_Site SNP A A T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:32597292A>T ENST00000378569.2 + 0 53 CCL7_ENST00000394630.3_De_novo_Start_InFrame|CCL7_ENST00000394627.1_De_novo_Start_InFrame|CCL7_ENST00000200307.4_Missense_Mutation_p.M5L NM_006273.2 NP_006264.2 P80098 CCL7_HUMAN chemokine (C-C motif) ligand 7 7 Breast(3;0.00224) Breast(31;0.151)|Ovarian(249;0.17) GTGGAAGCCCATGCCCTCACC 0.547000 0 ENST00000378569.2 1 0 hg19 CCDS11278.1 . . . . . . . . . . A 0.081 -1.184197 0.01620 . . ENSG00000108688 ENST00000378569;ENST00000394630;ENST00000394627 . . . 3.89 0.269 0.15631 . 10.005000 0.00166 N 0.000004 T 0.18635 0.0447 . . . 0.09310 N 1 . . . . . . T 0.12477 -1.0546 6 0.11182 T 0.66 . 5.9178 0.19065 0.5474:0.0:0.4526:0.0 . . . . L 5 . ENSP00000367832:M5L M + 1 0 CCL7 29621405 0.000000 0.05858 0.000000 0.03702 0.010000 0.07245 -2.026000 0.01434 -0.061000 0.13110 0.528000 0.53228 ATG TCGA-IB-A7LX-01A-12D-A36O-08 CCL7-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256386.2 0 0 1 60 89 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 1.000000 57 87 0 50 2 0 0 0 0 50 2 -20.000000 1 1 0 0 1 2 2 4 2.274668 1 0.550000 3.150000 0.700100 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 AP2B1 163 broad.mit.edu 37 17 33954701 33954701 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:33954701C>A ENST00000262325.7 + 9 1664 c.1111C>A c.(1111-1113)Cga>Aga p.R371R AP2B1_ENST00000589344.1_Silent_p.R371R|AP2B1_ENST00000538556.1_Silent_p.R314R|AP2B1_ENST00000312678.8_Silent_p.R371R|AP2B1_ENST00000592545.1_Silent_p.R333R|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Silent_p.R371R NM_001282.2 NP_001273.1 P63010 AP2B1_HUMAN adaptor-related protein complex 2, beta 1 subunit p.R371*(1) 28 Ovarian(249;0.17) TGACTTTGTTCGAAAAGCTGT 0.443000 1 Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000262325.7 1 0 hg19 CCDS32622.1 TCGA-IB-A7LX-01A-12D-A36O-08 AP2B1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000448969.1 1 0 0 13 269 0 65 0 9.989629e-01 0 246 0 65 2 0 0 0 0 0 2 1 0.999535 13 266 0 63 2 0 0 0 0 65 2 -2.806910 1 1 0 0 1 2 2 4 2.274668 1 0.550000 3.150000 0.700100 0.260000 0.140000 1.000000 0.260000 0.321758 0.260000 0 1.900000e-01 3.700000e-01 TOP2A 7153 broad.mit.edu 37 17 38564239 38564239 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:38564239G>T ENST00000423485.1 - 12 1638 c.1480C>A c.(1480-1482)Cga>Aga p.R494R NM_001067.3 NP_001058.2 P11388 TOP2A_HUMAN topoisomerase (DNA) II alpha 170kDa 39 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GAAGCTTCTCGAACATTGAGT 0.368000 0 SO:0001819 synonymous_variant ENST00000423485.1 1 0 hg19 CCDS45672.1 TCGA-IB-A7LX-01A-12D-A36O-08 TOP2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338035.1 1 0 0 21 469 0 102 0 8.623733e-01 0 81 0 102 2 0 0 0 0 0 2 1 0.999997 21 466 0 101 2 0 0 0 0 102 2 -3.071207 1 1 0 0 1 2 2 4 2.267005 1 0.550000 3.150000 0.698997 0.240000 0.140000 1.000000 0.230000 0.304127 0.240000 0 1.800000e-01 3.200000e-01 KRT28 162605 broad.mit.edu 37 17 38949428 38949428 + Missense_Mutation SNP T T A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:38949428T>A ENST00000306658.7 - 7 1296 c.1231A>T c.(1231-1233)Agc>Tgc p.S411C NM_181535.3 NP_853513.2 keratin 28 30 Breast(137;0.000301) TTCCCAGGGCTTCCTGATCCA 0.313000 Melanoma(19;789 869 15380 26882 39836) 0 SO:0001583 missense ENST00000306658.7 1 1 hg19 CCDS11376.1 . . . . . . . . . . T 14.22 2.471242 0.43942 . . ENSG00000173908 ENST00000306658 D 0.83419 -1.72 5.35 0.343 0.16001 . 0.768911 0.12060 N 0.503255 T 0.76586 0.4008 L 0.38175 1.15 0.22081 N 0.999376 P 0.35192 0.489 B 0.41299 0.353 T 0.66968 -0.5789 10 0.62326 D 0.03 . 7.4993 0.27509 0.0:0.4287:0.0:0.5713 . 411 Q7Z3Y7 K1C28_HUMAN C 411 ENSP00000305263:S411C ENSP00000305263:S411C S - 1 0 KRT28 36202954 0.023000 0.18921 0.940000 0.37924 0.992000 0.81027 -0.298000 0.08265 0.108000 0.17862 0.533000 0.62120 AGC TCGA-IB-A7LX-01A-12D-A36O-08 KRT28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257201.2 1 0 1 55 296 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 1.000000 54 287 0 77 2 0 0 0 0 77 2 -20.000000 1 1 0 0 1 2 2 4 2.267005 1 0.550000 3.150000 0.698997 0.860000 0.660000 1.000000 1.000000 0.867460 0.860000 1 7.500000e-01 1 HEATR6 63897 broad.mit.edu 37 17 58128258 58128258 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:58128258C>A ENST00000184956.6 - 15 2386 c.2370G>T c.(2368-2370)gcG>gcT p.A790A HEATR6_ENST00000585976.1_Intron NM_022070.4 NP_071353.4 Q6AI08 HEAT6_HUMAN HEAT repeat containing 6 44 all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922) BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10) CACAGGCGCTCGCCTGGAGAG 0.532000 0 SO:0001819 synonymous_variant ENST00000184956.6 1 0 hg19 CCDS11623.1 TCGA-IB-A7LX-01A-12D-A36O-08 HEATR6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449165.1 1 0 0 10 235 0 55 0 2.734309e-01 0 22 0 55 2 0 0 0 0 0 2 1 0.996991 10 234 0 53 2 0 0 0 0 55 2 -2.802442 1 1 0 0 1 2 2 4 2.231336 1 0.550000 3.150000 0.694501 0.230000 0.110000 1.000000 0.220000 0.323144 0.230000 0 1.600000e-01 3.600000e-01 CHD3 1107 broad.mit.edu 37 17 7794350 7794350 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:7794350C>A ENST00000330494.7 + 4 627 c.477C>A c.(475-477)ctC>ctA p.L159L CHD3_ENST00000358181.4_Silent_p.L159L|CHD3_ENST00000380358.4_Silent_p.L218L NM_001005273.2 NP_001005273.1 Q12873 CHD3_HUMAN chromodomain helicase DNA binding protein 3 65 Prostate(122;0.202) ACCACACGCTCACCAACTACA 0.527000 0 SO:0001819 synonymous_variant ENST00000330494.7 1 0 hg19 CCDS32554.1 . . . . . . . . . . C 9.430 1.085307 0.20390 . . ENSG00000170004 ENST00000452447 . . . 4.54 -3.21 0.05140 . . . . . T 0.40222 0.1108 . . . 0.80722 D 1 . . . . . . T 0.34750 -0.9816 4 . . . -15.2706 3.1578 0.06510 0.1046:0.1724:0.1951:0.5278 . . . . N 34 . . H + 1 0 CHD3 7735075 0.764000 0.28473 0.974000 0.42286 0.988000 0.76386 -0.190000 0.09615 -0.301000 0.08882 -0.259000 0.10710 CAC TCGA-IB-A7LX-01A-12D-A36O-08 CHD3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318050.1 1 0 0 25 535 0 137 0 9.948179e-01 0 176 0 137 2 0 0 0 0 0 2 1 1.000000 24 529 0 133 2 0 0 0 0 137 2 -3.018473 1 1 0 0 1 1 2 3 1.950712 1 0.550000 3.150000 0.647059 0.200000 0.130000 0.300000 0.210000 0.214279 0.200000 0 1.600000e-01 2.500000e-01 MYH10 4628 broad.mit.edu 37 17 8439125 8439125 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr17:8439125C>A ENST00000269243.4 - 14 1838 c.1700G>T c.(1699-1701)cGa>cTa p.R567L MYH10_ENST00000360416.3_Missense_Mutation_p.R577L|MYH10_ENST00000396239.1_Missense_Mutation_p.R567L|MYH10_ENST00000379980.4_Missense_Mutation_p.R583L NM_005964.3 NP_005955.3 P35580 MYH10_HUMAN myosin, heavy chain 10, non-muscle 52 TTTTAATTGTCGAGGTTTCTG 0.368000 0 SO:0001583 missense ENST00000269243.4 1 0 hg19 CCDS11144.1 . . . . . . . . . . C 21.7 4.182476 0.78677 . . ENSG00000133026 ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980 T;T;D;T 0.88509 -0.74;-0.74;-2.39;-0.74 5.29 5.29 0.74685 Myosin head, motor domain (2); 0.000000 0.85682 D 0.000000 D 0.94997 0.8381 M 0.90977 3.165 0.58432 D 0.99999 P;P;P 0.51057 0.941;0.928;0.941 P;P;P 0.56751 0.805;0.705;0.805 D 0.95680 0.8731 10 0.87932 D 0 . 19.1238 0.93374 0.0:1.0:0.0:0.0 . 576;577;567 B2RWP9;F8VTL3;P35580 .;.;MYH10_HUMAN L 567;577;567;583 ENSP00000269243:R567L;ENSP00000353590:R577L;ENSP00000379539:R567L;ENSP00000369315:R583L ENSP00000269243:R567L R - 2 0 MYH10 8379850 0.401000 0.25303 0.999000 0.59377 0.542000 0.35054 3.206000 0.51098 2.752000 0.94435 0.557000 0.71058 CGA TCGA-IB-A7LX-01A-12D-A36O-08 MYH10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000227001.2 1 0 0 14 413 0 109 0 5.657491e-02 0 11 0 109 2 0 0 0 0 0 2 1 0.999739 14 407 0 109 2 0 0 0 0 109 2 -3.256806 1 1 0 0 1 1 2 3 1.950712 1 0.550000 3.150000 0.647059 0.150000 0.080000 0.250000 0.150000 0.161897 0.150000 0 1.100000e-01 2.000000e-01 DSG2 1829 broad.mit.edu 37 18 29115333 29115333 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr18:29115333C>A ENST00000261590.8 + 10 1590 c.1381C>A c.(1381-1383)Caa>Aaa p.Q461K NM_001943.3 NP_001934.2 Q14126 DSG2_HUMAN desmoglein 2 49 OV - Ovarian serous cystadenocarcinoma(10;0.0068) TAGATATGTTCAAAATGGCAC 0.279000 0 SO:0001583 missense ENST00000261590.8 1 0 hg19 CCDS42423.1 . . . . . . . . . . C 10.63 1.405016 0.25378 . . ENSG00000046604 ENST00000261590 T 0.59906 0.23 5.66 2.39 0.29439 Cadherin (4);Cadherin-like (1); 1.115670 0.06754 N 0.780562 T 0.32971 0.0847 N 0.05554 -0.025 0.09310 N 1 B 0.17667 0.023 B 0.15052 0.012 T 0.14839 -1.0458 10 0.02654 T 1 . 8.9226 0.35621 0.4051:0.4015:0.1934:0.0 . 461 Q14126 DSG2_HUMAN K 461 ENSP00000261590:Q461K ENSP00000261590:Q461K Q + 1 0 DSG2 27369331 0.000000 0.05858 0.955000 0.39395 0.836000 0.47400 -0.080000 0.11339 0.663000 0.31027 0.462000 0.41574 CAA TCGA-IB-A7LX-01A-12D-A36O-08 DSG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447506.1 1 0 0 22 468 0 170 0 9.998950e-01 0 312 0 170 2 0 0 0 0 0 2 1 0.999999 22 461 0 169 2 0 0 0 0 170 2 -3.210889 1 1 0 0 1 0 3 3 1.685847 1 0.550000 3.150000 0.626091 0.200000 0.120000 1.000000 0.190000 0.350999 0.200000 0 1.600000e-01 1 SLC14A2 8170 broad.mit.edu 37 18 43224013 43224013 + Silent SNP G G T rs149835341 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr18:43224013G>T ENST00000255226.6 + 10 2055 c.1239G>T c.(1237-1239)acG>acT p.T413T SLC14A2_ENST00000586448.1_Silent_p.T413T|RP11-116O18.1_ENST00000590535.1_RNA NM_007163.3 NP_009094.3 Q15849 UT2_HUMAN solute carrier family 14 (urea transporter), member 2 63 TGCTCCTGACGACAAACAACC 0.542000 0 SO:0001819 synonymous_variant ENST00000255226.6 1 0 hg19 CCDS11924.1 TCGA-IB-A7LX-01A-12D-A36O-08 SLC14A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255858.1 1 0 0 14 373 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 0.999753 14 370 0 148 2 0 0 0 0 148 2 -2.841885 1 1 0 0 1 0 3 3 1.685847 1 0.550000 3.150000 0.626091 0.170000 0.080000 1.000000 0.160000 0.321760 0.170000 0 1.200000e-01 1 ZNF491 126069 broad.mit.edu 37 19 11918032 11918032 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:11918032C>A ENST00000323169.5 + 3 1595 c.1264C>A c.(1264-1266)Cgt>Agt p.R422S ZNF491_ENST00000492230.1_Intron NM_152356.3 NP_689569.2 Q8N8L2 ZN491_HUMAN zinc finger protein 491 26 AGCCTTCATTCGTTCCAGTTA 0.333000 0 SO:0001583 missense ENST00000323169.5 1 0 hg19 CCDS12267.1 . . . . . . . . . . c 0.278 -0.988536 0.02162 . . ENSG00000177599 ENST00000323169;ENST00000455048 T 0.60424 0.19 0.737 -0.437 0.12272 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.32071 0.0817 N 0.13003 0.285 0.09310 N 1 B 0.20052 0.041 B 0.10450 0.005 T 0.14062 -1.0486 9 0.32370 T 0.25 . 2.3692 0.04326 0.2684:0.4281:0.0:0.3035 . 422 Q8N8L2 ZN491_HUMAN S 422;394 ENSP00000313443:R422S ENSP00000313443:R422S R + 1 0 ZNF491 11779032 0.000000 0.05858 0.002000 0.10522 0.085000 0.17905 -0.354000 0.07681 -0.163000 0.10946 -0.451000 0.05528 CGT TCGA-IB-A7LX-01A-12D-A36O-08 ZNF491-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344518.1 1 0 0 10 244 0 66 0 0 0 1 0 66 2 0 0 0 0 0 2 1 0.996451 9 236 0 66 2 0 0 0 0 66 2 -3.087178 1 1 0 0 1 1 2 3 1.925710 1 0.550000 3.150000 0.647059 0.180000 0.090000 0.320000 0.180000 0.198787 0.180000 0 1.300000e-01 2.600000e-01 PLVAP 83483 broad.mit.edu 37 19 17488061 17488061 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:17488061G>T ENST00000252590.4 - 1 98 c.37C>A c.(37-39)Cgg>Agg p.R13R NM_031310.1 NP_112600.1 Q9BX97 PLVAP_HUMAN plasmalemma vesicle associated protein 27 CCCCCCGCCCGAGCGTAGGAC 0.652000 0 SO:0001819 synonymous_variant ENST00000252590.4 1 0 hg19 CCDS32952.1 TCGA-IB-A7LX-01A-12D-A36O-08 PLVAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463655.1 1 0 0 12 316 0 83 0 9.514635e-01 0 138 0 83 2 0 0 0 0 0 2 1 0.999076 12 311 0 83 2 0 0 0 0 83 2 -2.789037 1 1 0 0 1 2 4 6 2.114927 1 0.550000 3.150000 0.677650 0.210000 0.100000 1.000000 0.180000 0.377920 0.210000 0 1.400000e-01 1 ZNF99 7652 broad.mit.edu 37 19 22940990 22940990 + Missense_Mutation SNP A A C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:22940990A>C ENST00000596209.1 - 4 1811 c.1721T>G c.(1720-1722)tTt>tGt p.F574C ZNF99_ENST00000397104.3_Missense_Mutation_p.F483C NM_001080409.2 NP_001073878.2 A8MXY4 ZNF99_HUMAN zinc finger protein 99 124 Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102) AGATTGCTTAAAAGCTTTGCC 0.368000 0 SO:0001583 missense ENST00000596209.1 1 1 hg19 CCDS59369.1 . . . . . . . . . . - 10.29 1.308831 0.23821 . . ENSG00000213973 ENST00000397104 T 0.45668 0.89 1.44 0.101 0.14517 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.63570 0.2522 M 0.88377 2.95 0.09310 N 1 D 0.89917 1.0 D 0.91635 0.999 T 0.51348 -0.8717 9 0.66056 D 0.02 . 5.428 0.16438 0.7506:0.0:0.0:0.2493 . 483 A8MXY4 ZNF99_HUMAN C 483 ENSP00000380293:F483C ENSP00000380293:F483C F - 2 0 ZNF99 22732830 0.978000 0.34361 0.001000 0.08648 0.011000 0.07611 4.718000 0.61930 -0.219000 0.10003 0.163000 0.16589 TTT TCGA-IB-A7LX-01A-12D-A36O-08 ZNF99-001 NOVEL not_best_in_genome_evidence|basic|CCDS protein_coding protein_coding OTTHUMT00000464591.1 1 0 1 114 177 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 1.000000 112 175 0 103 2 0 0 0 0 104 2 -20.000000 1 1 0 0 1 2 4 6 2.027318 1 0.550000 3.150000 0.664430 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 FCGBP 8857 broad.mit.edu 37 19 40433627 40433627 + Silent SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:40433627G>A ENST00000221347.6 - 2 649 c.642C>T c.(640-642)gtC>gtT p.V214V NM_003890.2 NP_003881.2 Q9Y6R7 FCGBP_HUMAN Fc fragment of IgG binding protein 165 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) TACTAGCTGTGACCTTTGACC 0.562000 0 SO:0001819 synonymous_variant ENST00000221347.6 1 1 hg19 CCDS12546.1 TCGA-IB-A7LX-01A-12D-A36O-08 FCGBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462507.1 1 0 0 18 252 0 83 0 1.446437e-02 0 3 0 83 2 0 0 0 0 0 2 1 0.999982 18 248 0 82 2 0 0 0 0 83 2 -19.989210 1 1 0 0 1 1 2 3 1.979295 1 0.550000 3.150000 0.647059 0.310000 0.180000 0.470000 0.300000 0.323208 0.310000 0 2.400000e-01 3.900000e-01 BLOC1S3 388552 broad.mit.edu 37 19 45682658 45682658 + Missense_Mutation SNP A A C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:45682658A>C ENST00000433642.2 + 2 200 c.104A>C c.(103-105)gAg>gCg p.E35A BLOC1S3_ENST00000587722.1_Missense_Mutation_p.E35A|TRAPPC6A_ENST00000006275.4_5'Flank|TRAPPC6A_ENST00000592647.1_5'Flank|AC005779.2_ENST00000593083.1_5'Flank|TRAPPC6A_ENST00000585934.1_5'Flank|TRAPPC6A_ENST00000588062.1_5'Flank NM_212550.3 NP_997715.1 Q6QNY0 BL1S3_HUMAN biogenesis of lysosomal organelles complex-1, subunit 3 2 Ovarian(192;0.0728)|all_neural(266;0.112) TCCTCGTCGGAGGAGGAGGAG 0.761000 Hermansky-Pudlak syndrome 0 SO:0001583 missense Familial Cancer Database HPS, HPS1-8 ENST00000433642.2 0 1 hg19 CCDS12656.1 . . . . . . . . . . A 13.92 2.381951 0.42207 . . ENSG00000189114 ENST00000433642 . . . 2.93 1.77 0.24775 . 0.624228 0.12947 N 0.426136 T 0.16642 0.0400 N 0.08118 0 0.26487 N 0.975019 B 0.28128 0.201 B 0.20767 0.031 T 0.13980 -1.0489 9 0.62326 D 0.03 . 6.2471 0.20825 0.7472:0.2528:0.0:0.0 . 35 Q6QNY0 BL1S3_HUMAN A 35 . ENSP00000393840:E35A E + 2 0 BLOC1S3 50374498 0.697000 0.27767 0.994000 0.49952 0.982000 0.71751 0.657000 0.24963 1.121000 0.41925 0.374000 0.22700 GAG TCGA-IB-A7LX-01A-12D-A36O-08 BLOC1S3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457559.1 1 0 0 18 23 0 9 1 9.874824e-01 5 8 0 9 2 0 0 0 0 0 2 1 0.999998 18 23 0 8 2 0 0 0 0 9 2 -20.000000 1 1 119586 6 35 1 1 2 3 1.979295 1 0.550000 3.150000 0.647059 0.990000 0.990000 1.000000 1.000000 0.999957 0.990000 1 9.900000e-01 1 ZNF256 10172 broad.mit.edu 37 19 58453311 58453311 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:58453311G>T ENST00000282308.3 - 3 1061 c.865C>A c.(865-867)Cac>Aac p.H289N ZNF256_ENST00000598928.1_3'UTR NM_005773.2 NP_005764.2 Q9Y2P7 ZN256_HUMAN zinc finger protein 256 19 Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157) ACTCCAGTGTGAATTCTTCGG 0.393000 NSCLC(55;1313 1552 8040 11996) 0 SO:0001583 missense ENST00000282308.3 1 0 hg19 CCDS12966.1 . . . . . . . . . . . 23.0 4.368789 0.82463 . . ENSG00000152454 ENST00000282308 T 0.67345 -0.26 3.13 2.07 0.26955 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.81795 0.4898 M 0.89287 3.02 0.28223 N 0.926444 D 0.76494 0.999 D 0.73708 0.981 T 0.72047 -0.4408 9 0.87932 D 0 . 9.0328 0.36269 0.1174:0.0:0.8826:0.0 . 289 Q9Y2P7 ZN256_HUMAN N 289 ENSP00000282308:H289N ENSP00000282308:H289N H - 1 0 ZNF256 63145123 1.000000 0.71417 0.247000 0.24249 0.980000 0.70556 3.300000 0.51834 0.639000 0.30564 0.460000 0.39030 CAC TCGA-IB-A7LX-01A-12D-A36O-08 ZNF256-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466702.1 1 0 0 17 441 0 153 0 1.477809e-02 0 5 0 153 2 0 0 0 0 0 2 1 0.999964 17 437 0 152 2 0 0 0 0 153 2 -4.132772 1 1 0 0 1 1 2 3 1.990465 1 0.550000 3.150000 0.647059 0.170000 0.090000 0.270000 0.180000 0.181201 0.170000 0 1.300000e-01 2.200000e-01 C19orf18 147685 broad.mit.edu 37 19 58477954 58477954 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:58477954C>A ENST00000314391.3 - 4 416 c.315G>T c.(313-315)tcG>tcT p.S105S NM_152474.4 NP_689687.1 Q8NEA5 CS018_HUMAN chromosome 19 open reading frame 18 8 Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156) AGGCTACGCTCGAAATTAAAA 0.348000 0 SO:0001819 synonymous_variant ENST00000314391.3 1 0 hg19 CCDS12967.1 TCGA-IB-A7LX-01A-12D-A36O-08 C19orf18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466704.1 1 0 0 12 308 0 72 0 0 0 1 0 72 2 0 0 0 0 0 2 1 0.999094 11 305 0 72 2 0 0 0 0 72 2 -2.803158 1 1 0 0 1 1 2 3 1.990465 1 0.550000 3.150000 0.647059 0.170000 0.090000 0.290000 0.180000 0.186858 0.170000 0 1.300000e-01 2.400000e-01 ZNF606 80095 broad.mit.edu 37 19 58490276 58490276 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr19:58490276G>A ENST00000341164.4 - 7 2392 c.1772C>T c.(1771-1773)aCg>aTg p.T591M ZNF606_ENST00000536132.1_Missense_Mutation_p.T501M NM_025027.3 NP_079303.2 Q8WXB4 ZN606_HUMAN zinc finger protein 606 26 Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157) TTTCTCTCCCGTGTGAGTTCT 0.418000 0 SO:0001583 missense ENST00000341164.4 1 1 hg19 CCDS12968.1 . . . . . . . . . . G 14.81 2.647444 0.47258 . . ENSG00000166704 ENST00000341164;ENST00000536132 T;T 0.26373 1.74;1.74 4.91 4.91 0.64330 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.134588 0.34676 N 0.003775 T 0.53530 0.1802 M 0.79926 2.475 0.46416 D 0.999034 D 0.89917 1.0 D 0.68765 0.96 T 0.58973 -0.7541 10 0.87932 D 0 . 17.3812 0.87405 0.0:0.0:1.0:0.0 . 591 Q8WXB4 ZN606_HUMAN M 591;501 ENSP00000343617:T591M;ENSP00000445624:T501M ENSP00000343617:T591M T - 2 0 ZNF606 63182088 0.994000 0.37717 0.995000 0.50966 0.976000 0.68499 2.147000 0.42226 2.706000 0.92434 0.561000 0.74099 ACG TCGA-IB-A7LX-01A-12D-A36O-08 ZNF606-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405961.1 0 0 0 13 387 1 116 0 1.740299e-02 0 6 1 116 2 0 0 0 0 0 2 1 0.999461 12 377 0 113 2 0 0 0 1 116 2 -2.695491 1 1 121412 1 29 1 1 2 3 1.990465 1 0.550000 3.150000 0.647059 0.150000 0.070000 0.250000 0.150000 0.161239 0.150000 0 1.100000e-01 2.000000e-01 GPSM2 29899 broad.mit.edu 37 1 109428193 109428193 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:109428193C>A ENST00000406462.2 + 3 822 c.49C>A c.(49-51)Cgt>Agt p.R17S AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.R17S P81274 GPSM2_HUMAN G-protein signaling modulator 2 14 all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626) TTTTCATGTTCGTTACAGGTA 0.294000 0 SO:0001583 missense ENST00000406462.2 1 0 hg19 CCDS792.2 . . . . . . . . . . C 18.06 3.538254 0.65085 . . ENSG00000121957 ENST00000406462;ENST00000435987;ENST00000264126;ENST00000435475;ENST00000446797 D;D;D 0.93189 -3.18;-2.38;-3.18 5.62 5.62 0.85841 . 0.000000 0.85682 D 0.000000 T 0.78413 0.4279 N 0.03608 -0.345 0.39307 D 0.965015 P 0.43024 0.798 B 0.34779 0.189 D 0.84184 0.0441 10 0.46703 T 0.11 -5.4334 18.2007 0.89836 0.0:1.0:0.0:0.0 . 17 P81274 GPSM2_HUMAN S 17 ENSP00000385510:R17S;ENSP00000408664:R17S;ENSP00000264126:R17S ENSP00000264126:R17S R + 1 0 GPSM2 109229716 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 5.317000 0.65822 2.801000 0.96364 0.650000 0.86243 CGT TCGA-IB-A7LX-01A-12D-A36O-08 GPSM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032400.3 1 0 0 26 548 0 174 0 2.066676e-01 0 18 0 174 2 0 0 0 0 0 2 1 1.000000 26 547 0 174 2 0 0 0 0 174 2 -3.914346 1 1 0 0 1 0 2 2 1.629647 1 0.550000 3.150000 0.550000 0.160000 0.100000 0.230000 0.160000 0.170195 0.160000 0 1.300000e-01 2.000000e-01 PHTF1 10745 broad.mit.edu 37 1 114280825 114280825 + Silent SNP G G T rs78000844 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:114280825G>T ENST00000369604.1 - 5 721 c.238C>A c.(238-240)Cga>Aga p.R80R PHTF1_ENST00000393357.2_Silent_p.R80R|PHTF1_ENST00000447664.2_Silent_p.R80R|PHTF1_ENST00000369596.2_Intron|PHTF1_ENST00000357783.2_Silent_p.R80R|PHTF1_ENST00000369598.1_Silent_p.R80R|PHTF1_ENST00000369600.1_Intron Q9UMS5 PHTF1_HUMAN putative homeodomain transcription factor 1 27 Lung SC(450;0.184) all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05) AATACAACTCGAACAAGCCCC 0.358000 0 SO:0001819 synonymous_variant ENST00000369604.1 1 0 hg19 CCDS861.1 TCGA-IB-A7LX-01A-12D-A36O-08 PHTF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032666.1 1 0 0 11 207 0 85 0 1.971210e-01 0 15 0 85 2 0 0 0 0 0 2 1 0.998293 11 203 0 85 2 0 0 0 0 85 2 -4.545072 1 1 0 0 1 0 2 2 1.629647 1 0.550000 3.150000 0.550000 0.180000 0.090000 0.310000 0.180000 0.197590 0.180000 0 1.300000e-01 2.500000e-01 PTCHD2 57540 broad.mit.edu 37 1 11561859 11561859 + Silent SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:11561859C>T ENST00000294484.6 + 2 948 c.810C>T c.(808-810)caC>caT p.H270H PTCHD2_ENST00000389575.3_Silent_p.H270H NM_020780.1 NP_065831.1 Q9P2K9 PTHD2_HUMAN patched domain containing 2 76 Ovarian(185;0.249) Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255) CTCAGACGCACGCGCACTGGC 0.677000 0 SO:0001819 synonymous_variant ENST00000294484.6 1 1 hg19 CCDS41247.1 TCGA-IB-A7LX-01A-12D-A36O-08 PTCHD2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000005770.2 1 0 1 49 24 0 20 0 0 0 0 20 2 0 0 0 0 0 2 1 1.000000 47 24 0 19 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 0 3 3 1.682210 1 0.550000 3.150000 0.625234 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SPAG17 200162 broad.mit.edu 37 1 118609502 118609502 + Silent SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:118609502C>T ENST00000336338.5 - 18 2471 c.2406G>A c.(2404-2406)aaG>aaA p.K802K NM_206996.2 NP_996879.1 Q6Q759 SPG17_HUMAN sperm associated antigen 17 123 Esophageal squamous(2;0.0106) all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01) ACCTATATTGCTTATGGGCTT 0.358000 0 SO:0001819 synonymous_variant ENST00000336338.5 1 1 hg19 CCDS899.1 TCGA-IB-A7LX-01A-12D-A36O-08 SPAG17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033723.1 1 0 1 159 130 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 1.000000 158 129 0 120 2 0 0 0 0 121 2 -20.000000 1 1 0 0 1 0 2 2 1.629647 1 0.550000 3.150000 0.550000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 VPS13D 55187 broad.mit.edu 37 1 12383813 12383813 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:12383813C>A ENST00000358136.3 + 35 8096 c.7966C>A c.(7966-7968)Cgc>Agc p.R2656S VPS13D_ENST00000356315.4_Missense_Mutation_p.R2656S NM_015378.2 NP_056193.2 vacuolar protein sorting 13 homolog D (S. cerevisiae) 130 Ovarian(185;0.249) Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) GGATGATTGTCGCAAAGCTCT 0.383000 0 SO:0001583 missense ENST00000358136.3 1 0 hg19 CCDS30588.1 . . . . . . . . . . C 17.58 3.424276 0.62733 . . ENSG00000048707 ENST00000356315;ENST00000358136 T;T 0.25749 1.78;1.78 5.61 5.61 0.85477 Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1); 0.073997 0.52532 D 0.000062 T 0.45216 0.1331 M 0.64404 1.975 0.80722 D 1 D;B;B 0.62365 0.991;0.388;0.442 D;B;B 0.64595 0.927;0.088;0.142 T 0.20806 -1.0264 10 0.08179 T 0.78 . 19.6336 0.95721 0.0:1.0:0.0:0.0 . 563;2656;2656 B1AJZ2;Q5THJ4-2;Q5THJ4 .;.;VP13D_HUMAN S 2656 ENSP00000348666:R2656S;ENSP00000350854:R2656S ENSP00000348666:R2656S R + 1 0 VPS13D 12306400 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.089000 0.64492 2.646000 0.89796 0.637000 0.83480 CGC TCGA-IB-A7LX-01A-12D-A36O-08 VPS13D-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036897.2 1 0 0 18 387 0 125 0 3.254422e-01 0 24 0 125 2 0 0 0 0 0 2 1 0.999981 17 381 0 123 2 0 0 0 0 125 2 -3.658427 1 1 0 0 1 0 3 3 1.682210 1 0.550000 3.150000 0.625234 0.200000 0.110000 1.000000 0.190000 0.354122 0.200000 0 1.500000e-01 1 THBS3 7059 broad.mit.edu 37 1 155170966 155170966 + Silent SNP G G A rs150820199 byFrequency TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:155170966G>A ENST00000368378.3 - 12 1379 c.1359C>T c.(1357-1359)aaC>aaT p.N453N RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000541990.1_De_novo_Start_OutOfFrame|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000457183.2_Silent_p.N333N|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000541576.1_Intron|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA NM_001252607.1|NM_007112.4 NP_001239536.1|NP_009043.1 P49746 TSP3_HUMAN thrombospondin 3 p.N453N(1) 48 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) TCCCACACACGTTCCCATTCC 0.567000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000368378.3 0 1 hg19 CCDS1099.1 TCGA-IB-A7LX-01A-12D-A36O-08 THBS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086856.1 0 0 0 8 480 0 112 1 5.365262e-01 4 98 0 112 2 0 0 0 0 0 2 1 0.989030 8 475 0 111 2 0 0 0 0 112 2 -2.825541 1 0 121412 11 43 1 0 9 9 2.571479 1 0.550000 3.150000 0.728015 0.110000 0.030000 1.000000 0.090000 0.303379 0.110000 0 7.000000e-02 1 TPR 7175 broad.mit.edu 37 1 186304589 186304589 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:186304589G>T ENST00000367478.4 - 34 5088 c.4792C>A c.(4792-4794)Cgc>Agc p.R1598S NM_003292.2 NP_003283.2 P12270 TPR_HUMAN translocated promoter region, nuclear basket protein 123 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) GCAGTAATGCGAACATCCAAT 0.423000 T NTRK1 papillary thyroid Dom yes 1 1q25 7175 translocated promoter region E 0 SO:0001583 missense ENST00000367478.4 1 0 hg19 CCDS41446.1 . . . . . . . . . . G 29.2 4.989888 0.93106 . . ENSG00000047410 ENST00000367478 T 0.26518 1.73 5.14 5.14 0.70334 . 0.000000 0.85682 D 0.000000 T 0.54498 0.1862 M 0.79805 2.47 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 T 0.53585 -0.8418 10 0.36615 T 0.2 . 18.9661 0.92697 0.0:0.0:1.0:0.0 . 1598 P12270 TPR_HUMAN S 1598 ENSP00000356448:R1598S ENSP00000356448:R1598S R - 1 0 TPR 184571212 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 9.065000 0.93941 2.545000 0.85829 0.650000 0.86243 CGC TCGA-IB-A7LX-01A-12D-A36O-08 TPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086353.2 1 0 0 25 591 0 155 0 8.368645e-01 0 80 0 155 2 0 0 0 0 0 2 1 1.000000 24 583 0 155 2 0 0 0 0 155 2 -2.881965 1 1 0 0 1 0 4 4 2.292661 1 0.550000 3.150000 0.704433 0.220000 0.140000 1.000000 0.230000 0.261896 0.220000 0 1.800000e-01 2.900000e-01 TROVE2 6738 broad.mit.edu 37 1 193046072 193046072 + Silent SNP C C A rs55932617 by1000genomes TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:193046072C>A ENST00000367446.3 + 5 1188 c.978C>A c.(976-978)atC>atA p.I326I TROVE2_ENST00000367445.3_Silent_p.I326I|TROVE2_ENST00000416058.2_Silent_p.I51I|TROVE2_ENST00000432079.1_Silent_p.I51I|TROVE2_ENST00000400968.2_Silent_p.I326I|TROVE2_ENST00000367444.3_Silent_p.I326I|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000367441.1_Silent_p.I326I|TROVE2_ENST00000367443.1_Silent_p.I326I NM_004600.5 NP_004591.2 P10155 RO60_HUMAN TROVE domain family, member 2 21 ATATTTTGATCGCATTAGAAA 0.338000 0 SO:0001819 synonymous_variant ENST00000367446.3 1 0 hg19 CCDS1379.1 TCGA-IB-A7LX-01A-12D-A36O-08 TROVE2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000086688.1 1 0 0 14 312 0 71 0 3.962869e-01 0 30 0 71 2 0 0 0 0 0 2 1 0.999738 14 306 0 71 2 0 0 0 0 71 2 -2.966611 1 1 0 0 1 0 4 4 2.292661 1 0.550000 3.150000 0.704433 0.240000 0.130000 1.000000 0.240000 0.281234 0.240000 0 1.800000e-01 3.300000e-01 CRB1 23418 broad.mit.edu 37 1 197396927 197396927 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:197396927C>A ENST00000367400.3 + 7 2607 c.2472C>A c.(2470-2472)atC>atA p.I824I CRB1_ENST00000367399.2_Silent_p.I712I|CRB1_ENST00000544212.1_Silent_p.I305I|CRB1_ENST00000535699.1_Silent_p.I755I|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367397.1_Silent_p.I205I NM_201253.2 NP_957705.1 P82279 CRUM1_HUMAN crumbs family member 1, photoreceptor morphogenesis associated p.I824M(1) 132 CGTGGAAAATCGAAAAGGGAG 0.373000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000367400.3 1 0 hg19 CCDS1390.1 TCGA-IB-A7LX-01A-12D-A36O-08 CRB1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086565.2 1 0 0 13 284 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 0.999534 13 281 0 73 2 0 0 0 0 73 2 -4.390350 1 0 0 0 1 0 4 4 2.292661 1 0.550000 3.150000 0.704433 0.250000 0.130000 1.000000 0.240000 0.287006 0.250000 0 1.800000e-01 3.400000e-01 KDM5B 10765 broad.mit.edu 37 1 202724554 202724554 + Missense_Mutation SNP C C A rs76768289 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:202724554C>A ENST00000367265.3 - 11 2547 c.1383G>T c.(1381-1383)ttG>ttT p.L461F KDM5B_ENST00000456180.1_5'UTR|KDM5B_ENST00000367264.2_Missense_Mutation_p.L497F NM_006618.3 NP_006609.3 Q9UGL1 KDM5B_HUMAN lysine (K)-specific demethylase 5B 6 GCATGTTGTTCAAATTCCAGC 0.378000 0 SO:0001583 missense ENST00000367265.3 0 1 hg19 CCDS30974.1 . . . . . . . . . . C 18.80 3.700822 0.68501 . . ENSG00000117139 ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790 T;T;T 0.72505 -0.66;-0.66;-0.66 5.73 4.82 0.62117 Transcription factor jumonji/aspartyl beta-hydroxylase (2); 0.000000 0.85682 D 0.000000 D 0.86351 0.5912 M 0.93328 3.405 0.58432 D 0.999999 D;D 0.89917 0.999;1.0 D;D 0.91635 0.961;0.999 D 0.88022 0.2769 10 0.87932 D 0 -12.7178 9.1277 0.36826 0.0:0.7688:0.0:0.2312 . 497;461 Q9UGL1-2;Q9UGL1 .;KDM5B_HUMAN F 461;303;497;303 ENSP00000356234:L461F;ENSP00000356233:L497F;ENSP00000235790:L303F ENSP00000235790:L303F L - 3 2 KDM5B 200991177 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.022000 0.41030 1.425000 0.47237 0.655000 0.94253 TTG TCGA-IB-A7LX-01A-12D-A36O-08 KDM5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099184.2 0 0 0 18 487 0 127 0 7.712277e-01 1 77 0 127 2 0 0 0 0 0 2 1 0.999976 16 472 0 125 2 0 0 0 0 127 2 -1.828307 0 1 121390 23 41 1 0 4 4 2.292661 1 0.550000 3.150000 0.704433 0.200000 0.110000 1.000000 0.200000 0.237404 0.200000 0 1.500000e-01 2.600000e-01 CNIH3 149111 broad.mit.edu 37 1 224868723 224868723 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:224868723C>A ENST00000272133.3 + 2 1027 c.145C>A c.(145-147)Cat>Aat p.H49N NM_152495.1 NP_689708.1 Q8TBE1 CNIH3_HUMAN cornichon family AMPA receptor auxiliary protein 3 9 Breast(184;0.218) CAATCCTGTTCATGCGGTAAG 0.483000 0 SO:0001583 missense ENST00000272133.3 1 0 hg19 CCDS1544.1 . . . . . . . . . . C 7.784 0.710231 0.15239 . . ENSG00000143786 ENST00000272133 . . . 5.45 5.45 0.79879 . 0.000000 0.85682 D 0.000000 T 0.24851 0.0603 N 0.00554 -1.385 0.80722 D 1 B 0.31705 0.336 B 0.39531 0.302 T 0.43734 -0.9373 9 0.02654 T 1 -24.8564 18.0599 0.89373 0.0:1.0:0.0:0.0 . 49 Q8TBE1 CNIH3_HUMAN N 49 . ENSP00000272133:H49N H + 1 0 CNIH3 222935346 0.997000 0.39634 0.970000 0.41538 0.845000 0.48019 5.322000 0.65852 2.573000 0.86826 0.643000 0.83706 CAT TCGA-IB-A7LX-01A-12D-A36O-08 CNIH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091752.2 1 0 0 15 457 0 131 0 3.651894e-01 0 38 0 131 2 0 0 0 0 0 2 1 0.999851 15 445 0 128 2 0 0 0 0 131 2 -3.049391 1 1 0 0 1 0 4 4 2.292661 1 0.550000 3.150000 0.704433 0.180000 0.090000 1.000000 0.190000 0.217597 0.180000 0 1.300000e-01 2.400000e-01 RYR2 6262 broad.mit.edu 37 1 237995882 237995882 + Missense_Mutation SNP A A T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:237995882A>T ENST00000366574.2 + 105 15156 c.14839A>T c.(14839-14841)Agg>Tgg p.R4947W RYR2_ENST00000542537.1_Missense_Mutation_p.R4931W|RYR2_ENST00000360064.6_Missense_Mutation_p.R4953W NM_001035.2 NP_001026.2 Q92736 RYR2_HUMAN ryanodine receptor 2 (cardiac) 586 Ovarian(103;0.103) all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225) OV - Ovarian serous cystadenocarcinoma(106;0.00606) GTATCAAGAAAGGTGTTGGGA 0.388000 0 SO:0001583 missense ENST00000366574.2 1 1 hg19 CCDS55691.1 . . . . . . . . . . A 17.22 3.333129 0.60853 . . ENSG00000198626 ENST00000366574;ENST00000360064;ENST00000542537 D;D;D 0.97232 -4.3;-4.26;-4.29 5.16 4.0 0.46444 . 0.000000 0.56097 D 0.000025 D 0.98460 0.9487 M 0.89968 3.075 0.80722 D 1 D 0.76494 0.999 D 0.77557 0.99 D 0.98802 1.0740 10 0.87932 D 0 -17.2433 11.8212 0.52238 0.7051:0.2949:0.0:0.0 . 4947 Q92736 RYR2_HUMAN W 4947;4953;4931 ENSP00000355533:R4947W;ENSP00000353174:R4953W;ENSP00000443798:R4931W ENSP00000353174:R4953W R + 1 2 RYR2 236062505 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 2.605000 0.46283 0.932000 0.37266 0.533000 0.62120 AGG TCGA-IB-A7LX-01A-12D-A36O-08 RYR2-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095402.2 0 0 0 8 155 0 33 0 9.424743e-03 0 3 0 33 2 0 0 0 0 0 2 1 0.989669 8 154 0 32 2 0 0 0 0 33 2 -4.539993 1 1 0 0 1 0 4 4 2.292661 1 0.550000 3.150000 0.704433 0.290000 0.130000 1.000000 0.270000 0.327747 0.290000 0 2.000000e-01 4.200000e-01 SDCCAG8 10806 broad.mit.edu 37 1 243507631 243507631 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:243507631C>A ENST00000366541.3 + 12 1589 c.1471C>A c.(1471-1473)Cag>Aag p.Q491K SDCCAG8_ENST00000355875.4_Missense_Mutation_p.Q448K|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.Q346K|MIR4677_ENST00000584153.1_RNA NM_006642.3 NP_006633.1 Q86SQ7 SDCG8_HUMAN serologically defined colon cancer antigen 8 29 all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218) all_cancers(173;0.00395) all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392) AATTAAAGATCAGGTAAGAGA 0.353000 0 SO:0001583 missense ENST00000366541.3 1 1 hg19 CCDS31075.1 . . . . . . . . . . C 16.26 3.072404 0.55646 . . ENSG00000054282 ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549 T;T;T;T 0.57273 0.7;0.66;0.66;0.41 6.07 5.16 0.70880 . 0.129373 0.52532 D 0.000063 T 0.39886 0.1095 L 0.29908 0.895 0.47245 D 0.999362 B;B 0.25441 0.075;0.126 B;B 0.28638 0.092;0.092 T 0.19614 -1.0300 10 0.15499 T 0.54 -7.4048 12.343 0.55105 0.1339:0.7375:0.1286:0.0 . 448;491 E9PFS7;Q86SQ7 .;SDCG8_HUMAN K 448;491;346;271 ENSP00000348137:Q448K;ENSP00000355499:Q491K;ENSP00000341260:Q346K;ENSP00000410200:Q271K ENSP00000341260:Q346K Q + 1 0 SDCCAG8 241574254 0.998000 0.40836 1.000000 0.80357 0.998000 0.95712 1.247000 0.32815 1.566000 0.49654 0.585000 0.79938 CAG TCGA-IB-A7LX-01A-12D-A36O-08 SDCCAG8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096485.1 1 0 1 32 199 0 53 1 9.703296e-01 9 29 0 53 2 0 0 0 0 0 2 1 1.000000 32 197 0 52 2 0 0 0 0 53 2 -15.859720 1 1 0 0 1 0 4 4 2.225328 1 0.550000 3.150000 0.698997 0.770000 0.530000 1.000000 1.000000 0.785166 0.770000 0 6.400000e-01 9.400000e-01 OR2W5 441932 broad.mit.edu 37 1 247655339 247655339 + RNA SNP A A T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr1:247655339A>T ENST00000522351.1 + 0 970 A6NFC9 OR2W5_HUMAN olfactory receptor, family 2, subfamily W, member 5 39 all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.222) OV - Ovarian serous cystadenocarcinoma(106;0.0188) CCATGAAGAAACTTCTGGGGT 0.507000 0 ENST00000522351.1 1 1 hg19 TCGA-IB-A7LX-01A-12D-A36O-08 OR2W5-002 KNOWN basic processed_transcript pseudogene OTTHUMT00000375789.1 0 0 0 123 246 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 1.000000 124 239 0 96 2 0 0 0 0 97 2 -20.000000 1 1 0 0 1 0 4 4 2.225328 1 0.550000 3.150000 0.698997 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CLDN8 9073 broad.mit.edu 37 21 31587596 31587596 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr21:31587596C>A ENST00000399899.1 - 1 795 c.648G>T c.(646-648)ccG>ccT p.P216P CLDN8_ENST00000286809.1_Silent_p.P216P NM_199328.2 NP_955360.1 P56748 CLD8_HUMAN claudin 8 15 AGTAGACGCTCGGTGACTTCT 0.378000 0 SO:0001819 synonymous_variant ENST00000399899.1 1 0 hg19 CCDS13587.1 TCGA-IB-A7LX-01A-12D-A36O-08 CLDN8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000182260.1 1 0 0 25 478 0 128 0 4.709011e-02 0 7 0 128 2 0 0 0 0 0 2 1 1.000000 24 470 0 126 2 0 0 0 0 128 2 -2.595282 1 1 0 0 1 0.550000 3.150000 0 0 ITSN1 6453 broad.mit.edu 37 21 35147105 35147105 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr21:35147105C>A ENST00000381318.3 + 13 1666 c.1378C>A c.(1378-1380)Caa>Aaa p.Q460K ITSN1_ENST00000437442.2_Missense_Mutation_p.Q460K|ITSN1_ENST00000399355.2_Missense_Mutation_p.Q460K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399353.1_Missense_Mutation_p.Q423K|ITSN1_ENST00000399338.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399352.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000381285.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399367.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399326.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399349.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000379960.5_Missense_Mutation_p.Q460K NM_003024.2 NP_003015.2 Q15811 ITSN1_HUMAN intersectin 1 (SH3 domain protein) 67 ACTACTAAATCAAAGAAACAA 0.373000 0 SO:0001583 missense ENST00000381318.3 1 0 hg19 CCDS33545.1 . . . . . . . . . . C 17.68 3.450044 0.63290 . . ENSG00000205726 ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960 T;T;T;T;T;T;T;T;T;T;T;T 0.49432 1.61;0.79;0.83;0.78;1.61;1.61;0.82;1.61;1.61;1.61;1.61;1.61 4.64 4.64 0.57946 . 0.120389 0.56097 D 0.000021 T 0.49236 0.1545 M 0.68317 2.08 0.80722 D 1 B;B;B;B;B;P;B;B;B;B 0.34864 0.064;0.064;0.064;0.023;0.106;0.473;0.023;0.023;0.106;0.064 B;B;B;B;B;B;B;B;B;B 0.33121 0.039;0.039;0.039;0.005;0.084;0.158;0.005;0.005;0.084;0.039 T 0.56703 -0.7935 10 0.54805 T 0.06 . 17.8738 0.88818 0.0:1.0:0.0:0.0 . 423;423;423;460;460;460;460;460;460;423 A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0 .;.;.;.;.;.;.;ITSN1_HUMAN;.;. K 423;460;460;460;460;460;460;460;460;460;460;460;460;460 ENSP00000382290:Q423K;ENSP00000370719:Q460K;ENSP00000370691:Q460K;ENSP00000370685:Q460K;ENSP00000382301:Q460K;ENSP00000382289:Q460K;ENSP00000382292:Q460K;ENSP00000382286:Q460K;ENSP00000382275:Q460K;ENSP00000387377:Q460K;ENSP00000382265:Q460K;ENSP00000369294:Q460K ENSP00000369294:Q460K Q + 1 0 ITSN1 34068975 1.000000 0.71417 0.855000 0.33649 0.948000 0.59901 5.820000 0.69250 2.289000 0.77006 0.655000 0.94253 CAA TCGA-IB-A7LX-01A-12D-A36O-08 ITSN1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000140070.4 1 0 0 13 316 0 82 0 7.013694e-01 0 60 0 82 2 0 0 0 0 0 2 1 0.999492 12 310 0 81 2 0 0 0 0 82 2 -3.920832 1 1 0 0 1 2 3 5 2.266323 1 0.550000 3.150000 0.698997 0.240000 0.120000 1.000000 0.230000 0.408668 0.240000 0 1.700000e-01 1 DSCAM 1826 broad.mit.edu 37 21 41423897 41423897 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr21:41423897G>T ENST00000400454.1 - 30 5650 c.5173C>A c.(5173-5175)Cgg>Agg p.R1725R NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) GTTCCCGGCCGAGCGTCTGAA 0.483000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001819 synonymous_variant ENST00000400454.1 1 0 hg19 CCDS42929.1 TCGA-IB-A7LX-01A-12D-A36O-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 1 0 0 27 516 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 1.000000 27 503 0 121 2 0 0 0 0 122 2 -2.870906 1 1 0 0 1 2 3 5 2.266323 1 0.550000 3.150000 0.698997 0.290000 0.180000 1.000000 0.270000 0.446621 0.290000 0 2.200000e-01 1 CACNG2 10369 broad.mit.edu 37 22 37098459 37098459 + Missense_Mutation SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr22:37098459C>T ENST00000300105.6 - 1 1144 c.163G>A c.(163-165)Gag>Aag p.E55K RP1-293L6.1_ENST00000430281.1_RNA NM_006078.3 NP_006069.1 Q9Y698 CCG2_HUMAN calcium channel, voltage-dependent, gamma subunit 2 18 ATAACTTCCTCGTTCTTTTTG 0.517000 0 SO:0001583 missense ENST00000300105.6 1 1 hg19 CCDS13931.1 . . . . . . . . . . c 16.52 3.145171 0.57044 . . ENSG00000166862 ENST00000300105 T 0.37584 1.19 4.37 4.37 0.52481 . 0.000000 0.85682 D 0.000000 T 0.22820 0.0551 N 0.12746 0.255 0.58432 D 0.999997 D 0.52996 0.957 P 0.44394 0.448 T 0.04281 -1.0963 10 0.06891 T 0.86 -10.3973 17.3494 0.87318 0.0:1.0:0.0:0.0 . 55 Q9Y698 CCG2_HUMAN K 55 ENSP00000300105:E55K ENSP00000300105:E55K E - 1 0 CACNG2 35428405 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.284000 0.78650 2.134000 0.65973 0.546000 0.68486 GAG TCGA-IB-A7LX-01A-12D-A36O-08 CACNG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075500.2 1 0 1 113 322 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 1.000000 112 318 0 130 2 0 0 0 0 133 2 -5.967919 1 1 0 0 1 2 3 5 1.795983 1 0.550000 3.150000 0.619128 0.990000 0.940000 1.000000 1.000000 0.996954 0.990000 1 9.900000e-01 1 LGALS1 3956 broad.mit.edu 37 22 38075643 38075643 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr22:38075643G>A ENST00000215909.5 + 4 390 c.295G>A c.(295-297)Gtc>Atc p.V99I LGALS1_ENST00000489315.1_3'UTR NM_002305.3 NP_002296.1 P09382 LEG1_HUMAN lectin, galactoside-binding, soluble, 1 3 Melanoma(58;0.0574) CAACCTGACCGTCAAGCTGCC 0.567000 Pancreas(23;406 890 14304 26016) 0 SO:0001583 missense ENST00000215909.5 1 1 hg19 CCDS13954.1 . . . . . . . . . . g 0.469 -0.885255 0.02511 0.0 1.16E-4 ENSG00000100097 ENST00000215909 T 0.04360 3.64 6.08 -0.0473 0.13844 Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1); 0.237165 0.42294 N 0.000737 T 0.03695 0.0105 L 0.31120 0.905 0.31764 N 0.632933 B 0.11235 0.004 B 0.19666 0.026 T 0.35051 -0.9804 10 0.19590 T 0.45 -0.9193 10.1288 0.42665 0.4005:0.0:0.5995:0.0 . 99 P09382 LEG1_HUMAN I 99 ENSP00000215909:V99I ENSP00000215909:V99I V + 1 0 LGALS1 36405589 0.451000 0.25705 0.997000 0.53966 0.127000 0.20565 0.715000 0.25822 -0.043000 0.13513 -1.057000 0.02308 GTC TCGA-IB-A7LX-01A-12D-A36O-08 LGALS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319482.1 1 0 1 50 159 0 71 1 1 665 2015 0 71 2 0 0 0 0 0 2 1 1.000000 50 155 0 71 2 0 0 0 0 71 2 -4.275326 1 1 121412 7 44 1 2 3 5 1.795983 1 0.550000 3.150000 0.619128 0.990000 0.800000 1.000000 1.000000 0.971288 0.990000 1 9.100000e-01 1 CHST10 9486 broad.mit.edu 37 2 101010109 101010109 + Silent SNP T T C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:101010109T>C ENST00000264249.3 - 7 1054 c.669A>G c.(667-669)agA>agG p.R223R CHST10_ENST00000542617.1_Silent_p.R271R|CHST10_ENST00000409701.1_Silent_p.R223R NM_004854.4 NP_004845.1 O43529 CHSTA_HUMAN carbohydrate sulfotransferase 10 16 TCCTGTATTTTCTGATGATGC 0.483000 0 SO:0001819 synonymous_variant ENST00000264249.3 1 1 hg19 CCDS2047.1 TCGA-IB-A7LX-01A-12D-A36O-08 CHST10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253162.1 1 0 0 68 464 0 150 0 8.442364e-02 0 4 0 150 2 0 0 0 0 0 2 1 1.000000 64 458 0 150 2 0 0 0 0 150 2 -20.000000 1 1 0 0 1 2 4 6 2.189758 1 0.550000 3.150000 0.685094 0.690000 0.530000 1.000000 0.670000 0.746654 0.690000 0 6.000000e-01 1 MYCN 4613 broad.mit.edu 37 2 16086208 16086208 + Silent SNP C C A rs144531796 by1000genomes TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:16086208C>A ENST00000281043.3 + 3 1681 c.1384C>A c.(1384-1386)Cgg>Agg p.R462R NM_005378.4 NP_005369.2 P04198 MYCN_HUMAN v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog 31 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) TGAACACGCTCGGACTTGCTA 0.428000 A neuroblastoma Dom yes 2 2p24.1 4613 v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) O 0 SO:0001819 synonymous_variant ENST00000281043.3 1 0 hg19 CCDS1687.1 TCGA-IB-A7LX-01A-12D-A36O-08 MYCN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095469.2 1 0 0 21 411 0 117 0 0 0 1 0 117 2 0 0 0 0 0 2 1 0.999997 22 400 0 117 2 0 0 0 0 117 2 -2.522253 1 1 121406 6 42 1 2 6 8 2.087735 1 0.550000 3.150000 0.673795 0.260000 0.150000 1.000000 0.240000 0.379979 0.260000 0 2.000000e-01 1 FAM49A 81553 broad.mit.edu 37 2 16743285 16743285 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:16743285G>T ENST00000381323.3 - 6 643 c.423C>A c.(421-423)ttC>ttA p.F141L FAM49A_ENST00000355549.2_Missense_Mutation_p.F141L|FAM49A_ENST00000406434.1_Missense_Mutation_p.F141L NM_030797.3 NP_110424.1 Q9H0Q0 FA49A_HUMAN family with sequence similarity 49, member A p.F141F(1) 23 Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088) GBM - Glioblastoma multiforme(3;0.00969) TCAGCTCATCGAATCGAAGGG 0.453000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000381323.3 1 0 hg19 CCDS1688.1 . . . . . . . . . . G 17.95 3.513807 0.64522 . . ENSG00000197872 ENST00000381323;ENST00000406434;ENST00000355549 T;T;T 0.57595 0.39;0.39;0.39 5.7 -3.83 0.04269 . 0.000000 0.85682 D 0.000000 T 0.71710 0.3372 M 0.90252 3.1 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 T 0.74899 -0.3507 10 0.45353 T 0.12 -22.1984 13.5016 0.61459 0.6789:0.0:0.3211:0.0 . 141 Q9H0Q0 FA49A_HUMAN L 141 ENSP00000370724:F141L;ENSP00000384771:F141L;ENSP00000347744:F141L ENSP00000347744:F141L F - 3 2 FAM49A 16606766 0.005000 0.15991 0.957000 0.39632 0.494000 0.33585 -0.804000 0.04535 -0.587000 0.05890 -0.136000 0.14681 TTC TCGA-IB-A7LX-01A-12D-A36O-08 FAM49A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207203.2 1 0 0 11 224 0 71 0 7.585464e-02 0 9 0 71 2 0 0 0 0 0 2 1 0.998333 11 221 0 71 2 0 0 0 0 71 2 -3.343013 1 1 0 0 1 2 6 8 2.087735 1 0.550000 3.150000 0.673795 0.260000 0.120000 1.000000 0.240000 0.379540 0.260000 0 1.800000e-01 1 LRP2 4036 broad.mit.edu 37 2 170025143 170025143 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:170025143G>T ENST00000263816.3 - 61 11826 c.11541C>A c.(11539-11541)ttC>ttA p.F3847L NM_004525.2 NP_004516.2 P98164 LRP2_HUMAN low density lipoprotein receptor-related protein 2 p.F3847F(1) 315 """Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)" TTTTGCATTCGAACATAGTAG 0.428000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000263816.3 1 0 hg19 CCDS2232.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 25.6|25.6 4.656719|4.656719 0.88154|0.88154 .|. .|. ENSG00000081479|ENSG00000081479 ENST00000263816|ENST00000536293 D|. 0.98889|. -5.21|. 5.82|5.82 -6.33|-6.33 0.01988|0.01988 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|. 0.79046|. 0.4380|. M|M 0.85462|0.85462 2.755|2.755 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.87578|. 0.998|. D|. 0.83997|. 0.0341|. 10|. 0.72032|0.72032 D|D 0.01|0.01 .|. 17.3947|17.3947 0.87442|0.87442 0.8962:0.0:0.1038:0.0|0.8962:0.0:0.1038:0.0 .|. 3847|. P98164|. LRP2_HUMAN|. L|X 3847|512 ENSP00000263816:F3847L|. ENSP00000263816:F3847L|ENSP00000438157:S512X F|S -|- 3|2 2|0 LRP2|LRP2 169733389|169733389 0.971000|0.971000 0.33674|0.33674 0.855000|0.855000 0.33649|0.33649 0.823000|0.823000 0.46562|0.46562 0.340000|0.340000 0.19892|0.19892 -1.073000|-1.073000 0.03137|0.03137 -0.367000|-0.367000 0.07326|0.07326 TTC|TCG TCGA-IB-A7LX-01A-12D-A36O-08 LRP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255231.2 1 0 0 10 223 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 0.996647 9 218 0 62 2 0 0 0 0 64 2 -4.333398 1 1 0 0 1 2 5 7 2.129539 1 0.550000 3.150000 0.678284 0.240000 0.110000 1.000000 0.210000 0.388524 0.240000 0 1.700000e-01 1 FASTKD1 79675 broad.mit.edu 37 2 170403116 170403116 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:170403116C>A ENST00000453153.2 - 8 1659 c.1313G>T c.(1312-1314)cGa>cTa p.R438L FASTKD1_ENST00000453929.2_Missense_Mutation_p.R438L NM_024622.3 NP_078898.3 Q53R41 FAKD1_HUMAN FAST kinase domains 1 37 GGCTTCAATTCGGGATATCCC 0.413000 0 SO:0001583 missense ENST00000453153.2 1 0 hg19 CCDS33318.1 . . . . . . . . . . C 18.33 3.600955 0.66332 . . ENSG00000138399 ENST00000453153;ENST00000453929 T;T 0.25414 1.82;1.8 4.44 2.59 0.31030 . 0.265024 0.35772 N 0.002992 T 0.37652 0.1011 L 0.59436 1.845 0.40632 D 0.981862 D;D 0.64830 0.994;0.99 P;P 0.60682 0.878;0.759 T 0.13255 -1.0516 10 0.56958 D 0.05 -29.0924 7.238 0.26079 0.0:0.6022:0.0:0.3978 . 438;438 Q53R41-2;Q53R41 .;FAKD1_HUMAN L 438 ENSP00000400513:R438L;ENSP00000403229:R438L ENSP00000400513:R438L R - 2 0 FASTKD1 170111362 0.678000 0.27586 0.245000 0.24217 0.899000 0.52679 1.083000 0.30815 0.585000 0.29608 0.563000 0.77884 CGA TCGA-IB-A7LX-01A-12D-A36O-08 FASTKD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000337788.2 1 0 0 13 309 0 65 0 3.550350e-01 0 29 0 65 2 0 0 0 0 0 2 1 0.999491 13 302 0 64 2 0 0 0 0 65 2 -3.222233 1 1 0 0 1 2 5 7 2.129539 1 0.550000 3.150000 0.678284 0.220000 0.110000 1.000000 0.210000 0.373971 0.220000 0 1.600000e-01 1 SF3B1 23451 broad.mit.edu 37 2 198265629 198265629 + Missense_Mutation SNP T T C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:198265629T>C ENST00000335508.6 - 18 2619 c.2528A>G c.(2527-2529)aAa>aGa p.K843R SF3B1_ENST00000462613.1_5'Flank NM_012433.2 NP_036565.2 O75533 SF3B1_HUMAN splicing factor 3b, subunit 1, 155kDa 633 OV - Ovarian serous cystadenocarcinoma(117;0.246) TGCACCTACTTTGTTTGCCAA 0.348000 Mis myelodysplastic syndrome Dom yes 2 2q33.1 23451 splicing factor 3b, subunit 1, 155kDa L 0 SO:0001583 missense ENST00000335508.6 1 1 hg19 CCDS33356.1 . . . . . . . . . . T 18.25 3.581538 0.65992 . . ENSG00000115524 ENST00000335508 T 0.65916 -0.18 5.77 5.77 0.91146 Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.68412 0.2998 M 0.76433 2.335 0.80722 D 1 B 0.28082 0.2 B 0.36030 0.216 T 0.68447 -0.5406 10 0.52906 T 0.07 . 16.3948 0.83586 0.0:0.0:0.0:1.0 . 843 O75533 SF3B1_HUMAN R 843 ENSP00000335321:K843R ENSP00000335321:K843R K - 2 0 SF3B1 197973874 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.936000 0.87665 2.326000 0.78906 0.533000 0.62120 AAA TCGA-IB-A7LX-01A-12D-A36O-08 SF3B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335245.2 1 0 1 65 241 0 78 1 1 100 381 0 78 2 1 1 54 255 0 577 2 1 1.000000 65 239 0 78 2 0 0 0 0 78 2 -20.000000 1 1 0 0 1 2 6 8 2.094740 1 0.550000 3.150000 0.677650 0.990000 0.860000 1.000000 1.000000 0.987063 0.990000 1 9.700000e-01 1 SF3B1 23451 broad.mit.edu 37 2 198266713 198266713 + Missense_Mutation SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:198266713C>T ENST00000335508.6 - 15 2310 c.2219G>A c.(2218-2220)gGa>gAa p.G740E SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank NM_012433.2 NP_036565.2 O75533 SF3B1_HUMAN splicing factor 3b, subunit 1, 155kDa p.G740E(1) 633 OV - Ovarian serous cystadenocarcinoma(117;0.246) ATTTACCTTTCCTCTGTGTTG 0.343000 Mis myelodysplastic syndrome Dom yes 2 2q33.1 23451 splicing factor 3b, subunit 1, 155kDa L 1 Substitution - Missense(1) SO:0001583 missense ENST00000335508.6 1 1 hg19 CCDS33356.1 . . . . . . . . . . C 29.8 5.036521 0.93630 . . ENSG00000115524 ENST00000335508 T 0.62364 0.03 5.58 5.58 0.84498 Armadillo-like helical (1);Armadillo-type fold (1); 0.107844 0.64402 D 0.000005 T 0.76449 0.3989 M 0.83692 2.655 0.80722 D 1 D 0.55800 0.973 P 0.51974 0.686 T 0.80183 -0.1488 10 0.66056 D 0.02 . 19.5659 0.95393 0.0:1.0:0.0:0.0 . 740 O75533 SF3B1_HUMAN E 740 ENSP00000335321:G740E ENSP00000335321:G740E G - 2 0 SF3B1 197974958 1.000000 0.71417 1.000000 0.80357 0.959000 0.62525 7.359000 0.79477 2.619000 0.88677 0.563000 0.77884 GGA TCGA-IB-A7LX-01A-12D-A36O-08 SF3B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335245.2 1 0 1 76 226 0 76 1 1 157 347 0 76 2 1 1 42 125 0 366 2 1 1.000000 75 219 0 76 2 0 0 0 0 76 2 -20.000000 1 1 0 0 1 2 6 8 2.094740 1 0.550000 3.150000 0.677650 0.990000 0.990000 1.000000 1.000000 0.999697 0.990000 1 9.900000e-01 1 ATIC 471 broad.mit.edu 37 2 216190751 216190751 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr2:216190751C>A ENST00000236959.9 + 6 747 c.421C>A c.(421-423)Cga>Aga p.R141R ATIC_ENST00000540518.1_Silent_p.R82R|ATIC_ENST00000435675.1_Silent_p.R140R NM_004044.6 NP_004035.2 P31939 PUR9_HUMAN 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase p.R141*(1) ATIC/ALK(24) 8 Renal(323;0.229) Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116) AAACCACGCTCGAGTGACAGT 0.483000 T ALK ALCL Dom yes 2 2q35 471 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase L 1 Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000236959.9 1 0 hg19 CCDS2398.1 TCGA-IB-A7LX-01A-12D-A36O-08 ATIC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256610.1 1 0 0 11 238 0 70 0 9.953872e-01 1 202 0 70 2 0 0 0 0 0 2 1 0.998213 11 232 0 68 2 0 0 0 0 70 2 -3.221883 1 1 0 0 1 2 6 8 2.094740 1 0.550000 3.150000 0.677650 0.250000 0.120000 1.000000 0.210000 0.374253 0.250000 0 1.700000e-01 1 CPNE4 131034 broad.mit.edu 37 3 131283152 131283152 + Missense_Mutation SNP G G C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:131283152G>C ENST00000512055.1 - 15 3095 c.969C>G c.(967-969)aaC>aaG p.N323K CPNE4_ENST00000512332.1_Missense_Mutation_p.N341K|CPNE4_ENST00000429747.1_Missense_Mutation_p.N323K|CPNE4_ENST00000502818.1_Missense_Mutation_p.N341K|CPNE4_ENST00000511604.1_Missense_Mutation_p.N323K Q96A23 CPNE4_HUMAN copine IV 39 AGGAACAGCTGTTCCTGGGGT 0.433000 0 SO:0001583 missense ENST00000512055.1 1 1 hg19 CCDS3072.1 . . . . . . . . . . G 16.88 3.243726 0.58995 . . ENSG00000196353 ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818 T;T;T;T;T 0.54071 0.6;0.6;0.59;0.6;0.59 5.52 4.65 0.58169 von Willebrand factor, type A (1); 0.000000 0.85682 D 0.000000 T 0.67173 0.2865 L 0.58510 1.815 0.80722 D 1 D;P 0.76494 0.999;0.81 D;B 0.74023 0.982;0.313 T 0.65994 -0.6033 10 0.35671 T 0.21 -36.7038 14.6356 0.68686 0.07:0.0:0.93:0.0 . 341;323 Q96A23-2;Q96A23 .;CPNE4_HUMAN K 323;323;341;323;341 ENSP00000421705:N323K;ENSP00000411904:N323K;ENSP00000424853:N341K;ENSP00000423811:N323K;ENSP00000421646:N341K ENSP00000411904:N323K N - 3 2 CPNE4 132765842 1.000000 0.71417 1.000000 0.80357 0.977000 0.68977 5.441000 0.66569 1.350000 0.45770 -0.221000 0.12465 AAC TCGA-IB-A7LX-01A-12D-A36O-08 CPNE4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356583.4 1 0 1 65 287 0 80 0 3.852143e-01 0 7 0 80 2 0 0 0 0 0 2 1 1.000000 64 282 0 79 2 0 0 0 0 80 2 -20.000000 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.990000 0.810000 1.000000 1.000000 0.972263 0.990000 1 9.200000e-01 1 GK5 256356 broad.mit.edu 37 3 141900367 141900367 + Silent SNP G G T rs9866012 byFrequency TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:141900367G>T ENST00000392993.2 - 11 1135 c.984C>A c.(982-984)gtC>gtA p.V328V NM_001039547.2 NP_001034636.1 Q6ZS86 GLPK5_HUMAN glycerol kinase 5 (putative) 10 CTAAGCATACGACTTCTTGCC 0.383000 0 SO:0001819 synonymous_variant ENST00000392993.2 1 0 hg19 CCDS33871.1 TCGA-IB-A7LX-01A-12D-A36O-08 GK5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353999.1 1 0 0 18 412 0 105 0 4.667193e-01 0 35 0 105 2 0 0 0 0 0 2 1 0.999979 17 403 0 104 2 0 0 0 0 105 2 -2.721274 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.230000 0.130000 0.380000 0.240000 0.253288 0.230000 0 1.800000e-01 3.000000e-01 ATR 545 broad.mit.edu 37 3 142188288 142188288 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:142188288C>A ENST00000350721.4 - 38 6564 c.6443G>T c.(6442-6444)cGa>cTa p.R2148L RP11-383G6.3_ENST00000460977.1_RNA|ATR_ENST00000383101.3_Missense_Mutation_p.R2084L NM_001184.3 NP_001175.2 Q13535 ATR_HUMAN ATR serine/threonine kinase p.R2148Q(1) 122 ATGACAAATTCGAGAGATCAA 0.343000 Other conserved DNA damage response genes 1 Substitution - Missense(1) SO:0001583 missense ENST00000350721.4 1 0 hg19 CCDS3124.1 . . . . . . . . . . C 29.5 5.009379 0.93346 . . ENSG00000175054 ENST00000350721;ENST00000383101 T;T 0.15256 2.44;2.58 5.15 5.15 0.70609 PIK-related kinase (1); 0.126462 0.52532 D 0.000080 T 0.25494 0.0620 M 0.71871 2.18 0.80722 D 1 B 0.30068 0.267 B 0.28991 0.097 T 0.07404 -1.0774 10 0.87932 D 0 -3.8171 18.5955 0.91228 0.0:1.0:0.0:0.0 . 2148 Q13535 ATR_HUMAN L 2148;2084 ENSP00000343741:R2148L;ENSP00000372581:R2084L ENSP00000343741:R2148L R - 2 0 ATR 143670978 1.000000 0.71417 1.000000 0.80357 0.941000 0.58515 7.805000 0.86005 2.378000 0.81104 0.591000 0.81541 CGA TCGA-IB-A7LX-01A-12D-A36O-08 ATR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353995.2 1 0 0 22 462 0 118 0 5.986506e-01 0 43 0 118 2 0 0 0 0 0 2 1 0.999999 22 461 0 118 2 0 0 0 0 118 2 -4.388978 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.250000 0.150000 0.400000 0.240000 0.271826 0.250000 0 2.000000e-01 3.200000e-01 C3orf20 84077 broad.mit.edu 37 3 14769996 14769996 + Silent SNP C C A rs144350421 byFrequency TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:14769996C>A ENST00000253697.3 + 12 2193 c.1741C>A c.(1741-1743)Cgg>Agg p.R581R C3orf20_ENST00000435614.1_Silent_p.R459R|C3orf20_ENST00000412910.1_Silent_p.R459R NM_032137.4 NP_115513.4 Q8ND61 CC020_HUMAN chromosome 3 open reading frame 20 40 AGAATTTGTTCGGTTCAAGAT 0.463000 0 SO:0001819 synonymous_variant ENST00000253697.3 1 0 hg19 CCDS33706.1 TCGA-IB-A7LX-01A-12D-A36O-08 C3orf20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340586.1 1 0 0 13 204 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 0.999542 13 201 0 87 2 0 0 0 0 89 2 -2.842149 1 1 0 0 1 1 2 3 1.822614 1 0.550000 3.150000 0.635258 0.280000 0.150000 1.000000 0.260000 0.370845 0.280000 0 2.100000e-01 4.200000e-01 FAM194A 0 broad.mit.edu 37 3 150391782 150391782 + Missense_Mutation SNP T T G TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:150391782T>G ENST00000295910.6 - 11 1356 c.1304A>C c.(1303-1305)aAg>aCg p.K435T FAM194A_ENST00000491361.1_Missense_Mutation_p.K289T NM_152394.3 NP_689607.2 38 AGTCAGAAACTTGCTCCCATG 0.333000 0 SO:0001583 missense ENST00000295910.6 1 1 hg19 CCDS3151.2 . . . . . . . . . . T 17.11 3.306745 0.60305 . . ENSG00000163645 ENST00000295910;ENST00000491361;ENST00000313811 T;T 0.12984 2.63;2.63 4.94 4.94 0.65067 . 0.220254 0.31461 N 0.007604 T 0.25457 0.0619 L 0.45228 1.405 0.30174 N 0.801058 D 0.76494 0.999 D 0.79784 0.993 T 0.05131 -1.0904 10 0.46703 T 0.11 -12.9558 8.3833 0.32486 0.0:0.0893:0.0:0.9107 . 435 Q7L0X2 F194A_HUMAN T 435;289;393 ENSP00000295910:K435T;ENSP00000419366:K289T ENSP00000295910:K435T K - 2 0 FAM194A 151874472 1.000000 0.71417 1.000000 0.80357 0.969000 0.65631 3.661000 0.54503 2.053000 0.61076 0.533000 0.62120 AAG TCGA-IB-A7LX-01A-12D-A36O-08 FAM194A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257666.1 0 0 1 53 371 0 114 0 0 0 0 114 2 0 0 0 0 0 2 1 1.000000 52 363 0 111 2 0 0 0 0 114 2 -20.000000 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.700000 0.530000 0.920000 0.710000 0.711508 0.700000 0 6.100000e-01 8.000000e-01 IFT80 57560 broad.mit.edu 37 3 159998536 159998536 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:159998536C>A ENST00000326448.7 - 15 2015 c.1583G>T c.(1582-1584)cGa>cTa p.R528L RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.R699L|IFT80_ENST00000496589.1_Missense_Mutation_p.R391L|IFT80_ENST00000483465.1_Missense_Mutation_p.R391L NM_020800.2 NP_065851.1 Q9P2H3 IFT80_HUMAN intraflagellar transport 80 36 Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523) CACTATAAATCGAGTATCTTG 0.348000 0 SO:0001583 missense ENST00000326448.7 1 0 hg19 CCDS3188.1 . . . . . . . . . . C 15.47 2.843076 0.51057 . . ENSG00000068885 ENST00000326448;ENST00000483465;ENST00000496589 T;T;T 0.70164 2.32;-0.46;-0.46 5.59 5.59 0.84812 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.281880 0.24645 U 0.036780 T 0.64283 0.2584 M 0.65975 2.015 0.47659 D 0.999489 B 0.09022 0.002 B 0.06405 0.002 T 0.59511 -0.7441 10 0.33940 T 0.23 . 13.3036 0.60338 0.0:0.9182:0.0:0.0818 . 528 Q9P2H3 IFT80_HUMAN L 528;391;391 ENSP00000312778:R528L;ENSP00000418196:R391L;ENSP00000420646:R391L ENSP00000312778:R528L R - 2 0 IFT80 161481230 0.960000 0.32886 0.970000 0.41538 0.974000 0.67602 1.262000 0.32992 2.635000 0.89317 0.460000 0.39030 CGA TCGA-IB-A7LX-01A-12D-A36O-08 IFT80-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352651.2 1 0 0 13 334 0 80 0 5.624329e-01 0 48 0 80 2 0 0 0 0 0 2 1 0.999521 13 330 0 80 2 0 0 0 0 80 2 -3.096837 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.210000 0.110000 0.370000 0.200000 0.231830 0.210000 0 1.500000e-01 2.900000e-01 SMC4 10051 broad.mit.edu 37 3 160132228 160132228 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:160132228C>A ENST00000357388.3 + 9 1646 c.1195C>A c.(1195-1197)Caa>Aaa p.Q399K SMC4_ENST00000462787.1_Missense_Mutation_p.Q399K|SMC4_ENST00000469762.1_Missense_Mutation_p.Q374K|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000344722.5_Missense_Mutation_p.Q399K|SMC4_ENST00000360111.2_Missense_Mutation_p.Q399K NM_001002800.1 NP_001002800.1 Q9NTJ3 SMC4_HUMAN structural maintenance of chromosomes 4 48 Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523) GGAAGATGTTCAAGTTAGAGA 0.289000 0 SO:0001583 missense ENST00000357388.3 1 0 hg19 CCDS3189.1 . . . . . . . . . . C 6.676 0.493216 0.12702 . . ENSG00000113810 ENST00000357388;ENST00000360111;ENST00000392788;ENST00000469762;ENST00000489573;ENST00000462787;ENST00000344722 T;T;T;T;T;T 0.73152 -0.69;-0.72;-0.7;0.41;-0.72;-0.69 5.49 5.49 0.81192 RecF/RecN/SMC (1); 0.163089 0.53938 D 0.000045 T 0.41282 0.1152 N 0.02765 -0.5 0.35709 D 0.816222 B;B;B;B 0.12013 0.0;0.001;0.0;0.005 B;B;B;B 0.14023 0.002;0.002;0.001;0.01 T 0.48399 -0.9039 10 0.05833 T 0.94 -13.6609 10.8952 0.47019 0.1516:0.7182:0.1301:0.0 . 399;374;374;399 Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3 .;.;.;SMC4_HUMAN K 399;399;399;374;399;399;399 ENSP00000349961:Q399K;ENSP00000353225:Q399K;ENSP00000417964:Q374K;ENSP00000420121:Q399K;ENSP00000420734:Q399K;ENSP00000341382:Q399K ENSP00000341382:Q399K Q + 1 0 SMC4 161614922 1.000000 0.71417 1.000000 0.80357 0.487000 0.33371 3.146000 0.50631 2.583000 0.87209 0.650000 0.86243 CAA TCGA-IB-A7LX-01A-12D-A36O-08 SMC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352862.1 1 0 0 15 358 0 84 0 7.318526e-01 0 63 0 84 2 0 0 0 0 0 2 1 0.999866 15 353 0 84 2 0 0 0 0 84 2 -3.221883 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.230000 0.120000 0.380000 0.230000 0.245974 0.230000 0 1.700000e-01 3.000000e-01 MFN1 55669 broad.mit.edu 37 3 179069714 179069714 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:179069714C>A ENST00000471841.1 + 3 265 c.139C>A c.(139-141)Cga>Aga p.R47R MFN1_ENST00000263969.5_Silent_p.R47R|MFN1_ENST00000280653.7_Silent_p.R47R NM_033540.2 NP_284941 Q8IWA4 MFN1_HUMAN mitofusin 1 p.R47*(1) 31 all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923) GGAACTTGATCGAATAGCCAC 0.353000 1 Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000471841.1 1 0 hg19 CCDS3228.1 TCGA-IB-A7LX-01A-12D-A36O-08 MFN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348654.2 1 0 0 18 479 0 117 0 6.098508e-01 0 54 0 117 2 0 0 0 0 0 2 1 0.999979 18 470 0 117 2 0 0 0 0 117 2 -3.302474 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.200000 0.110000 0.330000 0.200000 0.220622 0.200000 0 1.500000e-01 2.600000e-01 ACTL6A 86 broad.mit.edu 37 3 179291168 179291168 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:179291168G>A ENST00000429709.2 + 4 502 c.289G>A c.(289-291)Gat>Aat p.D97N ACTL6A_ENST00000392662.1_Missense_Mutation_p.D55N|ACTL6A_ENST00000450518.2_Missense_Mutation_p.D55N NM_004301.3 NP_004292.1 O96019 ACL6A_HUMAN actin-like 6A 21 all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191) OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169) TGAAGACTGGGATAGTTTCCA 0.353000 0 SO:0001583 missense ENST00000429709.2 0 1 hg19 CCDS3231.1 . . . . . . . . . . G 34 5.398826 0.96030 . . ENSG00000136518 ENST00000429709;ENST00000450518;ENST00000392662 D;D;D 0.95853 -3.83;-3.83;-3.83 5.28 5.28 0.74379 . 0.000000 0.85682 D 0.000000 D 0.96439 0.8838 M 0.64260 1.97 0.80722 D 1 D 0.52996 0.957 P 0.53954 0.738 D 0.96821 0.9604 10 0.87932 D 0 . 19.2768 0.94034 0.0:0.0:1.0:0.0 . 97 O96019 ACL6A_HUMAN N 97;55;55 ENSP00000397552:D97N;ENSP00000394014:D55N;ENSP00000376430:D55N ENSP00000376430:D55N D + 1 0 ACTL6A 180773862 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 9.686000 0.98664 2.625000 0.88918 0.555000 0.69702 GAT TCGA-IB-A7LX-01A-12D-A36O-08 ACTL6A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349599.1 0 0 0 13 607 0 144 1 8.162320e-01 4 144 0 144 2 0 0 0 0 0 2 1 0.999457 13 593 0 143 2 0 0 0 0 144 2 -3.068190 1 0 121412 1 27 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.110000 0.050000 0.210000 0.120000 0.134363 0.110000 0 8.000000e-02 1.600000e-01 MCF2L2 23101 broad.mit.edu 37 3 182923997 182923997 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:182923997C>A ENST00000328913.3 - 24 3015 c.2718G>T c.(2716-2718)atG>atT p.M906I MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Missense_Mutation_p.M906I NM_015078.2 NP_055893 Q86YR7 MF2L2_HUMAN MCF.2 cell line derived transforming sequence-like 2 72 all_cancers(143;1.26e-12)|Ovarian(172;0.0355) all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21) TTGAAAGTGTCATCAGCTATT 0.408000 0 SO:0001583 missense ENST00000328913.3 1 0 hg19 CCDS3243.1 . . . . . . . . . . C 4.420 0.077657 0.08485 . . ENSG00000053524 ENST00000328913;ENST00000473233 T;T 0.11063 2.81;2.81 4.28 1.25 0.21368 Pleckstrin homology-type (1);Pleckstrin homology domain (2); 1.050980 0.07506 N 0.908130 T 0.08179 0.0204 L 0.29908 0.895 0.20975 N 0.999815 B 0.06786 0.001 B 0.04013 0.001 T 0.38112 -0.9676 10 0.56958 D 0.05 . 3.9497 0.09363 0.0:0.5782:0.1998:0.222 . 906 Q86YR7 MF2L2_HUMAN I 906 ENSP00000328118:M906I;ENSP00000420070:M906I ENSP00000328118:M906I M - 3 0 MCF2L2 184406691 0.023000 0.18921 0.360000 0.25837 0.118000 0.20060 0.077000 0.14738 0.553000 0.29044 0.563000 0.77884 ATG TCGA-IB-A7LX-01A-12D-A36O-08 MCF2L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350868.1 1 0 0 16 367 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 0.999930 16 362 0 79 2 0 0 0 0 79 2 -4.050431 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.230000 0.130000 0.390000 0.240000 0.254224 0.230000 0 1.800000e-01 3.100000e-01 TP63 8626 broad.mit.edu 37 3 189612250 189612250 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:189612250C>A ENST00000264731.3 + 14 2091 c.2002C>A c.(2002-2004)Cgc>Agc p.R668S TP63_ENST00000440651.2_Missense_Mutation_p.R664S|TP63_ENST00000449992.1_Missense_Mutation_p.R489S|TP63_ENST00000456148.1_Missense_Mutation_p.R570S|TP63_ENST00000382063.4_Missense_Mutation_p.R583S|TP63_ENST00000320472.5_3'UTR|TP63_ENST00000354600.5_Missense_Mutation_p.R574S NM_001114978.1|NM_003722.4 NP_001108450.1|NP_003713.3 Q9H3D4 P63_HUMAN tumor protein p63 61 all_cancers(143;3.35e-10)|Ovarian(172;0.0925) Lung(62;3.33e-05) CATGGATGCTCGCCGCAATAA 0.542000 HNSCC(45;0.13) 0 SO:0001583 missense ENST00000264731.3 1 0 hg19 CCDS3293.1 . . . . . . . . . . C 16.73 3.202877 0.58234 . . ENSG00000073282 ENST00000264731;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000449992;ENST00000456148 D;D;D;D;D;D 0.90133 -2.62;-2.62;-2.62;-2.62;-2.62;-2.62 5.91 5.91 0.95273 . 0.108147 0.64402 D 0.000006 D 0.84701 0.5530 N 0.19112 0.55 0.80722 D 1 B;B;B 0.18968 0.028;0.028;0.032 B;B;B 0.20955 0.032;0.032;0.026 T 0.78620 -0.2133 9 . . . -11.7075 19.2867 0.94077 0.0:1.0:0.0:0.0 . 489;574;668 Q9H3D4-10;Q9H3D4-2;Q9H3D4 .;.;P63_HUMAN S 668;664;583;574;489;570 ENSP00000264731:R668S;ENSP00000394337:R664S;ENSP00000371495:R583S;ENSP00000346614:R574S;ENSP00000387839:R489S;ENSP00000389485:R570S . R + 1 0 TP63 191094944 1.000000 0.71417 0.990000 0.47175 0.746000 0.42486 5.598000 0.67585 2.793000 0.96121 0.655000 0.94253 CGC TCGA-IB-A7LX-01A-12D-A36O-08 TP63-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000343865.1 1 0 0 13 263 0 59 0 1.400073e-01 0 13 0 59 2 0 0 0 0 0 2 1 0.999462 13 254 0 58 2 0 0 0 0 59 2 -3.094281 1 1 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.270000 0.140000 0.460000 0.270000 0.288450 0.270000 0 2.000000e-01 3.600000e-01 RPL35A 6165 broad.mit.edu 37 3 197680900 197680900 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:197680900C>A ENST00000464167.1 + 4 458 c.191C>A c.(190-192)cCa>cAa p.P64Q RPL35A_ENST00000329092.8_3'UTR|IQCG_ENST00000480302.1_Intron|IQCG_ENST00000265239.6_Intron|RPL35A_ENST00000448864.1_Missense_Mutation_p.P64Q NM_000996.2 NP_000987.2 P18077 RL35A_HUMAN ribosomal protein L35a 3 all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976) Lung NSC(153;0.132) Epithelial(36;1.04e-23)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07) GGCGGCAAACCAAACAAAACC 0.453000 0 SO:0001583 missense ENST00000464167.1 1 0 hg19 CCDS33930.1 . . . . . . . . . . C 16.31 3.087892 0.55968 . . ENSG00000182899 ENST00000464167;ENST00000448864;ENST00000442341 . . . 5.35 5.35 0.76521 Translation elongation/initiation factor/Ribosomal, beta-barrel (1); 0.000000 0.85682 D 0.000000 T 0.71367 0.3331 M 0.80616 2.505 0.80722 D 1 B 0.12630 0.006 B 0.24269 0.052 T 0.67906 -0.5549 9 0.31617 T 0.26 -21.202 19.1227 0.93369 0.0:1.0:0.0:0.0 . 64 P18077 RL35A_HUMAN Q 64 . ENSP00000387688:P64Q P + 2 0 RPL35A 199165297 1.000000 0.71417 0.997000 0.53966 0.982000 0.71751 7.755000 0.85180 2.530000 0.85305 0.558000 0.71614 CCA TCGA-IB-A7LX-01A-12D-A36O-08 RPL35A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000339788.1 1 0 0 8 214 0 45 1 1 3 7282 0 45 2 0 0 0 0 0 2 1 0.989940 8 215 0 44 2 0 0 0 0 45 2 -3.079547 1 0 0 0 1 1 3 4 2.284976 1 0.550000 3.150000 0.707602 0.210000 0.090000 0.410000 0.200000 0.232034 0.210000 0 1.400000e-01 3.000000e-01 JAGN1 84522 broad.mit.edu 37 3 9934901 9934901 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr3:9934901G>A ENST00000307768.4 + 2 561 c.392G>A c.(391-393)cGc>cAc p.R131H NM_032492.3 NP_115881.3 jagunal homolog 1 (Drosophila) 10 Medulloblastoma(99;0.227) CAGCTCTACCGCCATGGCAAG 0.527000 0 SO:0001583 missense ENST00000307768.4 1 1 hg19 CCDS2588.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 20.6|20.6 4.014448|4.014448 0.75161|0.75161 .|. .|. ENSG00000171135|ENSG00000171135 ENST00000543379|ENST00000307768 .|. .|. .|. 5.73|5.73 3.76|3.76 0.43208|0.43208 .|. .|0.054409 .|0.64402 .|D .|0.000001 T|T 0.74099|0.74099 0.3672|0.3672 M|M 0.84082|0.84082 2.675|2.675 0.53005|0.53005 D|D 0.999963|0.999963 .|D .|0.63880 .|0.993 .|P .|0.55713 .|0.782 T|T 0.78671|0.78671 -0.2113|-0.2113 6|9 0.13853|0.66056 T|D 0.58|0.02 -22.0269|-22.0269 11.9619|11.9619 0.53013|0.53013 0.071:0.0:0.7989:0.13|0.071:0.0:0.7989:0.13 .|. .|131 .|Q8N5M9 .|JAGN1_HUMAN T|H 130|131 .|. ENSP00000442889:A130T|ENSP00000306106:R131H A|R +|+ 1|2 0|0 JAGN1|JAGN1 9909901|9909901 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.933000|0.933000 0.57130|0.57130 7.496000|7.496000 0.81526|0.81526 1.434000|1.434000 0.47414|0.47414 -0.339000|-0.339000 0.08088|0.08088 GCC|CGC TCGA-IB-A7LX-01A-12D-A36O-08 JAGN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250335.1 0 0 0 16 386 1 130 1 7.515957e-01 17 317 1 130 11 0 0 0 0 0 2 1 0.817874 16 379 1 130 12 0 0 0 1 130 2 -3.461198 1 1 121412 8 40 1 1 2 3 1.822614 1 0.550000 3.150000 0.635258 0.180000 0.100000 1.000000 0.170000 0.284895 0.180000 0 1.400000e-01 2.700000e-01 SPATA5 166378 broad.mit.edu 37 4 123859326 123859326 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:123859326G>T ENST00000274008.4 + 8 1449 c.1380G>T c.(1378-1380)ccG>ccT p.P460P SPATA5_ENST00000422835.2_3'UTR NM_145207.2 NP_660208.2 Q8NB90 SPAT5_HUMAN spermatogenesis associated 5 24 CACTTTGTCCGAAAAGAGAGG 0.353000 0 SO:0001819 synonymous_variant ENST00000274008.4 1 0 hg19 CCDS3730.1 TCGA-IB-A7LX-01A-12D-A36O-08 SPATA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256714.2 1 0 0 14 367 0 116 0 1.492716e-02 0 5 0 116 2 0 0 0 0 0 2 1 0.999743 14 362 0 114 2 0 0 0 0 116 2 -3.056472 1 1 0 0 1 2 3 5 1.795702 1 0.550000 3.150000 0.621769 0.170000 0.080000 1.000000 0.160000 0.309474 0.170000 0 1.200000e-01 1 FAT4 79633 broad.mit.edu 37 4 126411862 126411862 + Missense_Mutation SNP G G A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:126411862G>A ENST00000394329.3 + 17 13898 c.13885G>A c.(13885-13887)Gcc>Acc p.A4629T FAT4_ENST00000335110.5_Missense_Mutation_p.A2870T NM_024582.4 NP_078858.4 Q6V0I7 FAT4_HUMAN FAT atypical cadherin 4 355 CAGCAGCATCGCCCCTTCGGA 0.512000 0 SO:0001583 missense ENST00000394329.3 1 1 hg19 CCDS3732.3 . . . . . . . . . . G 17.86 3.493760 0.64186 . . ENSG00000196159 ENST00000394329;ENST00000335110 D;D 0.91945 -2.94;-2.39 4.95 4.95 0.65309 . 0.000000 0.34110 U 0.004241 D 0.94807 0.8323 L 0.54323 1.7 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.995;0.998 D 0.94547 0.7750 10 0.45353 T 0.12 . 17.186 0.86867 0.0:0.0:1.0:0.0 . 2870;4629;4628 Q6V0I7-2;Q6V0I7;Q6V0I7-3 .;FAT4_HUMAN;. T 4629;2870 ENSP00000377862:A4629T;ENSP00000335169:A2870T ENSP00000335169:A2870T A + 1 0 FAT4 126631312 1.000000 0.71417 1.000000 0.80357 0.694000 0.40290 9.440000 0.97547 2.275000 0.75901 0.561000 0.74099 GCC TCGA-IB-A7LX-01A-12D-A36O-08 FAT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256765.2 1 0 0 11 163 0 64 0 4.268310e-02 0 5 0 64 2 0 0 0 0 0 2 1 0.998503 11 163 0 64 2 0 0 0 0 64 2 -3.318043 1 1 121412 1 29 1 2 3 5 1.795702 1 0.550000 3.150000 0.621769 0.300000 0.150000 1.000000 0.270000 0.413185 0.300000 0 2.100000e-01 1 RPS3A 6189 broad.mit.edu 37 4 152021718 152021718 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:152021718C>A ENST00000274065.4 + 2 224 c.144C>A c.(142-144)ctC>ctA p.L48L RPS3A_ENST00000322686.6_Silent_p.L35L|SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000506126.1_Silent_p.L11L|RPS3A_ENST00000512690.1_Silent_p.L48L|RPS3A_ENST00000509736.1_Intron|RPS3A_ENST00000514682.1_Silent_p.L11L NM_001006.4 NP_000997.1 ribosomal protein S3A 4 all_hematologic(180;0.093) GAAAGACGCTCGTCACCAGGA 0.393000 0 SO:0001819 synonymous_variant ENST00000274065.4 1 0 hg19 CCDS3775.1 TCGA-IB-A7LX-01A-12D-A36O-08 RPS3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000364957.1 1 0 0 14 214 0 79 0 1 0 3517 0 79 2 0 0 0 0 0 2 1 0.999768 14 212 0 79 2 0 0 0 0 79 2 -3.076017 1 1 0 0 1 2 3 5 1.795702 1 0.550000 3.150000 0.621769 0.280000 0.150000 1.000000 0.270000 0.402755 0.280000 0 2.100000e-01 1 GPR125 166647 broad.mit.edu 37 4 22389706 22389706 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:22389706C>A ENST00000334304.5 - 19 3857 c.3588G>T c.(3586-3588)acG>acT p.T1196T GPR125_ENST00000282943.5_5'UTR NM_145290.3 NP_660333.2 Q8IWK6 GP125_HUMAN G protein-coupled receptor 125 56 Breast(46;0.198) CTTCCACGCTCGTTGGGACAT 0.517000 0 SO:0001819 synonymous_variant ENST00000334304.5 1 0 hg19 CCDS33964.1 TCGA-IB-A7LX-01A-12D-A36O-08 GPR125-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362960.3 1 0 0 25 534 0 188 0 9.846938e-01 0 144 0 188 2 0 0 0 0 0 2 1 1.000000 25 528 0 185 2 0 0 0 0 188 2 -2.774725 1 1 0 0 1 1 3 4 2.081941 1 0.550000 3.150000 0.664430 0.230000 0.140000 1.000000 0.220000 0.402285 0.230000 0 1.800000e-01 1 NOP14 8602 broad.mit.edu 37 4 2958537 2958537 + Splice_Site SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:2958537C>A ENST00000314262.6 - 3 380 c.332G>T c.(331-333)cGa>cTa p.R111L NOP14_ENST00000416614.2_Splice_Site_p.R111L|NOP14_ENST00000398071.4_Splice_Site_p.R111L|NOP14_ENST00000502735.1_Splice_Site_p.R111L|NOP14-AS1_ENST00000503709.1_RNA NM_003703.1 NP_003694.1 P78316 NOP14_HUMAN NOP14 nucleolar protein 30 CTCATGATGTCGCTGACAGAA 0.313000 0 SO:0001630 splice_region_variant ENST00000314262.6 1 0 hg19 CCDS33945.1 . . . . . . . . . . C 19.99 3.927925 0.73327 . . ENSG00000087269 ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137 T;T;T;T 0.35973 1.28;1.28;1.28;1.28 5.41 4.53 0.55603 . 0.227351 0.39615 N 0.001308 T 0.54481 0.1861 M 0.80982 2.52 0.80722 D 1 P;P 0.51057 0.897;0.941 P;P 0.61658 0.892;0.856 T 0.57682 -0.7769 10 0.87932 D 0 -6.5327 6.3695 0.21473 0.0:0.6616:0.0:0.3384 . 111;111 E9PFK5;P78316 .;NOP14_HUMAN L 111;111;111;111;10 ENSP00000405068:R111L;ENSP00000315674:R111L;ENSP00000427415:R111L;ENSP00000381146:R111L ENSP00000315674:R111L R - 2 0 NOP14 2928335 0.999000 0.42202 1.000000 0.80357 0.995000 0.86356 2.917000 0.48821 1.199000 0.43173 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 NOP14-002 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000358135.2 1 0 0 8 164 0 46 0 7.497036e-01 0 56 0 46 2 0 0 0 0 0 2 1 0.989394 8 162 0 45 2 0 0 0 0 46 2 -10.603720 1 1 0 0 1 1 3 4 2.081941 1 0.550000 3.150000 0.664430 0.270000 0.110000 1.000000 0.230000 0.422119 0.270000 0 1.700000e-01 1 TBC1D1 23216 broad.mit.edu 37 4 38134830 38134830 + Silent SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:38134830C>T ENST00000261439.4 + 19 3613 c.3258C>T c.(3256-3258)acC>acT p.T1086T TBC1D1_ENST00000508802.1_Silent_p.T1077T|TBC1D1_ENST00000407365.1_3'UTR NM_001253914.1|NM_001253915.1|NM_015173.3 NP_001240843.1|NP_001240844.1|NP_055988.2 Q86TI0 TBCD1_HUMAN TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 36 TAGAGAAAACCAACAGCAGCT 0.393000 0 SO:0001819 synonymous_variant ENST00000261439.4 1 1 hg19 CCDS33972.1 . . . . . . . . . . C 9.867 1.197786 0.22037 . . ENSG00000065882 ENST00000510573 . . . 4.97 4.13 0.48395 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -27.4575 6.939 0.24483 0.2837:0.6293:0.0:0.087 . . . . X 774 . . Q + 1 0 TBC1D1 37811225 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 2.306000 0.43673 1.445000 0.47624 0.655000 0.94253 CAA TCGA-IB-A7LX-01A-12D-A36O-08 TBC1D1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317443.2 0 0 0 15 222 0 81 1 9.802797e-01 9 91 0 81 2 0 0 0 0 0 2 1 0.999880 15 220 0 81 2 0 0 0 0 81 2 -3.017629 1 0 121412 1 28 1 2 2 4 1.763541 1 0.550000 3.150000 0.613734 0.290000 0.160000 1.000000 0.260000 0.427790 0.290000 0 2.100000e-01 1 FRYL 285527 broad.mit.edu 37 4 48584630 48584630 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:48584630G>T ENST00000503238.1 - 17 1869 c.1870C>A c.(1870-1872)Cgt>Agt p.R624S FRYL_ENST00000506685.1_Missense_Mutation_p.R330S|FRYL_ENST00000507711.1_Missense_Mutation_p.R624S|FRYL_ENST00000537810.1_Missense_Mutation_p.R624S|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Missense_Mutation_p.R624S O94915 FRYL_HUMAN FRY-like 91 GTCACTTCACGAACAATAAAA 0.398000 0 SO:0001583 missense ENST00000503238.1 1 0 hg19 CCDS43227.1 . . . . . . . . . . G 16.54 3.151439 0.57151 . . ENSG00000075539 ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711;ENST00000506685 T;T;T;T;T 0.64260 3.64;3.64;3.64;3.64;-0.09 5.63 5.63 0.86233 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.64402 U 0.000001 T 0.75459 0.3852 L 0.51422 1.61 0.80722 D 1 D;P 0.64830 0.994;0.869 D;P 0.74023 0.982;0.724 T 0.70872 -0.4754 10 0.34782 T 0.22 . 20.0499 0.97621 0.0:0.0:1.0:0.0 . 624;624 F2Z2S2;O94915 .;FRYL_HUMAN S 624;624;624;624;330 ENSP00000426064:R624S;ENSP00000351113:R624S;ENSP00000441114:R624S;ENSP00000421584:R624S;ENSP00000425592:R330S ENSP00000351113:R624S R - 1 0 FRYL 48279387 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 4.926000 0.63433 2.798000 0.96311 0.655000 0.94253 CGT TCGA-IB-A7LX-01A-12D-A36O-08 FRYL-011 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000369265.2 1 0 0 9 206 0 77 0 1.064061e-01 0 12 0 77 2 0 0 0 0 0 2 1 0.994144 9 203 0 76 2 0 0 0 0 77 2 -3.808958 1 1 0 0 1 2 2 4 1.763541 1 0.550000 3.150000 0.613734 0.200000 0.090000 1.000000 0.180000 0.357415 0.200000 0 1.300000e-01 1 TMPRSS11D 9407 broad.mit.edu 37 4 68725370 68725370 + Missense_Mutation SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr4:68725370C>T ENST00000283916.6 - 2 133 c.35G>A c.(34-36)aGa>aAa p.R12K TMPRSS11D_ENST00000545541.1_Intron|TMPRSS11D_ENST00000509584.1_Intron|UBA6-AS1_ENST00000500538.2_RNA NM_004262.2 NP_004253.1 O60235 TM11D_HUMAN transmembrane protease, serine 11D 23 ATTCAGAAATCTTGAAGTCGA 0.388000 0 SO:0001583 missense ENST00000283916.6 1 1 hg19 CCDS3518.1 . . . . . . . . . . C 19.86 3.905995 0.72868 . . ENSG00000153802 ENST00000283916 D 0.88046 -2.33 5.19 5.19 0.71726 . 0.000000 0.64402 D 0.000010 D 0.89529 0.6741 L 0.61387 1.9 0.80722 D 1 D 0.67145 0.996 P 0.54759 0.76 D 0.88677 0.3199 10 0.41790 T 0.15 . 14.0925 0.65000 0.0:1.0:0.0:0.0 . 12 O60235 TM11D_HUMAN K 12 ENSP00000283916:R12K ENSP00000283916:R12K R - 2 0 TMPRSS11D 68407965 1.000000 0.71417 0.997000 0.53966 0.591000 0.36615 1.993000 0.40747 2.704000 0.92352 0.563000 0.77884 AGA TCGA-IB-A7LX-01A-12D-A36O-08 TMPRSS11D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251430.3 1 0 1 66 188 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 1.000000 66 186 0 66 2 0 0 0 0 67 2 -20.000000 1 1 0 0 1 2 2 4 1.763541 1 0.550000 3.150000 0.613734 0.990000 0.890000 1.000000 1.000000 0.991382 0.990000 1 9.900000e-01 1 MCC 4163 broad.mit.edu 37 5 112720776 112720776 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:112720776G>T ENST00000408903.3 - 2 719 c.304C>A c.(304-306)Cga>Aga p.R102R CTD-2201G3.1_ENST00000416046.2_RNA NM_001085377.1 NP_001078846 P23508 CRCM_HUMAN mutated in colorectal cancers 42 all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198) CTAATTTCTCGAACAAGCTGC 0.458000 0 SO:0001819 synonymous_variant ENST00000408903.3 1 0 hg19 CCDS43351.1 TCGA-IB-A7LX-01A-12D-A36O-08 MCC-003 PUTATIVE basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370839.1 1 0 0 14 374 0 116 0 3.704771e-02 0 8 0 116 2 0 0 0 0 0 2 1 0.999738 14 368 0 116 2 0 0 0 0 116 2 -3.267031 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.160000 0.090000 0.280000 0.170000 0.177686 0.160000 0 1.200000e-01 2.200000e-01 MYOT 9499 broad.mit.edu 37 5 137219194 137219194 + Missense_Mutation SNP T T A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:137219194T>A ENST00000239926.4 + 7 1312 c.938T>A c.(937-939)gTc>gAc p.V313D MYOT_ENST00000509812.1_Intron|RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.V198D|MYOT_ENST00000421631.2_Missense_Mutation_p.V129D|RP11-381K20.2_ENST00000508281.2_RNA NM_006790.2 NP_006781 Q9UBF9 MYOTI_HUMAN myotilin 23 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109) TTTGAAGTAGTCAGAGCTTCA 0.443000 0 SO:0001583 missense ENST00000239926.4 1 1 hg19 CCDS4194.1 . . . . . . . . . . T 21.9 4.221755 0.79464 . . ENSG00000120729 ENST00000239926;ENST00000421631;ENST00000515645 T;T;T 0.72505 -0.66;-0.66;-0.66 5.08 5.08 0.68730 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.56097 D 0.000032 D 0.88276 0.6393 H 0.95816 3.725 0.80722 D 1 D 0.76494 0.999 D 0.71184 0.972 D 0.91887 0.5520 10 0.87932 D 0 . 15.1564 0.72746 0.0:0.0:0.0:1.0 . 313 Q9UBF9 MYOTI_HUMAN D 313;129;198 ENSP00000239926:V313D;ENSP00000391185:V129D;ENSP00000426281:V198D ENSP00000239926:V313D V + 2 0 MYOT 137247093 1.000000 0.71417 1.000000 0.80357 0.970000 0.65996 6.191000 0.72063 2.021000 0.59480 0.533000 0.62120 GTC TCGA-IB-A7LX-01A-12D-A36O-08 MYOT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251219.2 1 0 1 45 242 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 44 235 0 85 2 0 0 0 0 85 2 -19.998670 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.720000 0.540000 0.940000 0.720000 0.734723 0.720000 0 6.300000e-01 8.300000e-01 PCDHB14 56122 broad.mit.edu 37 5 140603942 140603942 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:140603942C>A ENST00000239449.4 + 1 865 c.865C>A c.(865-867)Cgt>Agt p.R289S PCDHB14_ENST00000515856.2_Missense_Mutation_p.R136S NM_018934.2 NP_061757.1 Q9Y5E9 PCDBE_HUMAN protocadherin beta 14 49 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) AGAAGATATTCGTAAAACATT 0.378000 Ovarian(141;50 1831 27899 33809 37648) 0 SO:0001583 missense ENST00000239449.4 1 0 hg19 CCDS4256.1 . . . . . . . . . . - 6.356 0.433698 0.12045 . . ENSG00000120327 ENST00000515856;ENST00000239449 T;T 0.50001 0.76;0.76 4.75 0.286 0.15710 Cadherin (4);Cadherin-like (1); . . . . T 0.22282 0.0537 N 0.16602 0.42 0.09310 N 1 B 0.15141 0.012 B 0.15052 0.012 T 0.28396 -1.0045 9 0.02654 T 1 . 4.3959 0.11363 0.2528:0.4394:0.2343:0.0735 . 289 Q9Y5E9 PCDBE_HUMAN S 136;289 ENSP00000444518:R136S;ENSP00000239449:R289S ENSP00000239449:R289S R + 1 0 PCDHB14 140584126 0.000000 0.05858 0.078000 0.20375 0.873000 0.50193 -0.821000 0.04452 0.109000 0.17891 0.655000 0.94253 CGT TCGA-IB-A7LX-01A-12D-A36O-08 PCDHB14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251814.2 1 0 0 11 240 0 66 0 3.963645e-01 0 29 0 66 2 0 0 0 0 0 2 1 0.998331 11 237 0 66 2 0 0 0 0 66 2 -12.871820 1 0 121402 1 31 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.200000 0.100000 0.360000 0.210000 0.218956 0.200000 0 1.500000e-01 2.800000e-01 TCERG1 10915 broad.mit.edu 37 5 145859431 145859431 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:145859431G>T ENST00000296702.5 + 11 1814 c.1776G>T c.(1774-1776)ccG>ccT p.P592P TCERG1_ENST00000394421.2_Silent_p.P571P NM_006706.3 NP_006697.2 O14776 TCRG1_HUMAN transcription elongation regulator 1 46 Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) ACCCAACTCCGACAATGCTGT 0.323000 0 SO:0001819 synonymous_variant ENST00000296702.5 1 0 hg19 CCDS4282.1 TCGA-IB-A7LX-01A-12D-A36O-08 TCERG1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251886.1 1 0 0 10 232 0 51 0 5.719337e-01 0 44 0 51 2 0 0 0 0 0 2 1 0.996725 10 227 0 51 2 0 0 0 0 51 2 -3.110063 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.190000 0.090000 0.350000 0.180000 0.208096 0.190000 0 1.400000e-01 2.700000e-01 SLU7 10569 broad.mit.edu 37 5 159839519 159839519 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:159839519C>A ENST00000297151.4 - 6 965 c.578G>T c.(577-579)cGa>cTa p.R193L NM_006425.4 NP_006416.3 O95391 SLU7_HUMAN SLU7 splicing factor homolog (S. cerevisiae) 20 Renal(175;0.00196) Medulloblastoma(196;0.0354)|all_neural(177;0.116) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) TTTCAATGTTCGTTTTGCCTT 0.274000 0 SO:0001583 missense ENST00000297151.4 1 0 hg19 CCDS4352.1 . . . . . . . . . . C 24.6 4.554570 0.86231 . . ENSG00000164609 ENST00000297151 T 0.45668 0.89 5.68 4.81 0.61882 Pre-mRNA splicing Prp18-interacting factor (1); 0.051383 0.85682 D 0.000000 T 0.57651 0.2068 M 0.75150 2.29 0.80722 D 1 P 0.51147 0.942 P 0.54140 0.743 T 0.64071 -0.6493 10 0.87932 D 0 -28.4394 14.4844 0.67606 0.0:0.9296:0.0:0.0704 . 193 O95391 SLU7_HUMAN L 193 ENSP00000297151:R193L ENSP00000297151:R193L R - 2 0 SLU7 159772097 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 6.749000 0.74883 1.403000 0.46800 0.650000 0.86243 CGA TCGA-IB-A7LX-01A-12D-A36O-08 SLU7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252673.1 1 0 0 13 318 0 79 0 8.083668e-01 0 78 0 79 2 0 0 0 0 0 2 1 0.999404 13 307 0 76 2 0 0 0 0 79 2 -2.920853 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.180000 0.090000 0.310000 0.180000 0.194181 0.180000 0 1.300000e-01 2.500000e-01 TSPAN17 26262 broad.mit.edu 37 5 176084641 176084641 + Missense_Mutation SNP G G T rs141018454 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:176084641G>T ENST00000503045.1 + 9 927 c.872G>T c.(871-873)cGa>cTa p.R291L TSPAN17_ENST00000405525.2_3'UTR|TSPAN17_ENST00000515708.1_3'UTR|TSPAN17_ENST00000310032.8_Missense_Mutation_p.R314L|TSPAN17_ENST00000298564.10_3'UTR|TSPAN17_ENST00000508164.1_Missense_Mutation_p.R311L Q96FV3 TSN17_HUMAN tetraspanin 17 13 all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133) Medulloblastoma(196;0.00498)|all_neural(177;0.0212) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) ccacccagccgacatgttttc 0.537000 0 SO:0001583 missense ENST00000503045.1 1 0 hg19 . . . . . . . . . . G 13.99 2.403196 0.42613 . . ENSG00000048140 ENST00000310032;ENST00000508164;ENST00000503045 T;T;T 0.17528 3.13;3.14;2.27 2.8 -5.59 0.02505 . . . . . T 0.06142 0.0159 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.33317 -0.9873 9 0.87932 D 0 . 0.7854 0.01047 0.235:0.3522:0.1684:0.2445 . 311 Q96FV3-4 . L 314;311;291 ENSP00000309036:R314L;ENSP00000422053:R311L;ENSP00000425212:R291L ENSP00000309036:R314L R + 2 0 TSPAN17 176017247 0.000000 0.05858 0.000000 0.03702 0.121000 0.20230 -1.876000 0.01633 -1.978000 0.00993 -0.339000 0.08088 CGA TCGA-IB-A7LX-01A-12D-A36O-08 TSPAN17-008 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000372215.1 1 0 0 9 211 0 54 0 7.700399e-01 0 67 0 54 2 0 0 0 0 0 2 1 0.994019 9 207 0 54 2 0 0 0 0 54 2 -3.282755 1 1 121404 12 41 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.190000 0.090000 0.350000 0.180000 0.207878 0.190000 0 1.300000e-01 2.700000e-01 RUFY1 80230 broad.mit.edu 37 5 178994482 178994482 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:178994482G>T ENST00000319449.4 + 4 635 c.623G>T c.(622-624)cGa>cTa p.R208L RUFY1_ENST00000393438.2_Missense_Mutation_p.R100L|RUFY1_ENST00000377001.2_Missense_Mutation_p.R208L|RUFY1_ENST00000437570.2_Missense_Mutation_p.R100L NM_025158.4 NP_079434.3 Q96T51 RUFY1_HUMAN RUN and FYVE domain containing 1 26 all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195) all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GGAAGAGGCCGAGCGTGGCTT 0.403000 HNSCC(44;0.11) 0 SO:0001583 missense ENST00000319449.4 1 0 hg19 CCDS4445.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 33|33 5.271432|5.271432 0.95429|0.95429 .|. .|. ENSG00000176783|ENSG00000176783 ENST00000502984;ENST00000508609|ENST00000319449;ENST00000377001;ENST00000437570;ENST00000393438 .|T;T;T;T .|0.19105 .|2.17;2.17;2.17;2.17 5.43|5.43 5.43|5.43 0.79202|0.79202 .|RUN (3); .|0.000000 .|0.85682 .|D .|0.000000 .|T .|0.56171 .|0.1967 M|M 0.88241|0.88241 2.94|2.94 0.80722|0.80722 D|D 1|1 .|D .|0.89917 .|1.0 .|D .|0.97110 .|1.0 .|T .|0.63769 .|-0.6562 .|10 .|0.87932 .|D .|0 -15.4094|-15.4094 19.6173|19.6173 0.95639|0.95639 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|208 .|Q96T51 .|RUFY1_HUMAN X|L 166;19|208;208;100;100 .|ENSP00000325594:R208L;ENSP00000366200:R208L;ENSP00000390025:R100L;ENSP00000377087:R100L .|ENSP00000325594:R208L E|R +|+ 1|2 0|0 RUFY1|RUFY1 178927088|178927088 1.000000|1.000000 0.71417|0.71417 0.999000|0.999000 0.59377|0.59377 0.876000|0.876000 0.50452|0.50452 9.481000|9.481000 0.97933|0.97933 2.712000|2.712000 0.92718|0.92718 0.557000|0.557000 0.71058|0.71058 GAG|CGA TCGA-IB-A7LX-01A-12D-A36O-08 RUFY1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000253505.2 1 0 0 9 215 0 68 0 8.642011e-01 0 88 0 68 2 0 0 0 0 0 2 1 0.994264 9 213 0 68 2 0 0 0 0 68 2 -2.896596 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.190000 0.090000 0.350000 0.180000 0.204208 0.190000 0 1.300000e-01 2.700000e-01 SKIV2L2 23517 broad.mit.edu 37 5 54718748 54718748 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr5:54718748G>T ENST00000230640.5 + 26 3268 c.3014G>T c.(3013-3015)cGa>cTa p.R1005L SKIV2L2_ENST00000545714.1_Missense_Mutation_p.R904L NM_015360.4 NP_056175.3 P42285 SK2L2_HUMAN superkiller viralicidic activity 2-like 2 (S. cerevisiae) 41 Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194) GAATTGCTTCGACAAATGTGT 0.383000 Melanoma(2;92 134 23744 29976 33782) 0 SO:0001583 missense ENST00000230640.5 1 0 hg19 CCDS3967.1 . . . . . . . . . . G 26.0 4.694671 0.88830 . . ENSG00000039123 ENST00000230640;ENST00000545714 T;T 0.26373 1.74;1.74 5.79 5.79 0.91817 DSH, C-terminal (1); 0.062767 0.64402 D 0.000008 T 0.69079 0.3071 H 0.97983 4.12 0.80722 D 1 D;D 0.71674 0.998;0.984 D;D 0.71414 0.973;0.921 T 0.81202 -0.1040 10 0.87932 D 0 -10.8717 20.0281 0.97530 0.0:0.0:1.0:0.0 . 904;1005 F5H7E2;P42285 .;SK2L2_HUMAN L 1005;904 ENSP00000230640:R1005L;ENSP00000442583:R904L ENSP00000230640:R1005L R + 2 0 SKIV2L2 54754505 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 9.434000 0.97515 2.727000 0.93392 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 SKIV2L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214108.1 1 0 0 13 321 0 79 0 9.695676e-01 0 147 0 79 2 0 0 0 0 0 2 1 0.999531 13 318 0 79 2 0 0 0 0 79 2 -2.975620 1 1 0 0 1 1 2 3 1.889547 1 0.550000 3.150000 0.646296 0.180000 0.090000 0.300000 0.180000 0.192450 0.180000 0 1.300000e-01 2.400000e-01 AIM1 202 broad.mit.edu 37 6 106968971 106968971 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:106968971G>T ENST00000369066.3 + 2 3151 c.2664G>T c.(2662-2664)ttG>ttT p.L888F NM_001624.2 NP_001615 Q9UMX9 S45A2_HUMAN absent in melanoma 1 69 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) CCTGTGGTTTGAACAAAGAAC 0.478000 0 SO:0001583 missense ENST00000369066.3 1 0 hg19 CCDS34506.1 . . . . . . . . . . G 11.12 1.546580 0.27652 . . ENSG00000112297 ENST00000285105;ENST00000369066 T 0.72051 -0.62 5.99 0.198 0.15168 . 1.843970 0.02402 N 0.080812 T 0.29256 0.0728 N 0.22421 0.69 0.18873 N 0.999986 B 0.31931 0.347 B 0.25759 0.063 T 0.25187 -1.0139 10 0.52906 T 0.07 . 0.6497 0.00824 0.4479:0.1681:0.2214:0.1625 . 888 Q9Y4K1 AIM1_HUMAN F 1296;888 ENSP00000358062:L888F ENSP00000285105:L1296F L + 3 2 AIM1 107075664 0.970000 0.33590 0.009000 0.14445 0.980000 0.70556 0.373000 0.20484 0.078000 0.16900 -0.345000 0.07892 TTG TCGA-IB-A7LX-01A-12D-A36O-08 AIM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041669.1 1 0 0 15 264 0 119 0 2.318775e-01 0 16 0 119 2 0 0 0 0 0 2 1 0.999863 15 257 0 119 2 0 0 0 0 119 2 -4.788704 1 1 0 0 1 0 2 2 1.365333 1 0.550000 3.150000 0.550000 0.210000 0.110000 1.000000 0.200000 0.336034 0.210000 0 1.500000e-01 1 RTN4IP1 84816 broad.mit.edu 37 6 107070789 107070789 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:107070789G>T ENST00000369063.3 - 2 795 c.330C>A c.(328-330)atC>atA p.I110I RTN4IP1_ENST00000539449.1_Silent_p.I110I NM_032730.4 NP_116119.2 Q8WWV3 RT4I1_HUMAN reticulon 4 interacting protein 1 13 Breast(9;0.0107)|all_epithelial(6;0.14) all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144) Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394) CTTCTCCTTTGATTTTCACGT 0.413000 0 SO:0001819 synonymous_variant ENST00000369063.3 1 0 hg19 CCDS5056.1 TCGA-IB-A7LX-01A-12D-A36O-08 RTN4IP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041673.1 1 0 0 16 237 0 93 0 4.033831e-02 0 5 0 93 2 0 0 0 0 0 2 1 0.999935 15 235 0 93 2 0 0 0 0 93 2 -5.935248 1 1 0 0 1 0 2 2 1.365333 1 0.550000 3.150000 0.550000 0.240000 0.130000 1.000000 0.230000 0.365482 0.240000 0 1.800000e-01 1 ROS1 6098 broad.mit.edu 37 6 117710875 117710875 + Missense_Mutation SNP C C A rs140178288 byFrequency TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:117710875C>A ENST00000368508.3 - 12 1595 c.1397G>T c.(1396-1398)cGa>cTa p.R466L ROS1_ENST00000368507.3_Missense_Mutation_p.R475L|GOPC_ENST00000467125.1_Intron NM_002944.2 NP_002935.2 P08922 ROS1_HUMAN ROS proto-oncogene 1 , receptor tyrosine kinase TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7) 162 all_cancers(87;0.00846)|all_epithelial(87;0.0242) GTAAATGATTCGCTTGGCTTG 0.493000 T GOPC, SDC4, SLC34A2, EZR, LRIG3 glioblastoma, NSCLC Dom yes 6 6q22 6098 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) O, E 0 SO:0001583 missense ENST00000368508.3 1 0 hg19 CCDS5116.1 . . . . . . . . . . C 19.56 3.850642 0.71719 . . ENSG00000047936 ENST00000368508;ENST00000368507 D;D 0.91631 -2.88;-2.88 5.82 4.94 0.65067 . 0.112377 0.37348 N 0.002123 D 0.90253 0.6952 L 0.32530 0.975 0.80722 D 1 D 0.76494 0.999 D 0.65684 0.937 D 0.88337 0.2972 10 0.31617 T 0.26 . 11.6854 0.51483 0.0:0.9193:0.0:0.0807 . 466 P08922 ROS1_HUMAN L 466;475 ENSP00000357494:R466L;ENSP00000357493:R475L ENSP00000357493:R475L R - 2 0 ROS1 117817568 1.000000 0.71417 0.976000 0.42696 0.482000 0.33219 4.212000 0.58514 2.755000 0.94549 0.561000 0.74099 CGA TCGA-IB-A7LX-01A-12D-A36O-08 ROS1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000043464.1 1 0 0 8 121 0 31 0 1.475323e-02 0 3 0 31 2 0 0 0 0 0 2 1 0.985806 8 110 0 31 2 0 0 0 0 31 2 -3.326195 1 1 0 0 1 0 2 2 1.365333 1 0.550000 3.150000 0.550000 0.250000 0.110000 1.000000 0.220000 0.371014 0.250000 0 1.700000e-01 1 MAP3K5 4217 broad.mit.edu 37 6 137113237 137113237 + Missense_Mutation SNP C C G TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:137113237C>G ENST00000359015.4 - 1 419 c.59G>C c.(58-60)gGc>gCc p.G20A NM_005923.3 NP_005914.1 Q99683 M3K5_HUMAN mitogen-activated protein kinase kinase kinase 5 58 Colorectal(23;0.24) GGTGCAGAAGCCCGAGGGGGC 0.751000 0 SO:0001583 missense ENST00000359015.4 0 1 hg19 CCDS5179.1 . . . . . . . . . . C 9.984 1.228890 0.22542 . . ENSG00000197442 ENST00000359015;ENST00000367768 T 0.68624 -0.34 3.56 1.67 0.24075 . 0.634408 0.14920 N 0.290736 T 0.20170 0.0485 N 0.14661 0.345 0.18873 N 0.999985 B 0.13594 0.008 B 0.11329 0.006 T 0.29792 -1.0000 10 0.12103 T 0.63 . 7.361 0.26745 0.1664:0.7407:0.0:0.0929 . 20 Q99683 M3K5_HUMAN A 20;100 ENSP00000351908:G20A ENSP00000351908:G20A G - 2 0 MAP3K5 137154930 0.535000 0.26370 0.016000 0.15963 0.025000 0.11179 2.498000 0.45363 0.287000 0.22375 0.573000 0.79308 GGC TCGA-IB-A7LX-01A-12D-A36O-08 MAP3K5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042383.1 1 0 0 36 34 0 11 1 9.999725e-01 14 8 0 11 2 0 0 0 0 0 2 1 1.000000 34 34 0 11 2 0 0 0 0 11 2 -20.000000 1 1 0 0 1 2 8 10 4.331302 1 0.550000 3.150000 0.844398 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 UTRN 7402 broad.mit.edu 37 6 144768443 144768443 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:144768443C>A ENST00000367545.3 + 14 1711 c.1711C>A c.(1711-1713)Cga>Aga p.R571R NM_007124.2 NP_009055.2 P46939 UTRO_HUMAN utrophin p.R571*(2) 148 Ovarian(120;0.218) TGTCAGTGTTCGACGTCTGGC 0.383000 2 Substitution - Nonsense(2) SO:0001819 synonymous_variant ENST00000367545.3 1 0 hg19 CCDS34547.1 TCGA-IB-A7LX-01A-12D-A36O-08 UTRN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042551.1 1 0 0 8 174 0 52 0 1.025800e-01 0 11 0 52 2 0 0 0 0 0 2 1 0.989141 8 171 0 52 2 0 0 0 0 52 2 -4.312080 1 1 0 0 1 3 4 7 2.292266 1 0.550000 3.150000 0.701740 0.280000 0.120000 1.000000 0.230000 0.432807 0.280000 0 1.800000e-01 1 MAP3K4 4216 broad.mit.edu 37 6 161514029 161514029 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:161514029G>T ENST00000392142.4 + 14 3437 c.3289G>T c.(3289-3291)Gat>Tat p.D1097Y MAP3K4_ENST00000366919.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000366920.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000348824.7_Missense_Mutation_p.D1097Y NM_005922.2 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 77 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) TCAAGGATTTGATTTTCTACA 0.348000 0 SO:0001583 missense ENST00000392142.4 1 0 hg19 CCDS34565.1 . . . . . . . . . . G 23.5 4.421880 0.83559 . . ENSG00000085511 ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824 T;T;T;T 0.72167 -0.63;-0.61;-0.61;-0.63 5.84 4.97 0.65823 . 0.000000 0.85682 D 0.000000 T 0.76062 0.3935 L 0.51422 1.61 0.80722 D 1 D;D;D;D 0.89917 1.0;0.998;1.0;1.0 D;P;D;D 0.91635 0.998;0.898;0.999;0.999 T 0.80400 -0.1398 10 0.87932 D 0 -38.942 16.2904 0.82747 0.0:0.0:0.8664:0.1336 . 1097;87;1097;1097 F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4 .;.;.;M3K4_HUMAN Y 1097 ENSP00000355886:D1097Y;ENSP00000375986:D1097Y;ENSP00000355887:D1097Y;ENSP00000297332:D1097Y ENSP00000297332:D1097Y D + 1 0 MAP3K4 161434019 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.476000 0.97823 1.461000 0.47929 0.655000 0.94253 GAT TCGA-IB-A7LX-01A-12D-A36O-08 MAP3K4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000042988.3 1 0 0 13 284 0 104 0 3.591268e-01 0 27 0 104 2 0 0 0 0 0 2 1 0.999523 13 279 0 103 2 0 0 0 0 104 2 -3.193374 1 1 0 0 1 0 2 2 1.366277 1 0.550000 3.150000 0.550000 0.170000 0.080000 1.000000 0.160000 0.290527 0.170000 0 1.200000e-01 2.800000e-01 IMPG1 3617 broad.mit.edu 37 6 76751711 76751711 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr6:76751711C>A ENST00000369950.3 - 2 389 c.200G>T c.(199-201)cGa>cTa p.R67L IMPG1_ENST00000369963.3_Intron NM_001282368.1|NM_001563.2 NP_001269297.1|NP_001554.2 interphotoreceptor matrix proteoglycan 1 63 Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222) TCTTTTTGTTCGATGCTTTGC 0.363000 Pancreas(37;839 1141 2599 26037) 0 SO:0001583 missense ENST00000369950.3 1 0 hg19 CCDS4985.1 . . . . . . . . . . C 26.8 4.768403 0.90020 . . ENSG00000112706 ENST00000369950 T 0.79940 -1.32 6.07 5.21 0.72293 . 0.125602 0.36591 N 0.002519 D 0.87877 0.6288 M 0.82323 2.585 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 D 0.89118 0.3501 9 . . . . 15.5075 0.75753 0.0:0.9339:0.0:0.0661 . 67 Q17R60 IMPG1_HUMAN L 67 ENSP00000358966:R67L . R - 2 0 IMPG1 76808431 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.573000 0.53856 1.581000 0.49865 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 IMPG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041288.1 1 0 0 12 290 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 0.999037 12 283 0 131 2 0 0 0 0 131 2 -3.065444 1 1 0 0 1 0 2 2 1.369231 1 0.550000 3.150000 0.550000 0.150000 0.070000 1.000000 0.140000 0.277952 0.150000 0 1.100000e-01 2.600000e-01 PMPCB 9512 broad.mit.edu 37 7 102950912 102950912 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:102950912C>A ENST00000249269.4 + 9 1182 c.1144C>A c.(1144-1146)Caa>Aaa p.Q382K PMPCB_ENST00000420236.2_Missense_Mutation_p.Q277K|PMPCB_ENST00000428154.1_Missense_Mutation_p.Q382K NM_004279.2 NP_004270.2 O75439 MPPB_HUMAN peptidase (mitochondrial processing) beta 21 ACATGTTGTTCAAAAAGAATG 0.308000 0 SO:0001583 missense ENST00000249269.4 1 0 hg19 CCDS5730.1 . . . . . . . . . . C 24.7 4.556733 0.86231 . . ENSG00000105819 ENST00000249269;ENST00000428154;ENST00000420236 T;T;T 0.06608 3.28;3.28;3.28 5.71 4.83 0.62350 Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1); 0.000000 0.85682 D 0.000000 T 0.30166 0.0756 M 0.89287 3.02 0.80722 D 1 P;D;D;D;D;D 0.89917 0.937;1.0;1.0;1.0;1.0;1.0 P;D;D;D;D;D 0.76071 0.839;0.985;0.985;0.985;0.985;0.987 T 0.18147 -1.0346 10 0.51188 T 0.08 . 14.8943 0.70633 0.0:0.931:0.0:0.069 . 277;277;382;373;382;382 E7ERZ4;B4DM90;A8K1E9;Q96CP5;O75439;G3V0E4 .;.;.;.;MPPB_HUMAN;. K 382;382;277 ENSP00000249269:Q382K;ENSP00000390035:Q382K;ENSP00000410393:Q277K ENSP00000249269:Q382K Q + 1 0 PMPCB 102738148 1.000000 0.71417 0.992000 0.48379 0.963000 0.63663 6.026000 0.70873 1.423000 0.47198 0.585000 0.79938 CAA TCGA-IB-A7LX-01A-12D-A36O-08 PMPCB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347913.1 1 0 0 14 267 0 101 0 9.813653e-01 0 129 0 101 2 0 0 0 0 0 2 1 0.782532 14 265 1 99 11 0 0 0 0 101 2 -4.627886 1 1 0 0 1 0 3 3 1.672992 1 0.550000 3.150000 0.627792 0.230000 0.120000 1.000000 0.220000 0.366243 0.230000 0 1.700000e-01 1 LAMB4 22798 broad.mit.edu 37 7 107743496 107743496 + Silent SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:107743496C>T ENST00000388781.3 - 10 1256 c.1173G>A c.(1171-1173)gcG>gcA p.A391A LAMB4_ENST00000414450.2_Silent_p.A391A|LAMB4_ENST00000205386.4_Silent_p.A391A|LAMB4_ENST00000388780.3_Silent_p.A391A|LAMB4_ENST00000418464.1_Silent_p.A391A NM_007356.2 NP_031382.2 A4D0S4 LAMB4_HUMAN laminin, beta 4 97 CACGAATGCACGCGTAGGGAT 0.577000 0 SO:0001819 synonymous_variant ENST00000388781.3 1 1 hg19 CCDS34732.1 TCGA-IB-A7LX-01A-12D-A36O-08 LAMB4-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000337442.1 1 0 1 22 78 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.999999 22 75 0 34 2 0 0 0 0 34 2 -20.000000 1 1 121408 1 33 1 0 3 3 1.672992 1 0.550000 3.150000 0.627792 0.990000 0.660000 1.000000 1.000000 0.934200 0.990000 1 8.200000e-01 1 TSPAN33 340348 broad.mit.edu 37 7 128801559 128801559 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:128801559C>A ENST00000289407.4 + 2 251 c.142C>A c.(142-144)Cgg>Agg p.R48R NM_178562.3 NP_848657.1 Q86UF1 TSN33_HUMAN tetraspanin 33 14 TGTCTACGCTCGGCTAATGAA 0.582000 0 SO:0001819 synonymous_variant ENST00000289407.4 1 0 hg19 CCDS5810.1 TCGA-IB-A7LX-01A-12D-A36O-08 TSPAN33-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350983.1 1 0 0 13 275 0 92 0 7.192633e-03 0 3 0 92 2 0 0 0 0 0 2 1 0.999523 13 271 0 91 2 0 0 0 0 92 2 -2.890505 1 1 0 0 1 0 3 3 1.672992 1 0.550000 3.150000 0.627792 0.210000 0.110000 1.000000 0.200000 0.349124 0.210000 0 1.500000e-01 1 ZC3HC1 51530 broad.mit.edu 37 7 129658541 129658541 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:129658541C>A ENST00000358303.4 - 10 1556 c.1472G>T c.(1471-1473)cGa>cTa p.R491L RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.R420L|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R470L|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R448L|RP11-306G20.1_ENST00000587038.1_RNA NM_016478.3 NP_057562.3 Q86WB0 NIPA_HUMAN zinc finger, C3HC-type containing 1 p.R491Q(1) 22 Melanoma(18;0.0435) CCGAAATATTCGGAATACTTT 0.393000 Melanoma(115;540 1606 16325 28853 48167) 1 Substitution - Missense(1) SO:0001583 missense ENST00000358303.4 1 0 hg19 CCDS34753.1 . . . . . . . . . . C 21.0 4.081950 0.76528 . . ENSG00000091732 ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503 T;T;T;T 0.54675 1.21;0.62;1.24;0.56 6.17 6.17 0.99709 . 0.237648 0.36628 N 0.002486 T 0.71099 0.3300 M 0.62723 1.935 0.47737 D 0.9995 D;D;D 0.89917 1.0;0.974;0.987 D;P;P 0.77004 0.989;0.576;0.698 T 0.70651 -0.4813 10 0.66056 D 0.02 -8.1694 17.5987 0.88020 0.0:1.0:0.0:0.0 . 420;491;448 Q86WB0-3;Q86WB0;C9J0I9 .;NIPA_HUMAN;. L 491;420;470;448 ENSP00000351052:R491L;ENSP00000353933:R420L;ENSP00000309301:R470L;ENSP00000418533:R448L ENSP00000309301:R470L R - 2 0 ZC3HC1 129445777 1.000000 0.71417 1.000000 0.80357 0.384000 0.30261 3.871000 0.56077 2.941000 0.99782 0.655000 0.94253 CGA TCGA-IB-A7LX-01A-12D-A36O-08 ZC3HC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349316.1 1 0 0 13 304 0 88 0 2.680249e-01 0 23 0 88 2 0 0 0 0 0 2 1 0.999502 12 299 0 86 2 0 0 0 0 88 2 -3.027710 1 1 0 0 1 0 3 3 1.672992 1 0.550000 3.150000 0.627792 0.190000 0.100000 1.000000 0.190000 0.333253 0.190000 0 1.400000e-01 1 UBE3C 9690 broad.mit.edu 37 7 156961790 156961790 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:156961790C>A ENST00000348165.5 + 3 529 c.169C>A c.(169-171)Cga>Aga p.R57R UBE3C_ENST00000389103.4_Intron NM_014671.2 NP_055486.2 Q15386 UBE3C_HUMAN ubiquitin protein ligase E3C 63 all_hematologic(28;0.0185)|all_epithelial(9;0.0664) OV - Ovarian serous cystadenocarcinoma(82;0.00448) GTCATTTATTCGAGGCTATAG 0.363000 0 SO:0001819 synonymous_variant ENST00000348165.5 1 0 hg19 CCDS34789.1 TCGA-IB-A7LX-01A-12D-A36O-08 UBE3C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348108.1 1 0 0 12 238 0 65 0 6.664925e-01 0 46 0 65 2 0 0 0 0 0 2 1 0.999140 12 236 0 65 2 0 0 0 0 65 2 -2.926263 1 1 0 0 1 0 3 3 1.671923 1 0.550000 3.150000 0.626943 0.230000 0.110000 1.000000 0.210000 0.364627 0.230000 0 1.600000e-01 1 UBE2D4 51619 broad.mit.edu 37 7 43990227 43990227 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:43990227G>T ENST00000222402.3 + 6 423 c.334G>T c.(334-336)Gac>Tac p.D112Y RP5-1165K10.2_ENST00000454572.1_RNA|POLR2J4_ENST00000427076.1_RNA|UBE2D4_ENST00000394798.4_Missense_Mutation_p.D74Y NM_015983.3 NP_057067.1 Q9Y2X8 UB2D4_HUMAN ubiquitin-conjugating enzyme E2D 4 (putative) 5 GCTGCTCTGCGACCCCAACCC 0.562000 Esophageal Squamous(27;401 815 16344 30604) 0 SO:0001583 missense ENST00000222402.3 1 0 hg19 CCDS5474.1 . . . . . . . . . . G 20.6 4.025689 0.75390 . . ENSG00000078967 ENST00000222402;ENST00000394798 T;T 0.73789 -0.78;-0.78 4.49 3.61 0.41365 Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2); 0.055533 0.64402 D 0.000002 D 0.86834 0.6028 M 0.90369 3.11 0.58432 D 0.999999 D;D 0.89917 0.999;1.0 D;D 0.77557 0.976;0.99 D 0.87620 0.2509 10 0.87932 D 0 . 10.2569 0.43403 0.0996:0.0:0.9004:0.0 . 74;112 Q9UQL0;Q9Y2X8 .;UB2D4_HUMAN Y 112;74 ENSP00000222402:D112Y;ENSP00000378277:D74Y ENSP00000222402:D112Y D + 1 0 UBE2D4 43956752 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 8.286000 0.89916 0.885000 0.36088 0.655000 0.94253 GAC TCGA-IB-A7LX-01A-12D-A36O-08 UBE2D4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250958.2 1 0 0 11 185 0 41 0 6.120975e-01 0 35 0 41 2 0 0 0 0 0 2 1 0.998390 11 183 0 39 2 0 0 0 0 41 2 -3.220448 1 1 0 0 1 2 4 6 2.227293 1 0.550000 3.150000 0.694501 0.340000 0.160000 1.000000 0.300000 0.484510 0.340000 0 2.400000e-01 1 DYNC1I1 1780 broad.mit.edu 37 7 95665004 95665004 + Missense_Mutation SNP T T A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr7:95665004T>A ENST00000324972.6 + 13 1548 c.1355T>A c.(1354-1356)gTc>gAc p.V452D DYNC1I1_ENST00000537881.1_Missense_Mutation_p.V415D|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.V432D|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.V435D|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.V435D|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.V415D NM_004411.4 NP_004402.1 O14576 DC1I1_HUMAN dynein, cytoplasmic 1, intermediate chain 1 54 all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191) STAD - Stomach adenocarcinoma(171;0.0957) ACGGGAGACGTCAATAACTTC 0.463000 0 SO:0001583 missense ENST00000324972.6 1 1 hg19 CCDS5644.1 . . . . . . . . . . T 16.60 3.168707 0.57584 . . ENSG00000158560 ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059 T;T;T;T;T;T 0.77098 -1.07;-1.07;-1.07;-1.07;-1.07;-1.07 5.1 5.1 0.69264 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.000000 0.85682 D 0.000000 D 0.85673 0.5751 M 0.74546 2.27 0.80722 D 1 D;D;D;D;D 0.76494 0.999;0.999;0.999;0.997;0.996 D;D;D;D;D 0.78314 0.979;0.991;0.991;0.969;0.923 T 0.82631 -0.0362 10 0.11182 T 0.66 0.0118 15.3616 0.74478 0.0:0.0:0.0:1.0 . 435;432;435;452;415 Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3 .;.;.;DC1I1_HUMAN;. D 435;452;415;432;415;435 ENSP00000392337:V435D;ENSP00000320130:V452D;ENSP00000438377:V415D;ENSP00000398118:V432D;ENSP00000352348:V415D;ENSP00000412444:V435D ENSP00000320130:V452D V + 2 0 DYNC1I1 95502940 1.000000 0.71417 1.000000 0.80357 0.120000 0.20174 7.868000 0.87116 2.283000 0.76528 0.477000 0.44152 GTC TCGA-IB-A7LX-01A-12D-A36O-08 DYNC1I1-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000333432.1 1 0 0 103 1111 0 231 0 0 0 1 0 231 2 0 0 0 0 0 2 1 1.000000 102 1092 0 227 2 0 0 0 0 231 2 -19.999790 1 1 0 0 1 3 6 9 3.443848 1 0.550000 3.150000 0.801806 0.720000 0.570000 1.000000 0.730000 0.769685 0.720000 0 6.400000e-01 1 CSMD3 114788 broad.mit.edu 37 8 113599442 113599442 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr8:113599442C>A ENST00000297405.5 - 23 3982 c.3738G>T c.(3736-3738)acG>acT p.T1246T CSMD3_ENST00000352409.3_Silent_p.T1246T|CSMD3_ENST00000455883.2_Silent_p.T1142T|CSMD3_ENST00000343508.3_Silent_p.T1206T NM_198123.1 NP_937756.1 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 646 CTTCATTATTCGTTGCAGATG 0.353000 HNSCC(6;0.00088)|TCGA Ovarian(7;0.080) 0 SO:0001819 synonymous_variant ENST00000297405.5 1 0 hg19 CCDS6315.1 TCGA-IB-A7LX-01A-12D-A36O-08 CSMD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347141.1 1 0 0 25 628 0 124 0 0 0 0 124 2 0 0 0 0 0 2 1 0.885077 24 622 1 124 18 0 0 0 0 124 2 -3.079016 1 1 0 0 1 2 4 6 3.192915 1 0.550000 3.150000 0.785714 0.290000 0.180000 0.420000 0.300000 0.302985 0.290000 0 2.300000e-01 3.600000e-01 KCTD9 54793 broad.mit.edu 37 8 25296876 25296876 + Silent SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr8:25296876G>T ENST00000221200.4 - 6 638 c.418C>A c.(418-420)Cga>Aga p.R140R KCTD9_ENST00000518067.1_5'UTR NM_017634.3 NP_060104.2 Q7L273 KCTD9_HUMAN potassium channel tetramerization domain containing 9 12 all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191) TCAGGACTTCGGTCAATTAAG 0.368000 0 SO:0001819 synonymous_variant ENST00000221200.4 1 1 hg19 CCDS6048.1 TCGA-IB-A7LX-01A-12D-A36O-08 KCTD9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216890.1 1 0 0 6 206 0 73 0 2.118032e-01 0 26 0 73 2 0 0 0 0 0 2 1 0.962974 6 201 0 73 2 0 0 0 0 73 2 -2.614836 1 1 0 0 1 0 2 2 1.555864 1 0.550000 3.150000 0.550000 0.100000 0.040000 0.210000 0.100000 0.118473 0.100000 0 6.000000e-02 1.600000e-01 PREX2 80243 broad.mit.edu 37 8 68981315 68981315 + Missense_Mutation SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr8:68981315C>T ENST00000288368.4 + 12 1664 c.1387C>T c.(1387-1389)Cgc>Tgc p.R463C PREX2_ENST00000529398.1_3'UTR NM_024870.2|NM_025170.4 NP_079146.2|NP_079446.3 Q70Z35 PREX2_HUMAN phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 p.R463C(2) 178 ATATAGATTTCGCTATGATGA 0.348000 2 Substitution - Missense(2) SO:0001583 missense ENST00000288368.4 1 1 hg19 CCDS6201.1 . . . . . . . . . . C 26.6 4.751767 0.89753 . . ENSG00000046889 ENST00000288368;ENST00000396539;ENST00000354677 T 0.14391 2.51 5.72 4.84 0.62591 DEP domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1); 0.000000 0.85682 D 0.000000 T 0.34193 0.0889 L 0.60904 1.88 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.85130 0.997;0.991;0.996 T 0.08576 -1.0715 10 0.87932 D 0 . 15.0201 0.71624 0.0:0.9317:0.0:0.0683 . 463;463;463 Q70Z35-2;Q70Z35;Q70Z35-3 .;PREX2_HUMAN;. C 463 ENSP00000288368:R463C ENSP00000288368:R463C R + 1 0 PREX2 69143869 1.000000 0.71417 0.998000 0.56505 0.998000 0.95712 7.566000 0.82347 1.559000 0.49555 0.650000 0.86243 CGC TCGA-IB-A7LX-01A-12D-A36O-08 PREX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378620.1 1 0 1 74 122 0 51 0 4.872542e-01 0 4 0 51 2 0 0 0 0 0 2 1 1.000000 74 122 0 50 2 0 0 0 0 51 2 -11.491400 1 1 0 0 1 1 2 3 1.925306 1 0.550000 3.150000 0.641648 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 JPH1 56704 broad.mit.edu 37 8 75227735 75227735 + Missense_Mutation SNP C C T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr8:75227735C>T ENST00000342232.4 - 2 540 c.500G>A c.(499-501)cGc>cAc p.R167H NM_020647.2 NP_065698.1 Q9HDC5 JPH1_HUMAN junctophilin 1 24 Breast(64;0.00576) BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176) CTGCTCGCTGCGCAGCGAGGC 0.721000 0 SO:0001583 missense ENST00000342232.4 1 1 hg19 CCDS6217.1 . . . . . . . . . . C 33 5.214836 0.95104 . . ENSG00000104369 ENST00000342232 T 0.63913 -0.07 4.43 4.43 0.53597 . 0.000000 0.85682 D 0.000000 T 0.80428 0.4621 M 0.82193 2.58 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 T 0.82824 -0.0266 10 0.49607 T 0.09 . 17.2378 0.87004 0.0:1.0:0.0:0.0 . 167 Q9HDC5 JPH1_HUMAN H 167 ENSP00000344488:R167H ENSP00000344488:R167H R - 2 0 JPH1 75390290 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.489000 0.81451 2.284000 0.76573 0.655000 0.94253 CGC TCGA-IB-A7LX-01A-12D-A36O-08 JPH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379102.1 1 0 0 7 79 0 27 0 1.332411e-01 1 6 0 27 2 0 0 0 0 0 2 1 0.977793 7 74 0 27 2 0 0 0 0 27 2 -12.727030 1 1 0 0 1 1 2 3 1.925306 1 0.550000 3.150000 0.641648 0.400000 0.170000 1.000000 0.380000 0.445188 0.400000 0 2.700000e-01 5.900000e-01 PPP1R3B 79660 broad.mit.edu 37 8 8998916 8998916 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr8:8998916G>T ENST00000310455.3 - 2 396 c.246C>A c.(244-246)ttC>ttA p.F82L RP11-10A14.3_ENST00000520017.1_RNA|RP11-10A14.3_ENST00000522057.1_RNA|PPP1R3B_ENST00000519699.1_Missense_Mutation_p.F82L NM_001201329.1|NM_024607.3 NP_001188258.1|NP_078883.2 Q86XI6 PPR3B_HUMAN protein phosphatase 1, regulatory subunit 3B 12 GCGGGTCATCGAATTCCGAGA 0.532000 0 SO:0001583 missense ENST00000310455.3 1 0 hg19 CCDS5973.1 . . . . . . . . . . G 12.70 2.017814 0.35606 . . ENSG00000173281 ENST00000310455;ENST00000519699 T;T 0.43688 0.94;0.94 5.68 -8.12 0.01078 . 0.097783 0.64402 D 0.000001 T 0.30792 0.0776 L 0.51914 1.62 0.35771 D 0.820934 D 0.57571 0.98 P 0.46543 0.52 T 0.62464 -0.6849 10 0.09590 T 0.72 -25.5449 13.8132 0.63276 0.6793:0.0811:0.2396:0.0 . 82 Q86XI6 PPR3B_HUMAN L 82 ENSP00000308318:F82L;ENSP00000428642:F82L ENSP00000308318:F82L F - 3 2 PPP1R3B 9036326 0.005000 0.15991 0.630000 0.29268 0.844000 0.47949 -0.829000 0.04415 -1.404000 0.02050 -0.254000 0.11334 TTC TCGA-IB-A7LX-01A-12D-A36O-08 PPP1R3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251472.1 1 0 0 11 306 1 117 0 1.171865e-01 0 31 1 117 3 0 0 0 0 0 2 1 0.573693 11 303 1 117 11 0 0 0 1 117 2 -3.046002 1 1 0 0 1 0 2 2 1.565375 1 0.550000 3.150000 0.550000 0.120000 0.060000 0.220000 0.120000 0.136422 0.120000 0 9.000000e-02 1.700000e-01 IKBKAP 8518 broad.mit.edu 37 9 111679935 111679935 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr9:111679935C>A ENST00000374647.5 - 9 1063 c.756G>T c.(754-756)ttG>ttT p.L252F IKBKAP_ENST00000537196.1_5'UTR NM_003640.3 NP_003631.2 O95163 ELP1_HUMAN inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein 53 TAGATGCAATCAAACTGCCTG 0.373000 0 SO:0001583 missense ENST00000374647.5 1 0 hg19 CCDS6773.1 . . . . . . . . . . C 21.0 4.081679 0.76528 . . ENSG00000070061 ENST00000374647 T 0.37752 1.18 5.29 5.29 0.74685 Six-bladed beta-propeller, TolB-like (1); 0.000000 0.85682 D 0.000000 T 0.61350 0.2340 M 0.85859 2.78 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.65150 -0.6238 10 0.59425 D 0.04 -0.7514 10.2761 0.43510 0.0:0.9096:0.0:0.0904 . 252 O95163 ELP1_HUMAN F 252 ENSP00000363779:L252F ENSP00000363779:L252F L - 3 2 IKBKAP 110719756 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 2.861000 0.48380 2.642000 0.89623 0.561000 0.74099 TTG TCGA-IB-A7LX-01A-12D-A36O-08 IKBKAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053574.1 1 0 0 22 491 0 159 0 8.563759e-02 0 11 0 159 2 0 0 0 0 0 2 1 0.999999 22 483 0 158 2 0 0 0 0 159 2 -3.959990 1 1 0 0 1 0 2 2 1.589671 1 0.550000 3.150000 0.550000 0.150000 0.090000 0.230000 0.160000 0.162125 0.150000 0 1.200000e-01 1.900000e-01 SLC24A2 25769 broad.mit.edu 37 9 19516253 19516253 + Missense_Mutation SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chr9:19516253C>A ENST00000341998.2 - 10 1945 c.1884G>T c.(1882-1884)atG>atT p.M628I SLC24A2_ENST00000286344.3_Missense_Mutation_p.M611I NM_001193288.2|NM_020344.3 NP_001180217.1|NP_065077.1 Q9UI40 NCKX2_HUMAN solute carrier family 24 (sodium/potassium/calcium exchanger), member 2 33 GGATTTTGTTCATTCGCCACT 0.502000 0 SO:0001583 missense ENST00000341998.2 1 0 hg19 CCDS6493.1 . . . . . . . . . . C 26.2 4.710039 0.89018 . . ENSG00000155886 ENST00000341998;ENST00000286344 T;T 0.59502 0.26;0.26 5.07 5.07 0.68467 Sodium/calcium exchanger membrane region (1); 0.000000 0.85682 D 0.000000 T 0.67392 0.2888 L 0.33753 1.03 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.985;1.0 T 0.65492 -0.6155 9 . . . . 18.4603 0.90736 0.0:1.0:0.0:0.0 . 611;628 Q9UI40-2;Q9UI40 .;NCKX2_HUMAN I 628;611 ENSP00000344801:M628I;ENSP00000286344:M611I . M - 3 0 SLC24A2 19506253 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.771000 0.85420 2.351000 0.79841 0.655000 0.94253 ATG TCGA-IB-A7LX-01A-12D-A36O-08 SLC24A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051866.2 1 0 0 17 400 0 152 0 1.943403e-03 0 2 0 152 2 0 0 0 0 0 2 1 0.999965 17 397 0 152 2 0 0 0 0 152 2 -3.036471 1 1 0 0 1 0 3 3 1.727980 1 0.550000 3.150000 0.629477 0.190000 0.100000 1.000000 0.170000 0.321835 0.190000 0 1.400000e-01 1 SLC9A6 10479 broad.mit.edu 37 X 135076969 135076969 + Missense_Mutation SNP G G T rs146114052 TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:135076969G>T ENST00000370698.3 + 2 385 c.350G>T c.(349-351)cGg>cTg p.R117L SLC9A6_ENST00000370695.4_Missense_Mutation_p.R117L|SLC9A6_ENST00000370701.1_Missense_Mutation_p.R65L NM_006359.2 NP_006350.1 Q92581 SL9A6_HUMAN solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6 33 Acute lymphoblastic leukemia(192;0.000127) CTTGTGCTTCGGTATGGCATT 0.428000 0 SO:0001583 missense ENST00000370698.3 1 0 hg19 CCDS14654.1 . . . . . . . . . . G 29.9 5.048396 0.93740 . . ENSG00000198689 ENST00000370701;ENST00000370698;ENST00000370695 T;T;T 0.09817 2.94;2.94;2.94 5.07 5.07 0.68467 Cation/H+ exchanger (1); 0.658813 0.16648 N 0.205338 T 0.20210 0.0486 L 0.39692 1.235 0.80722 D 1 P;P;P 0.50443 0.871;0.701;0.935 P;P;P 0.53809 0.667;0.462;0.735 T 0.00728 -1.1591 10 0.66056 D 0.02 . 16.6984 0.85342 0.0:0.0:1.0:0.0 . 65;117;117 B4DU30;Q92581-2;Q92581 .;.;SL9A6_HUMAN L 65;117;117 ENSP00000359735:R65L;ENSP00000359732:R117L;ENSP00000359729:R117L ENSP00000359729:R117L R + 2 0 SLC9A6 134904635 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 9.361000 0.97122 2.234000 0.73211 0.544000 0.68410 CGG TCGA-IB-A7LX-01A-12D-A36O-08 SLC9A6-001 KNOWN non_canonical_U12|basic|CCDS protein_coding protein_coding OTTHUMT00000058450.1 1 0 0 14 399 0 78 0 1.269711e-01 0 17 0 78 2 0 0 0 0 0 2 1 0.999752 14 396 0 77 2 0 0 0 0 78 2 -2.220510 0 1 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.050000 0.030000 0.100000 0.060000 0.065579 0.050000 0 4.000000e-02 8.000000e-02 EGFL6 25975 broad.mit.edu 37 X 13645269 13645269 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:13645269C>A ENST00000361306.1 + 11 1682 c.1425C>A c.(1423-1425)gtC>gtA p.V475V EGFL6_ENST00000380602.3_Silent_p.V476V NM_001167890.1|NM_015507.3 NP_001161362.1|NP_056322.2 Q8IUX8 EGFL6_HUMAN EGF-like-domain, multiple 6 23 GAGACAAAGTCGGGAAACTTC 0.468000 0 SO:0001819 synonymous_variant ENST00000361306.1 1 0 hg19 CCDS14155.1 TCGA-IB-A7LX-01A-12D-A36O-08 EGFL6-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000055800.1 1 0 0 12 180 0 76 0 9.920691e-02 0 8 0 76 2 0 0 0 0 0 2 1 0.999130 12 176 0 74 2 0 0 0 0 76 2 -2.917043 1 1 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.110000 0.060000 0.190000 0.110000 0.121313 0.110000 0 8.000000e-02 1.500000e-01 GABRE 2564 broad.mit.edu 37 X 151124313 151124313 + Silent SNP C C A TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:151124313C>A ENST00000370328.3 - 7 857 c.804G>T c.(802-804)acG>acT p.T268T AF274855.1_ENST00000582865.1_RNA|GABRE_ENST00000370325.1_Silent_p.T268T|GABRE_ENST00000483564.1_5'UTR|MIR224_ENST00000384889.1_RNA NM_004961.3 NP_004952.2 P78334 GBRE_HUMAN gamma-aminobutyric acid (GABA) A receptor, epsilon 27 Acute lymphoblastic leukemia(192;6.56e-05) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) TGAAGAAAATCGTCATGACCA 0.478000 0 SO:0001819 synonymous_variant ENST00000370328.3 1 0 hg19 CCDS14703.1 TCGA-IB-A7LX-01A-12D-A36O-08 GABRE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060903.1 1 0 0 15 348 0 73 0 9.958631e-01 0 211 0 73 2 0 0 0 0 0 2 1 0.999877 16 346 0 73 2 0 0 0 0 73 2 -3.911315 1 1 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.070000 0.030000 0.120000 0.080000 0.079514 0.070000 0 5.000000e-02 1.000000e-01 CD99 4267 broad.mit.edu 37 X 2632474 2632474 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:2632474G>T ENST00000381192.3 + 2 261 c.79G>T c.(79-81)Gat>Tat p.D27Y CD99_ENST00000381187.3_Missense_Mutation_p.D27Y|CD99_ENST00000381184.1_Missense_Mutation_p.D27Y|CD99_ENST00000482405.2_3'UTR NM_001277710.1|NM_002414.3 NP_001264639.1|NP_002405.1 P14209 CD99_HUMAN CD99 molecule 11 TGGTGGTTTCGATTTATCCGA 0.294000 0 SO:0001583 missense ENST00000381192.3 1 0 hg19 CCDS14119.1 . . . . . . . . . . g 9.633 1.136817 0.21123 . . ENSG00000002586 ENST00000381192;ENST00000381187;ENST00000381184;ENST00000449611 T;T;T;T 0.49432 1.28;0.78;1.28;1.28 1.14 1.14 0.20703 . 0.162784 0.36932 U 0.002338 T 0.56499 0.1989 L 0.59436 1.845 0.09310 N 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.79784 0.993;0.993;0.993 T 0.37663 -0.9696 10 0.72032 D 0.01 . 5.2921 0.15733 0.0:0.0:1.0:0.0 . 27;27;27 A6NIW1;B2R932;P14209 .;.;CD99_HUMAN Y 27;27;27;70 ENSP00000370588:D27Y;ENSP00000370582:D27Y;ENSP00000370579:D27Y;ENSP00000405544:D70Y ENSP00000370579:D27Y D + 1 0 CD99 2642474 0.069000 0.21087 0.025000 0.17156 0.016000 0.09150 1.398000 0.34554 0.857000 0.35407 0.429000 0.28392 GAT TCGA-IB-A7LX-01A-12D-A36O-08 CD99-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055624.1 1 0 0 25 577 0 296 0 1 0 866 0 296 2 0 0 0 0 0 2 1 1.000000 24 567 0 295 2 0 0 0 0 296 2 -3.651936 1 1 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.070000 0.040000 0.110000 0.080000 0.078151 0.070000 0 5.000000e-02 9.000000e-02 CXorf21 80231 broad.mit.edu 37 X 30577624 30577624 + Silent SNP A A G TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:30577624A>G ENST00000378962.3 - 3 1171 c.849T>C c.(847-849)atT>atC p.I283I NM_025159.2 NP_079435.1 Q9HAI6 CX021_HUMAN chromosome X open reading frame 21 20 TAATTTCAGTAATTTCAGTTG 0.378000 0 SO:0001819 synonymous_variant ENST00000378962.3 0 1 hg19 CCDS14224.1 TCGA-IB-A7LX-01A-12D-A36O-08 CXorf21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056164.1 0 0 0 4 124 0 53 0 5.097955e-03 0 3 0 53 2 0 0 0 0 0 2 1 0.885915 4 121 0 53 2 0 0 0 0 53 2 -7.304968 1 0 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.050000 0.010000 0.130000 0.060000 0.069476 0.050000 0 3.000000e-02 1.000000e-01 BRWD3 254065 broad.mit.edu 37 X 79939559 79939559 + Missense_Mutation SNP G G T TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:79939559G>T ENST00000373275.4 - 37 4399 c.4183C>A c.(4183-4185)Cgc>Agc p.R1395S BRWD3_ENST00000473691.1_Intron NM_153252.4 NP_694984 Q6RI45 BRWD3_HUMAN bromodomain and WD repeat domain containing 3 87 AATATTTGGCGAACATCCTTA 0.348000 0 SO:0001583 missense ENST00000373275.4 1 0 hg19 CCDS14447.1 . . . . . . . . . . G 25.0 4.596937 0.87055 . . ENSG00000165288 ENST00000373275 T 0.29142 1.58 4.66 4.66 0.58398 Bromodomain (6); 0.051438 0.85682 D 0.000000 T 0.64571 0.2610 M 0.91459 3.21 0.58432 D 0.999999 D 0.89917 1.0 D 0.97110 1.0 T 0.74671 -0.3587 9 . . . 0.4745 16.8308 0.85944 0.0:0.0:1.0:0.0 . 1395 Q6RI45 BRWD3_HUMAN S 1395 ENSP00000362372:R1395S . R - 1 0 BRWD3 79826215 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.298000 0.78815 2.149000 0.67028 0.502000 0.49764 CGC TCGA-IB-A7LX-01A-12D-A36O-08 BRWD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057344.1 1 0 0 11 242 0 37 0 2.091063e-01 0 17 0 37 2 0 0 0 0 0 2 1 0.998438 12 241 0 35 2 0 0 0 0 37 2 -4.155208 1 1 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.070000 0.030000 0.130000 0.080000 0.085278 0.070000 0 5.000000e-02 1.100000e-01 NAP1L3 4675 broad.mit.edu 37 X 92926869 92926869 + Missense_Mutation SNP T T C TCGA-IB-A7LX-01A-12D-A36O-08 TCGA-IB-A7LX-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx b42e059c-cdb8-4a32-83d3-298334042c3e 1ad317bb-1738-4a90-a9a5-17f34cb9357e g.chrX:92926869T>C ENST00000373079.3 - 1 1698 c.1435A>G c.(1435-1437)Aaa>Gaa p.K479E FAM133A_ENST00000538690.1_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.K472E|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000332647.4_5'Flank NM_004538.5 NP_004529.2 Q99457 NP1L3_HUMAN nucleosome assembly protein 1-like 3 34 TAGATTGATTTCAGGATGACA 0.363000 0 SO:0001583 missense ENST00000373079.3 0 1 hg19 CCDS14465.1 . . . . . . . . . . T 12.32 1.902300 0.33628 . . ENSG00000186310 ENST00000373079;ENST00000543136 T 0.25912 1.77 3.42 3.42 0.39159 . 0.053033 0.64402 D 0.000001 T 0.34774 0.0909 L 0.46947 1.48 0.09310 N 1 D 0.63046 0.992 D 0.64410 0.925 T 0.07385 -1.0775 10 0.62326 D 0.03 . 4.6798 0.12729 0.0:0.1434:0.0:0.8566 . 479 Q99457 NP1L3_HUMAN E 479;472 ENSP00000362171:K479E ENSP00000362171:K479E K - 1 0 NAP1L3 92813525 0.998000 0.40836 0.715000 0.30552 0.719000 0.41307 1.448000 0.35112 1.588000 0.49971 0.430000 0.28490 AAA TCGA-IB-A7LX-01A-12D-A36O-08 NAP1L3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057449.1 0 0 0 5 132 0 22 0 1.199328e-02 0 4 0 22 2 0 0 0 0 0 2 1 0.937518 5 131 0 22 2 0 0 0 0 22 2 -8.153669 1 1 0 0 1 0 1 1 0.550000 3.150000 0.550000 0.060000 0.020000 0.140000 0.070000 0.078009 0.060000 0 4.000000e-02 1.100000e-01