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 PER1 5187 broad.mit.edu 37 17 8049954 8049955 + Frame_Shift_Ins INS - - T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr17:8049954_8049955insT ENST00000317276.4 - 15 2101_2102 c.1864_1865insA c.(1864-1866)agcfs p.S622fs PER1_ENST00000581082.1_Frame_Shift_Ins_p.S602fs|PER1_ENST00000354903.5_Frame_Shift_Ins_p.S606fs|PER1_ENST00000578089.1_5'Flank NM_002616.2 NP_002607.2 O15534 PER1_HUMAN period circadian clock 1 47 GTAGGAGCAGCTGGAGGCTTCT 0.639000 T ETV6 AML, CMML Other conserved DNA damage response genes Dom yes 17 17p13.1-17p12 5187 period homolog 1 (Drosophila) L 0 SO:0001589 frameshift_variant ENST00000317276.4 0 1 hg19 CCDS11131.1 TCGA-IB-A7M4-01A-11D-A36O-08 PER1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000441481.2 1 0 0 37 281 0 62 0 9.135793e-01 0 34 0 62 2 0 0 0 0 0 0 1 1.000000 37 276 0 60 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.681783 1 0.440000 1.980000 0.284071 0.410000 0.290000 0.540000 0.410000 0.418874 0.410000 0 0.350000 0.480000 ANKRD13C 81573 broad.mit.edu 37 1 70819981 70819981 + Frame_Shift_Del DEL G G - TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:70819981delG ENST00000370944.4 - 1 424 c.111delC c.(109-111)accfs p.T37fs HHLA3_ENST00000531950.1_5'Flank|HHLA3_ENST00000432224.1_5'Flank|HHLA3_ENST00000370940.5_5'Flank|HHLA3_ENST00000361764.4_5'Flank|ANKRD13C_ENST00000262346.6_Frame_Shift_Del_p.T37fs|HHLA3_ENST00000359875.5_5'Flank NM_030816.4 NP_110443.3 Q8N6S4 AN13C_HUMAN ankyrin repeat domain 13C 19 TTCTGGTAAAGGTACCGCCGA 0.602000 0 SO:0001589 frameshift_variant ENST00000370944.4 1 1 hg19 CCDS648.2 TCGA-IB-A7M4-01A-11D-A36O-08 ANKRD13C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025903.1 1 0 0 62 503 0 131 0 4.308822e-01 1 12 0 131 2 0 0 0 0 0 0 1 0.999724 106 485 4 129 33 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 1.943490 0 0.440000 1.980000 0.419569 0.470000 0.370000 0.600000 0.480000 0.486081 0.470000 0 0.420000 0.540000 RPL15 6138 broad.mit.edu 37 3 23960714 23960715 + Frame_Shift_Ins INS - - T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 - T - - Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr3:23960714_23960715insT ENST00000307839.5 + 4 976_977 c.337_338insT c.(337-339)ctgfs p.L113fs NKIRAS1_ENST00000437230.1_5'Flank|NKIRAS1_ENST00000412028.1_5'Flank|RPL15_ENST00000435882.1_Frame_Shift_Ins_p.L113fs|RPL15_ENST00000415719.1_Frame_Shift_Ins_p.L113fs|NKIRAS1_ENST00000415901.2_5'Flank|NKIRAS1_ENST00000421515.2_Intron|NKIRAS1_ENST00000416026.2_5'Flank|NKIRAS1_ENST00000388759.3_5'Flank|RPL15_ENST00000456530.2_Frame_Shift_Ins_p.L113fs|NKIRAS1_ENST00000425478.2_5'Flank|RPL15_ENST00000354811.5_Frame_Shift_Ins_p.L113fs|RPL15_ENST00000413699.1_Frame_Shift_Ins_p.L113fs|NKIRAS1_ENST00000443659.2_5'Flank NM_001253379.1|NM_001253380.1|NM_002948.3 NP_001240308.1|NP_001240309.1|NP_002939.2 P61313 RL15_HUMAN ribosomal protein L15 7 CTGTGGGGCTCTGAGAGTCCTG 0.421000 0 SO:0001589 frameshift_variant ENST00000307839.5 0 1 hg19 CCDS2640.1 TCGA-IB-A7M4-01A-11D-A36O-08 RPL15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252885.3 1 0 0 95 448 0 102 1 1 1374 7936 0 102 2 0 0 0 0 0 0 1 1.000000 90 412 0 102 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 2 2 4 2.113889 0 0.440000 1.980000 0.468085 0.840000 0.690000 1.000000 0.830000 0.855798 0.840000 0 0.760000 0.960000 NEURL 0 broad.mit.edu 37 10 105349367 105349367 + Missense_Mutation SNP A A C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr10:105349367A>C ENST00000369780.4 + 5 1845 c.1436A>C c.(1435-1437)gAc>gCc p.D479A NEURL_ENST00000369777.2_Missense_Mutation_p.D462A|SH3PXD2A_ENST00000427662.2_Intron NM_004210.4 NP_004201.3 O76050 NEUL1_HUMAN 17 CGCCTGTCTGACCCCTTGCTC 0.647000 0 SO:0001583 missense ENST00000369780.4 0 1 hg19 CCDS7551.1 . . . . . . . . . . A 15.49 2.850177 0.51270 . . ENSG00000107954 ENST00000369780;ENST00000369777 . . . 5.2 5.2 0.72013 . 0.100580 0.64402 D 0.000003 T 0.57272 0.2042 M 0.65498 2.005 0.80722 D 1 B 0.17852 0.024 B 0.12156 0.007 T 0.53493 -0.8431 9 0.20046 T 0.44 -30.6731 11.069 0.47993 0.9249:0.0:0.0751:0.0 . 479 O76050 NEU1A_HUMAN A 479;462 . ENSP00000358792:D462A D + 2 0 NEURL 105339357 1.000000 0.71417 0.998000 0.56505 0.990000 0.78478 5.976000 0.70484 1.980000 0.57719 0.459000 0.35465 GAC TCGA-IB-A7M4-01A-11D-A36O-08 NEURL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050170.1 0 0 0 11 498 0 161 1 5.567946e-02 2 14 0 161 2 0 0 0 0 0 2 1 0.997841 11 473 0 158 2 0 0 0 0 161 2 -2.851309 1 1 0 0 1 1 2 3 2.062135 0 0.440000 1.980000 0.448493 0.100000 0.040000 1.000000 0.100000 0.157845 0.100000 0 0.070000 0.150000 VDAC2 7417 broad.mit.edu 37 10 76979095 76979095 + Missense_Mutation SNP A A G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr10:76979095A>G ENST00000332211.6 + 6 550 c.337A>G c.(337-339)Acc>Gcc p.T113A VDAC2_ENST00000472137.1_3'UTR|VDAC2_ENST00000543351.1_Missense_Mutation_p.T113A|VDAC2_ENST00000313132.4_Missense_Mutation_p.T128A|VDAC2_ENST00000535553.1_Missense_Mutation_p.T74A NM_003375.3 NP_003366.2 P45880 VDAC2_HUMAN voltage-dependent anion channel 2 10 all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183) Dihydroxyaluminium(DB01375) ATTTGATACTACCTTCTCACC 0.239000 0 SO:0001583 missense ENST00000332211.6 1 1 hg19 CCDS7348.1 . . . . . . . . . . A 15.47 2.842620 0.51057 . . ENSG00000165637 ENST00000298468;ENST00000543351;ENST00000344036;ENST00000332211;ENST00000535553;ENST00000313132;ENST00000447677 T;T;T;T;T;T;T 0.42513 0.97;0.97;0.97;0.97;0.97;0.97;0.97 5.24 5.24 0.73138 . 0.000000 0.85682 D 0.000000 T 0.43478 0.1249 M 0.67569 2.06 0.80722 D 1 B;B;B 0.28082 0.033;0.2;0.149 B;B;B 0.30029 0.11;0.098;0.063 T 0.32161 -0.9917 10 0.23891 T 0.37 . 15.1356 0.72562 1.0:0.0:0.0:0.0 . 74;128;113 B4DKM5;P45880-1;P45880 .;.;VDAC2_HUMAN A 113;113;113;113;74;128;113 ENSP00000298468:T113A;ENSP00000443092:T113A;ENSP00000344876:T113A;ENSP00000361686:T113A;ENSP00000445901:T74A;ENSP00000361635:T128A;ENSP00000401492:T113A ENSP00000298468:T113A T + 1 0 VDAC2 76649101 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.574000 0.82434 1.978000 0.57642 0.460000 0.39030 ACC TCGA-IB-A7M4-01A-11D-A36O-08 VDAC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048792.1 1 0 1 85 321 0 89 1 1 223 171 0 89 2 0 0 0 0 0 2 1 1.000000 84 315 0 89 2 0 0 0 0 89 2 -20.000000 1 1 0 0 1 1 2 3 2.062135 0 0.440000 1.980000 0.448493 0.960000 0.790000 1.000000 1.000000 0.948667 0.960000 1 0.870000 1.000000 MUC2 4583 broad.mit.edu 37 11 1096405 1096405 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr11:1096405G>A ENST00000441003.2 + 34 6457 c.6430G>A c.(6430-6432)Gtg>Atg p.V2144M MUC2_ENST00000361558.6_Missense_Mutation_p.V282M NM_002457.2 NP_002448.2 Q02817 MUC2_HUMAN mucin 2, oligomeric mucus/gel-forming 102 all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191) Pranlukast(DB01411) CTGCACCTACGTGCTGGTGGA 0.602000 0 SO:0001583 missense ENST00000441003.2 1 1 hg19 . . . . . . . . . . g 15.11 2.735694 0.49045 . . ENSG00000198788 ENST00000441003;ENST00000361558 T;T 0.62364 0.03;0.03 3.95 3.04 0.35103 . . . . . T 0.75332 0.3835 M 0.80422 2.495 0.09310 N 1 D 0.76494 0.999 P 0.62014 0.897 T 0.63844 -0.6545 9 0.72032 D 0.01 . 9.045 0.36341 0.1805:0.0:0.8195:0.0 . 2144 E7EUV1 . M 2144;282 ENSP00000415183:V2144M;ENSP00000354885:V282M ENSP00000354885:V282M V + 1 0 MUC2 1086405 1.000000 0.71417 0.942000 0.38095 0.747000 0.42532 3.053000 0.49901 0.869000 0.35703 0.479000 0.44913 GTG TCGA-IB-A7M4-01A-11D-A36O-08 MUC2-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000345894.2 1 0 1 76 267 0 92 1 1 68 29 0 92 2 0 0 0 0 0 2 1 1.000000 75 264 0 92 2 0 0 0 0 92 2 -20.000000 1 1 0 0 1 1 2 3 2.078077 0 0.440000 1.980000 0.449686 0.990000 0.830000 1.000000 1.000000 0.973574 0.990000 1 0.920000 1.000000 MICAL2 9645 broad.mit.edu 37 11 12247727 12247727 + Missense_Mutation SNP C C G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr11:12247727C>G ENST00000256194.4 + 14 1986 c.1698C>G c.(1696-1698)gaC>gaG p.D566E MICAL2_ENST00000537344.1_Missense_Mutation_p.D566E|MICAL2_ENST00000527546.1_Missense_Mutation_p.D566E|MICAL2_ENST00000342902.5_Missense_Mutation_p.D566E|MICAL2_ENST00000379612.3_Missense_Mutation_p.D566E NM_001282663.1|NM_014632.2 NP_001269592.1|NP_055447.1 O94851 MICA2_HUMAN microtubule associated monooxygenase, calponin and LIM domain containing 2 47 GCAACTTTGACTCTTTGAATG 0.517000 0 SO:0001583 missense ENST00000256194.4 1 1 hg19 CCDS7809.1 . . . . . . . . . . C 15.48 2.846635 0.51164 . . ENSG00000133816 ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612 T;T;T;T;T 0.58940 0.3;0.3;0.3;0.3;0.3 5.39 5.39 0.77823 Calponin homology domain (5); 0.000000 0.85682 D 0.000000 T 0.46308 0.1386 L 0.37750 1.13 0.53005 D 0.999962 B;B;B;B;B 0.10296 0.0;0.001;0.002;0.003;0.0 B;B;B;B;B 0.20184 0.006;0.026;0.028;0.026;0.004 T 0.35450 -0.9788 10 0.28530 T 0.3 . 10.6994 0.45918 0.0:0.879:0.0:0.121 . 566;566;566;566;566 G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851 .;.;.;.;MICA2_HUMAN E 566;99;566;566;566;566 ENSP00000441689:D566E;ENSP00000256194:D566E;ENSP00000433965:D566E;ENSP00000344894:D566E;ENSP00000368932:D566E ENSP00000256194:D566E D + 3 2 MICAL2 12204303 0.979000 0.34478 1.000000 0.80357 0.988000 0.76386 0.260000 0.18424 2.526000 0.85167 0.563000 0.77884 GAC TCGA-IB-A7M4-01A-11D-A36O-08 MICAL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385993.1 0 0 0 12 449 0 114 1 2.278378e-01 2 30 0 114 2 0 0 0 0 0 2 1 0.999054 12 442 0 113 2 0 0 0 0 114 2 -3.276085 1 1 0 0 1 1 2 3 2.078077 0 0.440000 1.980000 0.449686 0.120000 0.060000 1.000000 0.120000 0.185530 0.120000 0 0.090000 0.180000 IGSF9B 22997 broad.mit.edu 37 11 133807360 133807360 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr11:133807360G>A ENST00000321016.8 - 5 820 c.590C>T c.(589-591)tCg>tTg p.S197L IGSF9B_ENST00000533871.2_Missense_Mutation_p.S197L Q9UPX0 TUTLB_HUMAN immunoglobulin superfamily, member 9B 44 all_hematologic(175;0.127) all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) CCGACTGACCGATGTCACTGT 0.607000 0 SO:0001583 missense ENST00000321016.8 1 1 hg19 . . . . . . . . . . G 18.11 3.551849 0.65311 . . ENSG00000080854 ENST00000321016;ENST00000533871;ENST00000527648;ENST00000533160 T;T;T;D 0.96459 -0.76;-1.21;-0.76;-4.02 5.54 4.6 0.57074 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . D 0.96380 0.8819 M 0.62266 1.93 0.09310 N 0.999997 D 0.52996 0.957 P 0.50537 0.643 D 0.91429 0.5164 9 0.52906 T 0.07 . 15.4985 0.75677 0.0:0.0:0.8604:0.1396 . 197 Q9UPX0 TUTLB_HUMAN L 197;39;197;187 ENSP00000317980:S197L;ENSP00000436552:S39L;ENSP00000436576:S197L;ENSP00000434026:S187L ENSP00000317980:S197L S - 2 0 IGSF9B 133312570 0.981000 0.34729 0.039000 0.18376 0.979000 0.70002 4.882000 0.63121 1.289000 0.44618 0.561000 0.74099 TCG TCGA-IB-A7M4-01A-11D-A36O-08 IGSF9B-201 KNOWN basic|appris_candidate protein_coding protein_coding 1 0 1 70 195 0 80 0 0 1 0 0 80 2 0 0 0 0 0 2 1 1.000000 68 190 0 80 2 0 0 0 0 80 2 -5.518651 1 1 121246 8 38 1 1 2 3 2.078077 0 0.440000 1.980000 0.449686 0.990000 0.980000 1.000000 1.000000 0.998713 0.990000 1 0.990000 1.000000 OR5B17 219965 broad.mit.edu 37 11 58126293 58126293 + Missense_Mutation SNP G G T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr11:58126293G>T ENST00000357377.3 - 1 249 c.250C>A c.(250-252)Ctt>Att p.L84I NM_001005489.1 NP_001005489.1 Q8NGF7 OR5BH_HUMAN olfactory receptor, family 5, subfamily B, member 17 30 Esophageal squamous(5;0.0027) Breast(21;0.0778) TCTTCTATAAGCAACCCAGTT 0.458000 0 SO:0001583 missense ENST00000357377.3 1 1 hg19 CCDS31548.1 . . . . . . . . . . g 3.439 -0.114369 0.06881 . . ENSG00000197786 ENST00000357377 T 0.00529 6.78 3.41 2.49 0.30216 GPCR, rhodopsin-like superfamily (1); 0.526148 0.14194 U 0.335150 T 0.00724 0.0024 M 0.73430 2.235 0.09310 N 1 B 0.20261 0.043 B 0.27608 0.081 T 0.34650 -0.9820 10 0.66056 D 0.02 -6.3521 9.1737 0.37098 0.1124:0.0:0.8876:0.0 . 84 Q8NGF7 OR5BH_HUMAN I 84 ENSP00000349945:L84I ENSP00000349945:L84I L - 1 0 OR5B17 57882869 0.000000 0.05858 0.005000 0.12908 0.013000 0.08279 -0.201000 0.09464 0.635000 0.30488 0.461000 0.40582 CTT TCGA-IB-A7M4-01A-11D-A36O-08 OR5B17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394708.2 1 0 1 53 182 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 53 182 0 55 2 0 0 0 0 55 2 -20.000000 1 1 0 0 1 1 2 3 2.078077 0 0.440000 1.980000 0.449686 0.990000 0.810000 1.000000 1.000000 0.972913 0.990000 1 0.920000 1.000000 KLC2 64837 broad.mit.edu 37 11 66029401 66029401 + Missense_Mutation SNP C C A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr11:66029401C>A ENST00000417856.1 + 3 660 c.417C>A c.(415-417)ttC>ttA p.F139L RP11-867G23.1_ENST00000530805.1_RNA|KLC2_ENST00000316924.5_Missense_Mutation_p.F139L|KLC2_ENST00000394066.2_Intron|KLC2_ENST00000394065.2_De_novo_Start_InFrame|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394078.1_Missense_Mutation_p.F139L|KLC2_ENST00000394067.2_Missense_Mutation_p.F139L|KLC2_ENST00000421552.1_Intron NM_001134775.1 NP_001128247.1 Q9H0B6 KLC2_HUMAN kinesin light chain 2 24 ACTTGCTGTTCATGAGCCAGA 0.632000 0 SO:0001583 missense ENST00000417856.1 1 0 hg19 CCDS8130.1 . . . . . . . . . . C 20.9 4.065877 0.76187 . . ENSG00000174996 ENST00000417856;ENST00000526758;ENST00000440228;ENST00000394067;ENST00000316924;ENST00000394078;ENST00000475757 T;T;T;T;T;T;T 0.75154 0.85;0.85;-0.91;0.85;0.85;0.85;-0.91 4.15 3.23 0.37069 Rabaptin, GTPase-Rab5 binding (1); 0.000000 0.64402 D 0.000001 D 0.84037 0.5384 M 0.87827 2.91 0.80722 D 1 D;D 0.69078 0.995;0.997 D;D 0.74348 0.983;0.973 T 0.82032 -0.0658 10 0.44086 T 0.13 -18.3166 5.6991 0.17873 0.0:0.6847:0.0:0.3153 . 139;139 A8MX29;Q9H0B6 .;KLC2_HUMAN L 139 ENSP00000399403:F139L;ENSP00000437026:F139L;ENSP00000396952:F139L;ENSP00000377631:F139L;ENSP00000314837:F139L;ENSP00000377641:F139L;ENSP00000431253:F139L ENSP00000314837:F139L F + 3 2 KLC2 65785977 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 1.567000 0.36407 0.953000 0.37825 0.561000 0.74099 TTC TCGA-IB-A7M4-01A-11D-A36O-08 KLC2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258200.1 1 0 0 9 224 0 73 0 6.789423e-01 0 58 0 73 2 0 0 0 0 0 2 1 0.994259 9 222 0 72 2 0 0 0 0 73 2 -3.222809 1 1 0 0 1 1 2 3 2.078077 0 0.440000 1.980000 0.449686 0.190000 0.080000 1.000000 0.180000 0.247540 0.190000 0 0.130000 0.280000 PWP1 11137 broad.mit.edu 37 12 108091262 108091262 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr12:108091262G>A ENST00000412830.3 + 7 800 c.632G>A c.(631-633)gGa>gAa p.G211E PWP1_ENST00000541166.1_Missense_Mutation_p.G149E NM_007062.1 NP_008993.1 Q13610 PWP1_HUMAN PWP1 homolog (S. cerevisiae) 23 ATTGCTGTAGGAAACATGACC 0.348000 0 SO:0001583 missense ENST00000412830.3 1 1 hg19 CCDS9114.1 . . . . . . . . . . G 28.6 4.936030 0.92458 . . ENSG00000136045 ENST00000412830;ENST00000258531;ENST00000546068;ENST00000538327;ENST00000541166 T;T 0.44083 0.93;1.7 5.88 5.88 0.94601 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.091825 0.85682 D 0.000000 T 0.73830 0.3637 M 0.93898 3.47 0.80722 D 1 D 0.59357 0.985 D 0.63488 0.915 T 0.80221 -0.1472 10 0.87932 D 0 . 19.8332 0.96644 0.0:0.0:1.0:0.0 . 211 Q13610 PWP1_HUMAN E 211;211;211;211;149 ENSP00000387365:G211E;ENSP00000445249:G149E ENSP00000258531:G211E G + 2 0 PWP1 106615392 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 9.039000 0.93777 2.779000 0.95612 0.637000 0.83480 GGA TCGA-IB-A7M4-01A-11D-A36O-08 PWP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406539.1 1 0 0 31 604 0 159 1 9.788459e-01 13 109 0 159 2 0 0 0 0 0 2 1 1.000000 30 595 0 159 2 0 0 0 0 159 2 -5.311288 1 1 0 0 1 2 3 5 2.383851 1 0.440000 1.980000 0.527346 0.270000 0.180000 1.000000 0.260000 0.411469 0.270000 0 0.220000 1.000000 ETV6 2120 broad.mit.edu 37 12 12037406 12037406 + Missense_Mutation SNP A A G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr12:12037406A>G ENST00000396373.4 + 6 1311 c.1037A>G c.(1036-1038)tAt>tGt p.Y346C NM_001987.4 NP_001978.1 P41212 ETV6_HUMAN ets variant 6 ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238) 45 all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36) GATTACGTCTATCAGTTGCTT 0.438000 T NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5 congenital fibrosarcoma, multiple leukemia and lymphoma, secretory breast, MDS, ALL Dom yes 12 12p13 2120 ets variant gene 6 (TEL oncogene) L, E, M 0 SO:0001583 missense ENST00000396373.4 1 1 hg19 CCDS8643.1 . . . . . . . . . . A 23.9 4.475803 0.84640 . . ENSG00000139083 ENST00000396373 T 0.14640 2.49 5.77 5.77 0.91146 Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4); 0.000000 0.85682 D 0.000000 T 0.34978 0.0916 L 0.56769 1.78 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.03068 -1.1076 10 0.62326 D 0.03 . 15.7572 0.78043 1.0:0.0:0.0:0.0 . 346 P41212 ETV6_HUMAN C 346 ENSP00000379658:Y346C ENSP00000379658:Y346C Y + 2 0 ETV6 11928673 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.339000 0.96797 2.199000 0.70637 0.533000 0.62120 TAT TCGA-IB-A7M4-01A-11D-A36O-08 ETV6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400130.2 1 0 1 153 676 0 244 1 9.998816e-01 22 37 0 244 2 0 0 0 0 0 2 1 1.000000 153 668 0 243 2 0 0 0 0 244 2 -20.000000 1 1 0 0 1 1 2 3 2.019051 0 0.440000 1.980000 0.441229 0.830000 0.720000 0.970000 0.840000 0.842768 0.830000 0 0.770000 0.900000 PITPNM2 57605 broad.mit.edu 37 12 123482085 123482085 + Missense_Mutation SNP G G T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr12:123482085G>T ENST00000542749.1 - 9 1322 c.1259C>A c.(1258-1260)tCc>tAc p.S420Y PITPNM2_ENST00000280562.5_Missense_Mutation_p.S420Y|PITPNM2_ENST00000320201.4_Missense_Mutation_p.S420Y|PITPNM2_ENST00000392428.1_Missense_Mutation_p.S141Y|PITPNM2_ENST00000451868.2_5'Flank Q9BZ72 PITM2_HUMAN phosphatidylinositol transfer protein, membrane-associated 2 39 all_neural(191;0.101)|Medulloblastoma(191;0.163) GTGGATCTTGGAGGGCGGTGC 0.657000 0 SO:0001583 missense ENST00000542749.1 1 1 hg19 CCDS9242.1 . . . . . . . . . . G 18.94 3.730448 0.69074 . . ENSG00000090975 ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749 T;T;T;T 0.20598 2.06;2.06;2.06;2.06 4.83 3.93 0.45458 . 0.417988 0.23797 N 0.044466 T 0.22360 0.0539 N 0.08118 0 0.37075 D 0.898715 D;D 0.62365 0.98;0.991 P;P 0.58721 0.844;0.73 T 0.35624 -0.9781 10 0.87932 D 0 -38.3331 14.0007 0.64431 0.0:0.4813:0.5187:0.0 . 420;420 Q9BZ72-2;Q9BZ72 .;PITM2_HUMAN Y 420;420;141;420 ENSP00000280562:S420Y;ENSP00000322218:S420Y;ENSP00000376223:S141Y;ENSP00000437611:S420Y ENSP00000280562:S420Y S - 2 0 PITPNM2 122048038 1.000000 0.71417 1.000000 0.80357 0.946000 0.59487 5.154000 0.64894 1.019000 0.39547 -0.300000 0.09419 TCC TCGA-IB-A7M4-01A-11D-A36O-08 PITPNM2-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401342.1 1 0 1 129 401 0 147 0 6.005868e-02 0 2 0 147 2 0 0 0 0 0 2 1 1.000000 128 392 0 145 2 0 0 0 0 147 2 -20.000000 1 1 0 0 1 0 1 1 2.005753 0 0.440000 1.980000 0.427403 0.990000 0.910000 1.000000 1.000000 0.993566 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a 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-A7M4-01A-11D-A36O-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 81 289 0 89 1 9.590678e-01 9 12 0 89 2 1 1 72 304 0 305 2 1 1.000000 81 288 0 88 2 1 1 1858 6158 0 89 2 -20.000000 1 1 121404 2 44 1 1 2 3 2.019051 0 0.440000 1.980000 0.441229 0.990000 0.810000 1.000000 1.000000 0.961391 0.990000 1 0.890000 1.000000 OR6C6 283365 broad.mit.edu 37 12 55688832 55688832 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr12:55688832C>T ENST00000358433.2 - 1 184 c.185G>A c.(184-186)cGt>cAt p.R62H NM_001005493.1 NP_001005493.1 A6NF89 OR6C6_HUMAN olfactory receptor, family 6, subfamily C, member 6 20 GGAGAAATTACGGAGAAAGAA 0.388000 0 SO:0001583 missense ENST00000358433.2 1 1 hg19 CCDS31817.1 . . . . . . . . . . - 3.881 -0.025966 0.07589 . . ENSG00000188324 ENST00000358433 T 0.01084 5.36 4.24 0.321 0.15883 GPCR, rhodopsin-like superfamily (1); 0.000000 0.43919 D 0.000517 T 0.01800 0.0057 M 0.84219 2.685 0.09310 N 1 B 0.15719 0.014 B 0.12837 0.008 T 0.43065 -0.9414 10 0.66056 D 0.02 . 2.1956 0.03910 0.1224:0.4226:0.1199:0.335 . 62 A6NF89 OR6C6_HUMAN H 62 ENSP00000351211:R62H ENSP00000351211:R62H R - 2 0 OR6C6 53975099 0.000000 0.05858 0.001000 0.08648 0.063000 0.16089 -1.335000 0.02662 -0.046000 0.13446 -1.274000 0.01402 CGT TCGA-IB-A7M4-01A-11D-A36O-08 OR6C6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398151.1 1 0 1 80 217 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 1.000000 80 214 0 79 2 0 0 0 0 79 2 -6.084236 1 1 121400 3 39 1 1 2 3 2.019051 0 0.440000 1.980000 0.441229 0.990000 0.990000 1.000000 1.000000 0.999175 0.990000 1 0.990000 1.000000 TMTC3 160418 broad.mit.edu 37 12 88568385 88568385 + Splice_Site SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr12:88568385G>A ENST00000266712.6 + 9 1421 c.1201G>A c.(1201-1203)Gta>Ata p.V401I NM_181783.3 NP_861448.2 Q6ZXV5 TMTC3_HUMAN transmembrane and tetratricopeptide repeat containing 3 p.V401I(1) 31 CTTAAACAGTGTATTTAAAAA 0.318000 1 Substitution - Missense(1) SO:0001630 splice_region_variant ENST00000266712.6 1 0 hg19 CCDS9032.1 . . . . . . . . . . G 10.75 1.439040 0.25900 . . ENSG00000139324 ENST00000266712 T 0.42131 0.98 5.71 4.83 0.62350 . 0.468547 0.24436 N 0.038556 T 0.28797 0.0714 L 0.27053 0.805 0.26494 N 0.974889 B 0.15930 0.015 B 0.20384 0.029 T 0.16188 -1.0411 10 0.22109 T 0.4 -12.395 9.9853 0.41839 0.2109:0.0:0.7891:0.0 . 401 Q6ZXV5-2 . I 401 ENSP00000266712:V401I ENSP00000266712:V401I V + 1 0 TMTC3 87092516 0.997000 0.39634 0.990000 0.47175 0.786000 0.44442 0.928000 0.28831 1.426000 0.47256 -0.136000 0.14681 GTA TCGA-IB-A7M4-01A-11D-A36O-08 TMTC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406421.1 1 0 1 89 233 0 106 1 3.097978e-01 4 0 0 106 2 0 0 0 0 0 2 1 1.000000 89 228 0 106 2 0 0 0 0 106 2 -20.000000 1 1 0 0 1 0 0 0 1.618708 1 0.440000 1.980000 0.297894 0.970000 0.810000 1.000000 1.000000 0.956618 0.970000 1 0.890000 1.000000 IRS2 8660 broad.mit.edu 37 13 110436560 110436560 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr13:110436560G>A ENST00000375856.3 - 1 2355 c.1841C>T c.(1840-1842)cCg>cTg p.P614L NM_003749.2 NP_003740.2 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 19 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) GGGGCAGGACGGGCAGAGGCG 0.697000 Melanoma(100;613 2409 40847) 0 SO:0001583 missense ENST00000375856.3 0 1 hg19 CCDS9510.1 . . . . . . . . . . G 1.859 -0.463098 0.04476 . . ENSG00000185950 ENST00000375856 T 0.17213 2.29 4.2 4.2 0.49525 . 0.965381 0.08540 U 0.930734 T 0.13670 0.0331 L 0.44542 1.39 0.42996 D 0.994506 B 0.34329 0.449 B 0.16722 0.016 T 0.15263 -1.0443 10 0.10636 T 0.68 -11.5 13.8503 0.63492 0.0:0.0:1.0:0.0 . 614 Q9Y4H2 IRS2_HUMAN L 614 ENSP00000365016:P614L ENSP00000365016:P614L P - 2 0 IRS2 109234561 0.977000 0.34250 0.980000 0.43619 0.886000 0.51366 2.612000 0.46343 2.156000 0.67533 0.549000 0.68633 CCG TCGA-IB-A7M4-01A-11D-A36O-08 IRS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045755.1 0 0 0 4 47 0 18 1 7.050339e-01 6 23 0 18 2 0 0 0 0 0 2 1 0.888377 4 46 0 18 2 0 0 0 0 18 2 -8.898715 1 1 119534 4 31 1 0 0 0 1.892462 0 0.440000 1.980000 0.406025 0.360000 0.120000 0.740000 0.320000 0.392743 0.360000 0 0.220000 0.550000 WASF3 10810 broad.mit.edu 37 13 27259854 27259854 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr13:27259854C>T ENST00000335327.5 + 10 1559 c.1381C>T c.(1381-1383)Cgg>Tgg p.R461W WASF3_ENST00000361042.4_Missense_Mutation_p.R458W 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) GCAGGAGCAGCGGGAGCAGGA 0.532000 0 SO:0001583 missense ENST00000335327.5 1 1 hg19 CCDS9318.1 . . . . . . . . . . C 25.6 4.650714 0.87958 . . ENSG00000132970 ENST00000361042;ENST00000335327 T;T 0.42900 0.96;0.96 5.75 5.75 0.90469 . 0.110713 0.64402 D 0.000004 T 0.61763 0.2373 L 0.52364 1.645 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.87578 0.998;0.91 T 0.58205 -0.7677 10 0.48119 T 0.1 -11.9041 19.9239 0.97097 0.0:1.0:0.0:0.0 . 458;461 Q86VQ2;Q9UPY6 .;WASF3_HUMAN W 458;461 ENSP00000354325:R458W;ENSP00000335055:R461W ENSP00000335055:R461W R + 1 2 WASF3 26157854 1.000000 0.71417 0.984000 0.44739 0.961000 0.63080 5.562000 0.67346 2.716000 0.92895 0.561000 0.74099 CGG TCGA-IB-A7M4-01A-11D-A36O-08 WASF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044258.1 1 0 1 53 259 0 77 0 1.404639e-01 0 4 0 77 2 0 0 0 0 0 2 1 1.000000 53 255 0 76 2 0 0 0 0 77 2 -3.187230 1 1 0 0 1 0 0 0 1.892462 0 0.440000 1.980000 0.406025 0.720000 0.550000 0.910000 0.730000 0.733442 0.720000 0 0.630000 0.820000 MTUS2 23281 broad.mit.edu 37 13 29600278 29600278 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr13:29600278G>A ENST00000431530.3 + 1 1531 c.1473G>A c.(1471-1473)acG>acA p.T491T NM_001033602.2 NP_001028774.2 Q5JR59 MTUS2_HUMAN microtubule associated tumor suppressor candidate 2 20 AGAACAAGACGGAGGTGCCTG 0.517000 0 SO:0001819 synonymous_variant ENST00000431530.3 1 1 hg19 CCDS45022.1 TCGA-IB-A7M4-01A-11D-A36O-08 MTUS2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000044336.3 1 0 1 38 167 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 37 166 0 70 2 0 0 0 0 70 2 -2.976986 1 1 120898 2 32 1 0 0 0 1.892462 0 0.440000 1.980000 0.406025 0.790000 0.580000 1.000000 1.000000 0.799003 0.790000 0 0.680000 0.910000 MTHFD1 4522 broad.mit.edu 37 14 64854981 64854981 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr14:64854981C>T ENST00000545908.1 + 1 233 c.4C>T c.(4-6)Cgc>Tgc p.R2C MTHFD1_ENST00000216605.8_5'Flank P11586 C1TC_HUMAN methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase 30 Tetrahydrofolic acid(DB00116) ACTGCGCATGCGCCACCGCGT 0.627000 Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519) 0 SO:0001583 missense ENST00000545908.1 0 1 hg19 . . . . . . . . . . C 13.22 2.172108 0.38315 . . ENSG00000100714 ENST00000545908;ENST00000216605 T;T 0.13089 2.62;2.7 4.54 0.576 0.17380 . . . . . T 0.08537 0.0212 . . . 0.20074 N 0.999934 B 0.06786 0.001 B 0.04013 0.001 T 0.37197 -0.9716 8 0.87932 D 0 . 1.4441 0.02360 0.1748:0.4661:0.1695:0.1896 . 2 F5H2F4 . C 2 ENSP00000438588:R2C;ENSP00000216605:R2C ENSP00000438588:R2C R + 1 0 MTHFD1 63924734 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 0.268000 0.18571 0.094000 0.17404 -0.140000 0.14226 CGC TCGA-IB-A7M4-01A-11D-A36O-08 MTHFD1-002 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000412167.1 0 0 0 5 43 0 13 0 4.434389e-02 0 3 0 13 2 0 0 0 0 0 2 1 0.941063 5 43 0 13 2 0 0 0 0 13 2 -11.159780 1 1 0 0 1 0 3 3 2.177319 1 0.440000 1.980000 0.488398 0.640000 0.230000 1.000000 1.000000 0.678621 0.640000 0 0.390000 1.000000 CSPG4 1464 broad.mit.edu 37 15 75977834 75977834 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr15:75977834G>A ENST00000308508.5 - 4 4090 c.3998C>T c.(3997-3999)tCg>tTg p.S1333L NM_001897.4 NP_001888.2 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 48 CACATCCAGCGAGAAGGCATC 0.662000 0 SO:0001583 missense ENST00000308508.5 0 1 hg19 CCDS10284.1 . . . . . . . . . . . 10.07 1.250306 0.22880 . . ENSG00000173546 ENST00000308508 T 0.19669 2.13 4.76 3.78 0.43462 . 0.428701 0.21773 N 0.069329 T 0.11110 0.0271 L 0.27053 0.805 0.30136 N 0.804328 B 0.31837 0.342 B 0.17098 0.017 T 0.08006 -1.0743 10 0.20519 T 0.43 . 8.5151 0.33242 0.0964:0.1601:0.7435:0.0 . 1333 Q6UVK1 CSPG4_HUMAN L 1333 ENSP00000312506:S1333L ENSP00000312506:S1333L S - 2 0 CSPG4 73764889 1.000000 0.71417 0.993000 0.49108 0.240000 0.25518 3.390000 0.52523 2.356000 0.79943 0.505000 0.49811 TCG TCGA-IB-A7M4-01A-11D-A36O-08 CSPG4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286472.1 1 0 1 24 34 0 18 1 9.982334e-01 17 2 0 18 2 0 0 0 0 0 2 1 1.000000 23 32 0 18 2 0 0 0 0 18 2 -20.000000 1 1 121050 2 31 1 0 1 1 1.648770 1 0.440000 1.980000 0.282051 0.940000 0.760000 1.000000 0.990000 0.933968 0.940000 1 0.870000 0.990000 TBL3 10607 broad.mit.edu 37 16 2024811 2024811 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr16:2024811G>A ENST00000568546.1 + 6 555 c.427G>A c.(427-429)Ggg>Agg p.G143R NM_006453.2 NP_006444.2 Q12788 TBL3_HUMAN transducin (beta)-like 3 18 GCGGCACTACGGGACACACCA 0.662000 Melanoma(118;616 1651 35077 38081 48633) 0 SO:0001583 missense ENST00000568546.1 0 1 hg19 CCDS10453.1 . . . . . . . . . . G 16.52 3.145173 0.57044 . . ENSG00000183751 ENST00000332704 . . . 4.97 4.97 0.65823 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.611855 0.18098 N 0.151764 T 0.40498 0.1119 N 0.02247 -0.625 0.42212 D 0.991811 D 0.89917 1.0 D 0.67548 0.952 T 0.50882 -0.8775 9 0.45353 T 0.12 -35.2202 11.1898 0.48679 0.0:0.0:0.7045:0.2955 . 143 Q12788 TBL3_HUMAN R 143 . ENSP00000331815:G143R G + 1 0 TBL3 1964812 1.000000 0.71417 0.943000 0.38184 0.307000 0.27823 6.648000 0.74359 2.301000 0.77427 0.561000 0.74099 GGG TCGA-IB-A7M4-01A-11D-A36O-08 TBL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250615.3 0 0 0 9 314 0 80 1 7.744434e-01 3 97 0 80 2 0 0 0 0 0 2 1 0.993707 9 306 0 78 2 0 0 0 0 80 2 -2.924339 1 1 121394 4 39 1 2 2 4 2.114976 0 0.440000 1.980000 0.468085 0.140000 0.060000 1.000000 0.130000 0.229200 0.140000 0 0.090000 0.220000 PKD1 5310 broad.mit.edu 37 16 2161454 2161454 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr16:2161454G>A ENST00000262304.4 - 15 3922 c.3714C>T c.(3712-3714)ggC>ggT p.G1238G RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.G1238G NM_001009944.2 NP_001009944 P98161 PKD1_HUMAN polycystic kidney disease 1 (autosomal dominant) 72 TGATGTTGTCGCCCGTCTGCA 0.672000 0 SO:0001819 synonymous_variant ENST00000262304.4 1 1 hg19 CCDS32369.1 TCGA-IB-A7M4-01A-11D-A36O-08 PKD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341688.1 0 0 1 50 124 1 35 1 5.511203e-01 2 4 1 35 2 0 0 0 0 0 2 1 0.999999 49 121 1 35 16 0 0 0 1 35 2 -20.000000 1 1 119332 9 37 1 2 2 4 2.114976 0 0.440000 1.980000 0.468085 0.990000 0.990000 1.000000 1.000000 0.999714 0.990000 1 0.990000 1.000000 SMCR8 140775 broad.mit.edu 37 17 18220237 18220237 + Silent SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr17:18220237C>T ENST00000406438.3 + 1 1614 c.1134C>T c.(1132-1134)gtC>gtT p.V378V TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank NM_144775.2 NP_658988.2 Q8TEV9 SMCR8_HUMAN Smith-Magenis syndrome chromosome region, candidate 8 21 TTGTGGAGGTCGATGACAGGA 0.448000 0 SO:0001819 synonymous_variant ENST00000406438.3 1 1 hg19 CCDS11195.2 TCGA-IB-A7M4-01A-11D-A36O-08 SMCR8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132065.2 1 0 1 84 239 0 107 1 8.828876e-01 12 1 0 107 2 0 0 0 0 0 2 1 1.000000 83 235 0 105 2 0 0 0 0 107 2 -20.000000 1 0 0 0 1 0 1 1 1.681783 1 0.440000 1.980000 0.284071 0.890000 0.740000 1.000000 0.920000 0.898563 0.890000 1 0.820000 0.970000 SLFN13 146857 broad.mit.edu 37 17 33767722 33767722 + Silent SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr17:33767722C>T ENST00000285013.6 - 6 2861 c.2586G>A c.(2584-2586)agG>agA p.R862R SLFN13_ENST00000360502.2_Silent_p.R544R|SLFN13_ENST00000534689.1_Silent_p.R544R|SLFN13_ENST00000526861.1_Silent_p.R862R|SLFN13_ENST00000533791.1_Silent_p.R862R|SLFN13_ENST00000542635.1_Silent_p.R862R NM_144682.5 NP_653283.3 Q68D06 SLN13_HUMAN schlafen family member 13 31 ACACTATGCTCCTTTCCAGGC 0.478000 0 SO:0001819 synonymous_variant ENST00000285013.6 0 1 hg19 CCDS32620.1 TCGA-IB-A7M4-01A-11D-A36O-08 SLFN13-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381883.1 0 0 0 15 808 0 195 0 1.043118e-01 0 28 0 195 2 0 0 0 0 0 2 1 0.999853 14 796 0 192 2 0 0 0 0 195 2 -2.205970 0 1 0 0 1 2 2 4 2.168698 1 0.440000 1.980000 0.481097 0.090000 0.040000 1.000000 0.090000 0.220875 0.090000 0 0.060000 0.150000 SPATA20 64847 broad.mit.edu 37 17 48631760 48631760 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr17:48631760G>A ENST00000356488.4 + 14 2141 c.2058G>A c.(2056-2058)gcG>gcA p.A686A CACNA1G-AS1_ENST00000508920.1_RNA|SPATA20_ENST00000393244.3_Silent_p.A642A|CACNA1G-AS1_ENST00000505495.1_RNA|SPATA20_ENST00000006658.6_Silent_p.A702A|CACNA1G-AS1_ENST00000505793.1_RNA|SPATA20_ENST00000511937.1_3'UTR NM_001258372.1 NP_001245301.1 Q8TB22 SPT20_HUMAN spermatogenesis associated 20 24 Breast(11;1.23e-18) BRCA - Breast invasive adenocarcinoma(22;9.38e-09) TCCCGGTGGCGTTGCCCGAGA 0.647000 0 SO:0001819 synonymous_variant ENST00000356488.4 0 1 hg19 CCDS58563.1 TCGA-IB-A7M4-01A-11D-A36O-08 SPATA20-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000367651.1 0 0 0 5 414 1 92 0 1.458673e-02 0 113 1 92 6 0 0 0 0 0 2 0 0.011357 5 409 1 91 16 0 0 0 1 92 2 -2.621283 1 1 121412 19 45 1 2 2 4 2.153852 1 0.440000 1.980000 0.478973 0.060000 0.010000 1.000000 0.060000 0.192714 0.060000 0 0.030000 0.130000 CLTC 1213 broad.mit.edu 37 17 57725004 57725004 + Missense_Mutation SNP C C A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr17:57725004C>A ENST00000269122.3 + 3 770 c.496C>A c.(496-498)Ctt>Att p.L166I CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Missense_Mutation_p.L166I NM_004859.3 NP_004850.1 Q00610 CLH1_HUMAN clathrin, heavy chain (Hc) CLTC/ALK(44)|CLTC/TFE3(2) 9 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) AAAGTGGTTACTTCTGACTGG 0.393000 T ALK, TFE3 ALCL, renal Dom yes 17 17q11-qter 1213 clathrin, heavy polypeptide (Hc) L 0 SO:0001583 missense ENST00000269122.3 1 1 hg19 CCDS32696.1 . . . . . . . . . . C 16.75 3.210186 0.58343 . . ENSG00000141367 ENST00000269122;ENST00000393043 T;T 0.42513 0.97;0.97 5.79 5.79 0.91817 Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1); 0.000000 0.85682 D 0.000000 T 0.58595 0.2133 L 0.50333 1.59 0.80722 D 1 D;B 0.56968 0.978;0.001 D;B 0.77557 0.99;0.015 T 0.53885 -0.8375 10 0.42905 T 0.14 . 15.153 0.72717 0.0:0.931:0.0:0.069 . 166;166 Q00610;Q00610-2 CLH1_HUMAN;. I 166 ENSP00000269122:L166I;ENSP00000376763:L166I ENSP00000269122:L166I L + 1 0 CLTC 55079786 1.000000 0.71417 1.000000 0.80357 0.498000 0.33706 4.985000 0.63845 2.739000 0.93911 0.655000 0.94253 CTT TCGA-IB-A7M4-01A-11D-A36O-08 CLTC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258859.1 1 0 1 101 388 0 122 1 1 53 71 0 122 2 0 0 0 0 0 2 1 1.000000 100 381 0 121 2 0 0 0 0 122 2 -20.000000 1 1 0 0 1 2 2 4 2.153852 1 0.440000 1.980000 0.478973 0.990000 0.840000 1.000000 1.000000 0.974259 0.990000 1 0.920000 1.000000 TP53 7157 broad.mit.edu 37 17 7577532 7577532 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr17:7577532G>A ENST00000269305.4 - 7 938 c.749C>T c.(748-750)cCc>cTc p.P250L TP53_ENST00000445888.2_Missense_Mutation_p.P250L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.P250L|TP53_ENST00000420246.2_Missense_Mutation_p.P250L|TP53_ENST00000359597.4_Missense_Mutation_p.P250L|TP53_ENST00000413465.2_Missense_Mutation_p.P250L NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.P250L(45)|p.0?(8)|p.?(5)|p.P250H(4)|p.P250F(3)|p.P250N(2)|p.M246_P250delMNRRP(2)|p.P250_L252delPIL(2)|p.P250Q(2)|p.R248_P250delRRP(1)|p.P250_T253delPILT(1)|p.N247_P250delNRRP(1)|p.R249_P250delRP(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_I251delRPI(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGTGAGGATGGGCCTCCGGTT 0.577000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 80 Substitution - Missense(56)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(1) GRCh37 CM973401 TP53 M SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 24.2 4.504438 0.85176 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D;D 0.99885 -7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5 4.62 4.62 0.57501 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99898 0.9951 M 0.91406 3.205 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 0.997;0.996;0.998;0.998;1.0 D 0.96045 0.9027 10 0.87932 D 0 -1.5308 15.3618 0.74483 0.0:0.0:1.0:0.0 . 250;250;250;250;250 P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7 .;.;P53_HUMAN;.;. L 250;250;250;250;250;250;239;118 ENSP00000410739:P250L;ENSP00000352610:P250L;ENSP00000269305:P250L;ENSP00000398846:P250L;ENSP00000391127:P250L;ENSP00000391478:P250L;ENSP00000425104:P118L ENSP00000269305:P250L P - 2 0 TP53 7518257 1.000000 0.71417 1.000000 0.80357 0.724000 0.41520 9.601000 0.98297 2.564000 0.86499 0.462000 0.41574 CCC TCGA-IB-A7M4-01A-11D-A36O-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 63 135 0 87 1 1 100 21 0 87 2 1 1 167 404 0 560 2 1 1.000000 63 132 0 87 2 0 0 0 0 87 2 -20.000000 1 1 0 0 1 0 1 1 1.681783 1 0.440000 1.980000 0.284071 0.960000 0.820000 1.000000 1.000000 0.954674 0.960000 1 0.900000 1.000000 ZNF521 25925 broad.mit.edu 37 18 22806481 22806481 + Silent SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr18:22806481C>T ENST00000361524.3 - 4 1549 c.1401G>A c.(1399-1401)ctG>ctA p.L467L ZNF521_ENST00000538137.2_Silent_p.L467L|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.L247L NM_015461.2 NP_056276.1 Q96K83 ZN521_HUMAN zinc finger protein 521 149 all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991) CAGAAACAATCAGACCTGGGT 0.463000 T PAX5 ALL Dom yes 18 18q11.2 25925 zinc finger protein 521 L 0 SO:0001819 synonymous_variant ENST00000361524.3 1 1 hg19 CCDS32806.1 TCGA-IB-A7M4-01A-11D-A36O-08 ZNF521-001 KNOWN overlapping_uORF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446781.2 1 0 0 21 418 0 98 0 0 0 0 98 2 0 0 0 0 0 2 1 0.999997 22 411 0 97 2 0 0 0 0 98 2 -19.985880 1 0 0 0 1 2 7 9 3.039103 1 0.440000 1.980000 0.632449 0.360000 0.210000 1.000000 0.340000 0.486926 0.360000 0 0.270000 1.000000 KLHL14 57565 broad.mit.edu 37 18 30322007 30322007 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr18:30322007C>T ENST00000359358.4 - 3 1391 c.953G>A c.(952-954)cGc>cAc p.R318H KLHL14_ENST00000358095.4_Missense_Mutation_p.R318H NM_020805.1 NP_065856.1 Q9P2G3 KLH14_HUMAN kelch-like family member 14 p.R318H(1) 31 CTTGTTAGAGCGAATTCTTCA 0.428000 1 Substitution - Missense(1) SO:0001583 missense ENST00000359358.4 0 1 hg19 CCDS32813.1 . . . . . . . . . . C 20.6 4.025617 0.75390 . . ENSG00000197705 ENST00000359358;ENST00000358095 T;D 0.81996 -1.21;-1.56 6.11 6.11 0.99139 Galactose oxidase, beta-propeller (1); 0.053328 0.85682 D 0.000000 D 0.92267 0.7547 M 0.84082 2.675 0.80722 D 1 D 0.71674 0.998 D 0.72075 0.976 D 0.92111 0.5696 10 0.87932 D 0 . 20.7342 0.99715 0.0:1.0:0.0:0.0 . 318 Q9P2G3 KLH14_HUMAN H 318 ENSP00000352314:R318H;ENSP00000350808:R318H ENSP00000350808:R318H R - 2 0 KLHL14 28576005 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.298000 0.78815 2.906000 0.99361 0.655000 0.94253 CGC TCGA-IB-A7M4-01A-11D-A36O-08 KLHL14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448376.1 0 0 0 9 345 0 53 0 0 0 1 0 53 2 0 0 0 0 0 2 1 0.993747 8 338 0 52 2 0 0 0 0 53 2 -3.427231 1 1 121412 1 29 1 1 3 4 2.800587 1 0.440000 1.980000 0.581715 0.170000 0.070000 1.000000 0.150000 0.310650 0.170000 0 0.110000 1.000000 CYP4F22 126410 broad.mit.edu 37 19 15655075 15655075 + Missense_Mutation SNP T T C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr19:15655075T>C ENST00000269703.3 + 10 1320 c.1121T>C c.(1120-1122)cTg>cCg p.L374P CYP4F22_ENST00000601005.2_Missense_Mutation_p.L374P NM_173483.3 NP_775754.2 Q6NT55 CP4FN_HUMAN cytochrome P450, family 4, subfamily F, polypeptide 22 37 GGCCGGGAGCTGGAGGAGCTG 0.542000 0 SO:0001583 missense ENST00000269703.3 0 1 hg19 CCDS12331.1 . . . . . . . . . . T 0.522 -0.861607 0.02610 . . ENSG00000171954 ENST00000269703 T 0.67523 -0.27 5.21 1.34 0.21922 . 0.814660 0.10833 N 0.629139 T 0.31009 0.0783 N 0.01493 -0.835 0.39648 D 0.970427 B 0.02656 0.0 B 0.06405 0.002 T 0.17715 -1.0360 10 0.13108 T 0.6 . 3.4617 0.07535 0.1692:0.2777:0.0:0.5531 . 374 Q6NT55 CP4FN_HUMAN P 374 ENSP00000269703:L374P ENSP00000269703:L374P L + 2 0 CYP4F22 15516075 0.170000 0.23016 0.998000 0.56505 0.993000 0.82548 0.276000 0.18716 0.272000 0.22027 0.496000 0.49642 CTG TCGA-IB-A7M4-01A-11D-A36O-08 CYP4F22-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461338.2 1 0 0 7 149 0 36 0 0 0 1 0 36 2 0 0 0 0 0 2 1 0.980016 6 147 0 36 2 0 0 0 0 36 2 -10.137330 1 1 0 0 1 0 0 0 1.979553 0 0.440000 1.980000 0.429967 0.200000 0.090000 0.380000 0.200000 0.224189 0.200000 0 0.140000 0.300000 EPS15L1 58513 broad.mit.edu 37 19 16547778 16547778 + Silent SNP C C T rs33914440 byFrequency TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr19:16547778C>T ENST00000248070.6 - 6 481 c.342G>A c.(340-342)ccG>ccA p.P114P EPS15L1_ENST00000455140.2_Silent_p.P114P|EPS15L1_ENST00000602009.1_5'Flank|EPS15L1_ENST00000535753.2_Silent_p.P114P|EPS15L1_ENST00000594975.1_Silent_p.P114P|EPS15L1_ENST00000597937.1_Silent_p.P114P NM_021235.2 NP_067058.1 Q9UBC2 EP15R_HUMAN epidermal growth factor receptor pathway substrate 15-like 1 30 CTGCAGAGGGCGGTGTGACCA 0.522000 0 SO:0001819 synonymous_variant ENST00000248070.6 1 0 hg19 CCDS32944.1 TCGA-IB-A7M4-01A-11D-A36O-08 EPS15L1-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000461040.1 0 0 1 47 306 0 83 1 8.456231e-01 7 17 0 83 2 0 0 0 0 0 2 1 1.000000 48 299 0 82 2 0 0 0 0 83 2 -2.857362 1 1 121412 6085 69 1 0 0 0 1.979553 0 0.440000 1.980000 0.429967 0.590000 0.440000 0.760000 0.590000 0.601519 0.590000 0 0.510000 0.680000 DPY19L3 147991 broad.mit.edu 37 19 32971419 32971419 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr19:32971419C>T ENST00000342179.5 + 18 2160 c.1945C>T c.(1945-1947)Cgg>Tgg p.R649W DPY19L3_ENST00000392250.2_Missense_Mutation_p.R649W|DPY19L3_ENST00000586987.1_Missense_Mutation_p.R649W NM_207325.2 NP_997208.2 Q6ZPD9 D19L3_HUMAN dpy-19-like 3 (C. elegans) 32 Esophageal squamous(110;0.162) GAGGCACCGCCGGGGCTGCCG 0.632000 0 SO:0001583 missense ENST00000342179.5 1 1 hg19 CCDS12422.1 . . . . . . . . . . C 25.0 4.596002 0.86953 . . ENSG00000178904 ENST00000392250;ENST00000342179 T;T 0.56776 0.44;0.44 5.43 3.18 0.36537 . 0.000000 0.85682 D 0.000000 T 0.70378 0.3217 M 0.77103 2.36 0.50813 D 0.999891 D 0.89917 1.0 D 0.91635 0.999 T 0.74172 -0.3751 10 0.72032 D 0.01 -13.2638 11.7833 0.52028 0.6264:0.3736:0.0:0.0 . 649 Q6ZPD9 D19L3_HUMAN W 649 ENSP00000376081:R649W;ENSP00000344937:R649W ENSP00000344937:R649W R + 1 2 DPY19L3 37663259 0.949000 0.32298 0.934000 0.37439 0.968000 0.65278 1.706000 0.37878 1.214000 0.43395 0.563000 0.77884 CGG TCGA-IB-A7M4-01A-11D-A36O-08 DPY19L3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450311.1 1 0 0 13 227 0 79 1 7.637243e-02 3 5 0 79 2 0 0 0 0 0 2 1 0.999564 13 225 0 79 2 0 0 0 0 79 2 -3.325330 1 0 121408 1 30 1 0 0 0 1.979553 0 0.440000 1.980000 0.429967 0.240000 0.130000 0.390000 0.240000 0.256911 0.240000 0 0.180000 0.320000 ZNF569 148266 broad.mit.edu 37 19 37903725 37903725 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr19:37903725C>T ENST00000316950.6 - 6 2392 c.1835G>A c.(1834-1836)gGa>gAa p.G612E ZNF569_ENST00000392150.2_Missense_Mutation_p.G453E|ZNF569_ENST00000392149.2_Missense_Mutation_p.G612E NM_152484.2 NP_689697.2 Q5MCW4 ZN569_HUMAN zinc finger protein 569 40 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) GAAGGCTTTTCCACATTTATT 0.408000 0 SO:0001583 missense ENST00000316950.6 1 1 hg19 CCDS12503.1 . . . . . . . . . . C 18.22 3.575704 0.65878 . . ENSG00000196437 ENST00000316950;ENST00000392149;ENST00000392150 T;T 0.58210 0.35;0.35 4.1 3.06 0.35304 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.62109 0.2401 L 0.46819 1.47 0.44890 D 0.997908 D;D 0.89917 1.0;1.0 D;D 0.69479 0.964;0.964 T 0.63328 -0.6662 9 0.62326 D 0.03 . 11.1105 0.48230 0.0:0.9057:0.0:0.0943 . 453;612 Q17RR6;Q5MCW4 .;ZN569_HUMAN E 612;268;453 ENSP00000325018:G612E;ENSP00000375993:G453E ENSP00000325018:G612E G - 2 0 ZNF569 42595565 0.996000 0.38824 0.999000 0.59377 0.998000 0.95712 2.285000 0.43487 1.061000 0.40601 0.655000 0.94253 GGA TCGA-IB-A7M4-01A-11D-A36O-08 ZNF569-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109594.2 1 0 1 171 514 0 147 0 6.277213e-02 1 1 0 147 2 0 0 0 0 0 2 1 1.000000 168 504 1 143 17 0 0 0 0 147 2 -20.000000 1 1 0 0 1 0 0 0 1.979553 0 0.440000 1.980000 0.429967 0.990000 0.960000 1.000000 1.000000 0.998340 0.990000 1 0.990000 1.000000 ZNF613 79898 broad.mit.edu 37 19 52448407 52448407 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr19:52448407G>A ENST00000293471.6 + 6 1950 c.1271G>A c.(1270-1272)gGa>gAa p.G424E ZNF613_ENST00000391794.4_Missense_Mutation_p.G388E|ZNF613_ENST00000601794.1_3'UTR NM_001031721.3 NP_001026891.2 Q6PF04 ZN613_HUMAN zinc finger protein 613 19 all_neural(266;0.117) ACTCACACTGGAGAGAAACCC 0.418000 0 SO:0001583 missense ENST00000293471.6 0 1 hg19 CCDS33089.1 . . . . . . . . . . G 16.41 3.114923 0.56505 . . ENSG00000176024 ENST00000293471;ENST00000391794;ENST00000535279 T;T 0.25749 1.78;4.74 3.36 3.36 0.38483 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.36932 N 0.002329 T 0.37732 0.1014 L 0.31476 0.935 0.31474 N 0.66797 D 0.89917 1.0 D 0.97110 1.0 T 0.43686 -0.9376 10 0.87932 D 0 . 14.0307 0.64613 0.0:0.0:1.0:0.0 . 424 Q6PF04 ZN613_HUMAN E 424;388;98 ENSP00000293471:G424E;ENSP00000375671:G388E ENSP00000293471:G424E G + 2 0 ZNF613 57140219 0.974000 0.33945 0.998000 0.56505 0.929000 0.56500 1.109000 0.31135 1.890000 0.54733 0.655000 0.94253 GGA TCGA-IB-A7M4-01A-11D-A36O-08 ZNF613-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461104.2 0 0 0 9 358 0 103 0 7.986632e-02 0 17 0 103 2 0 0 0 0 0 2 1 0.994067 9 354 0 100 2 0 0 0 0 103 2 -3.699657 1 1 0 0 1 1 2 3 2.033799 0 0.440000 1.980000 0.447296 0.110000 0.050000 1.000000 0.110000 0.165510 0.110000 0 0.080000 0.170000 ZNF773 374928 broad.mit.edu 37 19 58016113 58016113 + Missense_Mutation SNP G G T rs140869170 TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr19:58016113G>T ENST00000282292.4 + 2 262 c.122G>T c.(121-123)cGc>cTc p.R41L AC003005.4_ENST00000601674.1_3'UTR|ZNF773_ENST00000598770.1_Missense_Mutation_p.R40L|ZNF773_ENST00000599847.1_Missense_Mutation_p.R41L|ZNF773_ENST00000593916.1_Missense_Mutation_p.R40L NM_198542.1 NP_940944.1 Q6PK81 ZN773_HUMAN zinc finger protein 773 22 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221) CTCCTCTACCGCAATGTGATG 0.527000 0 SO:0001583 missense ENST00000282292.4 1 1 hg19 CCDS33134.1 . . . . . . . . . . G 0.697 -0.792230 0.02884 . . ENSG00000152439 ENST00000332030;ENST00000282292 T 0.02709 4.19 1.39 -0.898 0.10550 Krueppel-associated box (4); . . . . T 0.04861 0.0131 M 0.69523 2.12 0.09310 N 1 B;B 0.32573 0.376;0.1 B;B 0.37692 0.256;0.154 T 0.32955 -0.9887 9 0.45353 T 0.12 . 5.4787 0.16710 0.3572:0.0:0.6428:0.0 . 40;41 Q6PK81-2;Q6PK81 .;ZN773_HUMAN L 64;41 ENSP00000282292:R41L ENSP00000282292:R41L R + 2 0 ZNF773 62707925 0.000000 0.05858 0.001000 0.08648 0.769000 0.43574 -0.343000 0.07791 -0.200000 0.10300 0.305000 0.20034 CGC TCGA-IB-A7M4-01A-11D-A36O-08 ZNF773-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000466475.1 1 0 0 92 379 0 133 1 1.013782e-01 2 1 0 133 2 0 0 0 0 0 2 1 1.000000 87 353 0 150 2 0 0 0 0 133 2 -3.553700 1 0 0 0 1 1 2 3 2.049236 0 0.440000 1.980000 0.447296 0.900000 0.740000 1.000000 1.000000 0.902285 0.900000 1 0.810000 1.000000 AGL 178 broad.mit.edu 37 1 100382219 100382219 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:100382219G>A ENST00000294724.4 + 33 4891 c.4413G>A c.(4411-4413)ccG>ccA p.P1471P AGL_ENST00000370161.2_Silent_p.P1455P|AGL_ENST00000361522.4_Silent_p.P1454P|AGL_ENST00000361302.3_Silent_p.P1455P|AGL_ENST00000370165.3_Silent_p.P1471P|AGL_ENST00000361915.3_Silent_p.P1471P|AGL_ENST00000370163.3_Silent_p.P1471P NM_000028.2 NP_000019.2 P35573 GDE_HUMAN amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase 69 all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131) TGATGGGCCCGGAGACTACTG 0.353000 0 SO:0001819 synonymous_variant ENST00000294724.4 1 1 hg19 CCDS759.1 TCGA-IB-A7M4-01A-11D-A36O-08 AGL-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029778.1 1 0 0 17 286 0 82 1 2.658557e-01 3 14 0 82 2 0 0 0 0 0 2 1 0.999965 17 282 0 82 2 0 0 0 0 82 2 -2.807443 1 1 0 0 1 0 1 1 1.966678 0 0.440000 1.980000 0.429967 0.250000 0.150000 0.380000 0.250000 0.262386 0.250000 0 0.190000 0.320000 TBX15 6913 broad.mit.edu 37 1 119441695 119441695 + Missense_Mutation SNP C C T rs141002143 byFrequency TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:119441695C>T ENST00000369429.3 - 7 989 c.980G>A c.(979-981)cGc>cAc p.R327H TBX15_ENST00000207157.3_Missense_Mutation_p.R221H Q96SF7 TBX15_HUMAN T-box 15 37 all_neural(166;0.117) all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237) GGTGAGTGTGCGCACAGGAGG 0.493000 0 SO:0001583 missense ENST00000369429.3 1 0 hg19 4 0.0018315018315018315 1 0.0020325203252032522 1 0.0027624309392265192 2 0.0034965034965034965 0 0.0 C 33 5.284276 0.95517 0.004085 0.0 ENSG00000092607 ENST00000344218;ENST00000207157;ENST00000369429;ENST00000449873;ENST00000393149 D;D;D 0.88664 -2.41;-2.34;-1.7 5.65 5.65 0.86999 . 0.129767 0.49305 D 0.000159 D 0.92678 0.7673 L 0.54323 1.7 0.80722 D 1 D;D 0.89917 0.999;1.0 D;D 0.76071 0.987;0.98 D 0.92398 0.5927 10 0.66056 D 0.02 . 20.073 0.97731 0.0:1.0:0.0:0.0 . 91;327 E9PCG3;Q96SF7 .;TBX15_HUMAN H 91;221;327;22;21 ENSP00000207157:R221H;ENSP00000358437:R327H;ENSP00000398625:R22H ENSP00000207157:R221H R - 2 0 TBX15 119243218 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 7.181000 0.77682 2.811000 0.96726 0.655000 0.94253 CGC TCGA-IB-A7M4-01A-11D-A36O-08 TBX15-002 PUTATIVE not_organism_supported|upstream_ATG|basic|appris_principal protein_coding protein_coding OTTHUMT00000034351.1 1 0 1 44 257 0 83 0 0 0 1 0 83 2 0 0 0 0 0 2 1 1.000000 42 250 0 83 2 0 0 0 0 83 2 -2.718232 1 1 121404 57 50 1 0 0 0 1.936642 0 0.440000 1.980000 0.419569 0.630000 0.470000 0.820000 0.640000 0.648315 0.630000 0 0.550000 0.730000 IVL 3713 broad.mit.edu 37 1 152882593 152882593 + Missense_Mutation SNP A A G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:152882593A>G ENST00000368764.3 + 2 384 c.320A>G c.(319-321)cAg>cGg p.Q107R IVL_ENST00000392667.2_5'UTR P07476 INVO_HUMAN involucrin 29 Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) CCAGAGCAGCAGCTTAAGCAG 0.488000 0 SO:0001583 missense ENST00000368764.3 1 1 hg19 CCDS1030.1 . . . . . . . . . . A 10.78 1.447930 0.26074 . . ENSG00000163207 ENST00000368764 T 0.10573 2.86 4.46 3.29 0.37713 . . . . . T 0.07279 0.0184 N 0.19112 0.55 0.47407 D 0.999415 D 0.59357 0.985 D 0.65233 0.933 T 0.31081 -0.9956 9 0.33141 T 0.24 . 8.638 0.33959 0.8286:0.0:0.0:0.1714 . 107 P07476 INVO_HUMAN R 107 ENSP00000357753:Q107R ENSP00000357753:Q107R Q + 2 0 IVL 151149217 0.000000 0.05858 0.055000 0.19348 0.058000 0.15608 0.047000 0.14056 0.800000 0.34041 0.402000 0.26972 CAG TCGA-IB-A7M4-01A-11D-A36O-08 IVL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034664.1 1 0 1 38 178 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1.000000 38 174 0 67 2 0 0 0 0 68 2 -20.000000 1 1 0 0 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.760000 0.550000 0.980000 0.760000 0.771027 0.760000 0 0.650000 0.880000 ZBTB7B 51043 broad.mit.edu 37 1 154988280 154988280 + Silent SNP C C A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:154988280C>A ENST00000368426.3 + 3 1281 c.1144C>A c.(1144-1146)Cga>Aga p.R382R ZBTB7B_ENST00000417934.2_Silent_p.R416R|ZBTB7B_ENST00000535420.1_Silent_p.R382R|ZBTB7B_ENST00000292176.2_Silent_p.R382R NM_001256455.1 NP_001243384.1 O15156 ZBT7B_HUMAN zinc finger and BTB domain containing 7B 29 all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) BRCA - Breast invasive adenocarcinoma(34;0.00034) CTGCGGTGTTCGATTCACCAG 0.632000 0 SO:0001819 synonymous_variant ENST00000368426.3 1 0 hg19 CCDS1081.1 TCGA-IB-A7M4-01A-11D-A36O-08 ZBTB7B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091083.1 1 0 0 11 237 0 59 0 7.170339e-01 0 55 0 59 2 0 0 0 0 0 2 1 0.998253 11 232 0 58 2 0 0 0 0 59 2 -12.752270 1 1 0 0 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.190000 0.100000 0.330000 0.190000 0.207398 0.190000 0 0.140000 0.260000 FCRL2 79368 broad.mit.edu 37 1 157736756 157736756 + Missense_Mutation SNP C C G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:157736756C>G ENST00000361516.3 - 7 1216 c.1168G>C c.(1168-1170)Gat>Cat p.D390H FCRL2_ENST00000469986.1_Missense_Mutation_p.D137H|FCRL2_ENST00000392274.3_Missense_Mutation_p.D390H|FCRL2_ENST00000368181.4_Missense_Mutation_p.D106H NM_030764.3 NP_110391.2 Q96LA5 FCRL2_HUMAN Fc receptor-like 2 51 all_hematologic(112;0.0378) LUSC - Lung squamous cell carcinoma(543;0.24) CTATAGCCATCAGGTCCTGAG 0.443000 0 SO:0001583 missense ENST00000361516.3 0 1 hg19 CCDS1168.1 . . . . . . . . . . C 9.353 1.066107 0.20067 . . ENSG00000132704 ENST00000292389;ENST00000361516;ENST00000368181;ENST00000392274;ENST00000469986 T;T;T;T 0.22336 2.06;3.62;1.96;3.04 3.22 -4.53 0.03462 . 4.697510 0.00866 U 0.001962 T 0.06962 0.0177 L 0.40543 1.245 0.09310 N 1 P;P;B;B 0.47762 0.9;0.799;0.032;0.376 P;B;B;B 0.45913 0.497;0.263;0.025;0.071 T 0.10520 -1.0626 10 0.52906 T 0.07 . 1.3638 0.02197 0.1577:0.2103:0.156:0.476 . 390;106;390;137 B4DVJ9;Q96LA5-5;Q96LA5;Q96LA5-2 .;.;FCRL2_HUMAN;. H 106;390;106;390;137 ENSP00000355157:D390H;ENSP00000357163:D106H;ENSP00000376100:D390H;ENSP00000417393:D137H ENSP00000292389:D106H D - 1 0 FCRL2 156003380 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -3.231000 0.00548 -0.956000 0.03631 -0.140000 0.14226 GAT TCGA-IB-A7M4-01A-11D-A36O-08 FCRL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051408.2 0 0 0 4 220 0 65 0 5.451211e-03 0 5 0 65 2 0 0 0 0 0 2 1 0.887979 4 217 0 65 2 0 0 0 0 65 2 -2.860572 1 1 0 0 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.080000 0.020000 0.190000 0.080000 0.095521 0.080000 0 0.040000 0.140000 PLXNA2 5362 broad.mit.edu 37 1 208390894 208390894 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:208390894C>T ENST00000367033.3 - 2 1131 c.374G>A c.(373-375)cGc>cAc p.R125H NM_025179.3 NP_079455.3 O75051 PLXA2_HUMAN plexin A2 80 GGCCAGCAGGCGGTTCTCAGA 0.577000 0 SO:0001583 missense ENST00000367033.3 1 1 hg19 CCDS31013.1 . . . . . . . . . . C 27.0 4.793291 0.90453 . . ENSG00000076356 ENST00000367033 T 0.10573 2.86 5.64 5.64 0.86602 WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4); 0.000000 0.85682 D 0.000000 T 0.42086 0.1187 M 0.87682 2.9 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.43798 -0.9369 10 0.87932 D 0 . 19.7016 0.96057 0.0:1.0:0.0:0.0 . 179;125 O75051-2;O75051 .;PLXA2_HUMAN H 125 ENSP00000356000:R125H ENSP00000356000:R125H R - 2 0 PLXNA2 206457517 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 7.512000 0.81728 2.662000 0.90505 0.514000 0.50259 CGC TCGA-IB-A7M4-01A-11D-A36O-08 PLXNA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000088932.6 1 0 1 112 362 0 144 0 5.219958e-01 1 6 0 144 2 0 0 0 0 0 2 1 1.000000 110 357 0 142 2 0 0 0 0 144 2 -4.936967 1 1 121412 1 34 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.990000 0.860000 1.000000 1.000000 0.978796 0.990000 1 0.930000 1.000000 LYST 1130 broad.mit.edu 37 1 235944227 235944227 + Nonsense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:235944227G>A ENST00000389794.3 - 16 5326 c.5152C>T c.(5152-5154)Cga>Tga p.R1718* LYST_ENST00000389793.2_Nonsense_Mutation_p.R1718*|LYST_ENST00000536965.1_3'UTR Q99698 LYST_HUMAN lysosomal trafficking regulator 162 Ovarian(103;0.0634)|Breast(184;0.23) all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228) OV - Ovarian serous cystadenocarcinoma(106;0.000674) TGTTCACATCGCAAAATTTCT 0.294000 0 SO:0001587 stop_gained ENST00000389794.3 0 1 hg19 CCDS31062.1 . . . . . . . . . . G 45 12.019982 0.99627 . . ENSG00000143669 ENST00000389794;ENST00000389793 . . . 5.05 4.11 0.48088 . 0.354342 0.31872 N 0.006937 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 12.6163 0.56578 0.0:0.0:0.6889:0.3111 . . . . X 1718 . ENSP00000374443:R1718X R - 1 2 LYST 234010850 0.998000 0.40836 0.850000 0.33497 0.976000 0.68499 2.716000 0.47219 1.193000 0.43086 0.467000 0.42956 CGA TCGA-IB-A7M4-01A-11D-A36O-08 LYST-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097533.5 0 0 0 6 368 0 83 0 3.929659e-04 0 2 0 83 2 0 0 0 0 0 2 1 0.964699 6 366 0 82 2 0 0 0 0 83 2 -3.027400 1 1 0 0 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.070000 0.020000 0.140000 0.070000 0.080594 0.070000 0 0.040000 0.110000 RYR2 6262 broad.mit.edu 37 1 237780691 237780691 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:237780691C>T ENST00000366574.2 + 38 6138 c.5821C>T c.(5821-5823)Cgt>Tgt p.R1941C RYR2_ENST00000542537.1_Missense_Mutation_p.R1925C|RYR2_ENST00000360064.6_Missense_Mutation_p.R1939C 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) AGACAATCAACGTTTCCGATA 0.473000 0 SO:0001583 missense ENST00000366574.2 0 1 hg19 CCDS55691.1 . . . . . . . . . . C 16.54 3.152395 0.57259 . . ENSG00000198626 ENST00000366574;ENST00000360064;ENST00000542537 T;T;T 0.73897 -0.79;-0.79;-0.79 5.39 5.39 0.77823 . 0.000000 0.64402 D 0.000005 T 0.67078 0.2855 L 0.39397 1.21 0.80722 D 1 D 0.55800 0.973 B 0.41813 0.367 T 0.71708 -0.4511 10 0.56958 D 0.05 . 14.0546 0.64759 0.1508:0.8492:0.0:0.0 . 1941 Q92736 RYR2_HUMAN C 1941;1939;1925 ENSP00000355533:R1941C;ENSP00000353174:R1939C;ENSP00000443798:R1925C ENSP00000353174:R1939C R + 1 0 RYR2 235847314 0.849000 0.29639 0.949000 0.38748 0.983000 0.72400 1.765000 0.38481 2.517000 0.84864 0.650000 0.86243 CGT TCGA-IB-A7M4-01A-11D-A36O-08 RYR2-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095402.2 0 0 0 4 235 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.891119 4 235 0 52 2 0 0 0 0 52 2 -5.516103 1 0 120904 3 40 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.070000 0.020000 0.170000 0.070000 0.089607 0.070000 0 0.040000 0.130000 KIF26B 55083 broad.mit.edu 37 1 245772663 245772663 + Missense_Mutation SNP C C T rs115703444 by1000genomes TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:245772663C>T ENST00000407071.2 + 8 2187 c.1747C>T c.(1747-1749)Cgc>Tgc p.R583C KIF26B_ENST00000366518.4_Missense_Mutation_p.R202C NM_018012.3 NP_060482.2 Q2KJY2 KI26B_HUMAN kinesin family member 26B 51 all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127) OV - Ovarian serous cystadenocarcinoma(106;0.022) CATAAACGAACGCAAGGAAAA 0.567000 0 SO:0001583 missense ENST00000407071.2 1 1 hg19 CCDS44342.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 C 14.12 2.440500 0.43326 2.6E-4 0.0 ENSG00000162849 ENST00000407071;ENST00000366518;ENST00000413001 T;T 0.76060 -0.99;-0.99 5.22 5.22 0.72569 Kinesin, motor domain (4); . . . . T 0.79015 0.4375 L 0.52364 1.645 0.80722 D 1 P;P 0.48407 0.91;0.869 P;P 0.51550 0.488;0.673 T 0.80223 -0.1471 9 0.56958 D 0.05 . 19.1397 0.93443 0.0:1.0:0.0:0.0 . 202;583 B7WPD9;Q2KJY2 .;KI26B_HUMAN C 583;202;199 ENSP00000385545:R583C;ENSP00000355475:R202C ENSP00000355475:R202C R + 1 0 KIF26B 243839286 1.000000 0.71417 0.976000 0.42696 0.742000 0.42306 2.108000 0.41854 2.590000 0.87494 0.650000 0.86243 CGC TCGA-IB-A7M4-01A-11D-A36O-08 KIF26B-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381037.1 1 0 1 17 79 0 30 0 2.322260e-01 1 4 0 30 2 0 0 0 0 0 2 1 0.999975 17 76 0 29 2 0 0 0 0 30 2 -20.000000 1 1 120844 18 40 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.770000 0.480000 1.000000 1.000000 0.776739 0.770000 0 0.610000 0.950000 OR14C36 127066 broad.mit.edu 37 1 248513002 248513002 + Nonsense_Mutation SNP C C A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:248513002C>A ENST00000317861.1 + 1 926 c.926C>A c.(925-927)tCa>tAa p.S309* NM_001001918.1 NP_001001918.1 Q8NHC7 O14CZ_HUMAN olfactory receptor, family 14, subfamily C, member 36 43 ATTTTTTATTCAGAAAATGTG 0.328000 0 SO:0001587 stop_gained ENST00000317861.1 0 1 hg19 CCDS31112.1 . . . . . . . . . . C 13.04 2.118676 0.37436 . . ENSG00000177174 ENST00000317861 . . . 3.07 3.07 0.35406 . 1.879040 0.04039 U 0.302756 . . . . . . 0.09310 N 0.999999 . . . . . . . . . . 0.02654 T 1 . 9.9262 0.41494 0.0:1.0:0.0:0.0 . . . . X 309 . ENSP00000324534:S309X S + 2 0 OR14C36 246579625 0.000000 0.05858 0.235000 0.24058 0.127000 0.20565 -0.623000 0.05546 1.773000 0.52216 0.388000 0.25769 TCA TCGA-IB-A7M4-01A-11D-A36O-08 OR14C36-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097359.1 0 0 0 10 374 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 0.996848 9 372 0 107 2 0 0 0 0 107 2 -2.797699 1 1 0 0 1 0 0 0 1.927308 0 0.440000 1.980000 0.414226 0.110000 0.050000 0.200000 0.110000 0.123382 0.110000 0 0.080000 0.160000 MEGF6 1953 broad.mit.edu 37 1 3511972 3511972 + Silent SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:3511972C>T ENST00000356575.4 - 3 532 c.306G>A c.(304-306)acG>acA p.T102T NM_001409.3 NP_001400.3 O75095 MEGF6_HUMAN multiple EGF-like-domains 6 19 all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105) all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211) TCCGGGCCTCCGTGGTATACA 0.637000 Ovarian(73;978 3658) 0 SO:0001819 synonymous_variant ENST00000356575.4 1 1 hg19 CCDS41237.1 TCGA-IB-A7M4-01A-11D-A36O-08 MEGF6-007 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354866.1 1 0 0 23 285 0 102 0 6.223421e-03 0 2 0 102 2 0 0 0 0 0 2 1 0.999999 23 279 0 102 2 0 0 0 0 102 2 -2.879466 1 1 120880 14 42 1 0 0 0 1.902310 0 0.440000 1.980000 0.408784 0.320000 0.200000 0.460000 0.320000 0.331765 0.320000 0 0.260000 0.390000 STIL 6491 broad.mit.edu 37 1 47748097 47748097 + Missense_Mutation SNP T T C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr1:47748097T>C ENST00000360380.3 - 12 1531 c.1168A>G c.(1168-1170)Ata>Gta p.I390V STIL_ENST00000371877.3_Missense_Mutation_p.I390V|STIL_ENST00000396221.2_Missense_Mutation_p.I390V|STIL_ENST00000243182.6_Missense_Mutation_p.I390V|STIL_ENST00000337817.5_Missense_Mutation_p.I390V NM_001282936.1 NP_001269865.1 Q15468 STIL_HUMAN SCL/TAL1 interrupting locus 36 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) TGATCATGTATTGGCATCTTC 0.388000 0 SO:0001583 missense ENST00000360380.3 1 1 hg19 CCDS548.1 . . . . . . . . . . T 0.547 -0.850932 0.02651 . . ENSG00000123473 ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475 T;T;T;T;T;T 0.39592 1.07;1.07;1.07;1.07;1.07;1.07 5.74 -4.22 0.03800 . 0.663385 0.16965 N 0.192348 T 0.17916 0.0430 N 0.13043 0.29 0.09310 N 1 B;B;B;B;B 0.02656 0.0;0.0;0.0;0.0;0.0 B;B;B;B;B 0.08055 0.003;0.003;0.003;0.003;0.003 T 0.33701 -0.9858 10 0.08599 T 0.76 -1.1589 9.5812 0.39488 0.0:0.5654:0.122:0.3126 . 390;343;390;390;390 E9PSF2;Q5T0C7;B7ZLW5;Q15468-2;Q15468 .;.;.;.;STIL_HUMAN V 390;390;390;390;390;343 ENSP00000353544:I390V;ENSP00000337367:I390V;ENSP00000360944:I390V;ENSP00000379523:I390V;ENSP00000243182:I390V;ENSP00000411664:I343V ENSP00000243182:I390V I - 1 0 STIL 47520684 0.053000 0.20554 0.184000 0.23157 0.125000 0.20455 -0.250000 0.08830 -0.747000 0.04759 0.459000 0.35465 ATA TCGA-IB-A7M4-01A-11D-A36O-08 STIL-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000021649.2 1 0 1 95 364 0 116 0 2.800527e-01 1 4 0 116 2 0 0 0 0 0 2 1 1.000000 92 360 0 115 2 0 0 0 0 116 2 -20.000000 1 1 0 0 1 0 0 0 1.943490 0 0.440000 1.980000 0.419569 0.900000 0.740000 1.000000 1.000000 0.904158 0.900000 1 0.820000 0.990000 HM13 81502 broad.mit.edu 37 20 30125989 30125989 + Missense_Mutation SNP C C G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr20:30125989C>G ENST00000340852.5 + 3 414 c.290C>G c.(289-291)tCc>tGc p.S97C HM13_ENST00000335574.5_Missense_Mutation_p.S97C|HM13_ENST00000376127.3_Missense_Mutation_p.S97C|HM13_ENST00000398174.3_Missense_Mutation_p.S97C NM_030789.2 NP_110416.1 Q8TCT9 HM13_HUMAN histocompatibility (minor) 13 12 all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198) all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264) CAGATATTCTCCCAGGAGTAC 0.512000 0 SO:0001583 missense ENST00000340852.5 1 1 hg19 CCDS13182.1 . . . . . . . . . . C 27.4 4.826944 0.90955 . . ENSG00000101294 ENST00000335574;ENST00000340852;ENST00000398174;ENST00000376127;ENST00000344042 T;T;T;T;T 0.18960 2.18;2.18;2.18;2.18;2.18 5.46 5.46 0.80206 . 0.098626 0.64402 D 0.000001 T 0.57666 0.2069 M 0.92833 3.35 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.79108 0.992;0.987;0.982;0.987 T 0.67692 -0.5605 10 0.62326 D 0.03 -3.5946 17.8794 0.88835 0.0:1.0:0.0:0.0 . 97;97;97;97 Q8TCT9;Q8TCT9-4;Q8TCT9-2;Q8TCT9-5 HM13_HUMAN;.;.;. C 97 ENSP00000335294:S97C;ENSP00000343032:S97C;ENSP00000381237:S97C;ENSP00000365296:S97C;ENSP00000341347:S97C ENSP00000335294:S97C S + 2 0 HM13 29589650 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 6.840000 0.75369 2.567000 0.86603 0.655000 0.94253 TCC TCGA-IB-A7M4-01A-11D-A36O-08 HM13-011 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078527.2 1 0 1 68 385 0 76 1 1 67 247 0 76 2 0 0 0 0 0 2 1 1.000000 68 381 0 76 2 0 0 0 0 76 2 -3.019294 1 1 0 0 1 1 3 4 2.488582 1 0.440000 1.980000 0.561541 0.900000 0.690000 1.000000 1.000000 0.901692 0.900000 1 0.790000 1.000000 MYLK2 85366 broad.mit.edu 37 20 30414610 30414610 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr20:30414610G>A ENST00000375994.2 + 7 1366 c.1093G>A c.(1093-1095)Gga>Aga p.G365R MYLK2_ENST00000375985.4_Missense_Mutation_p.G365R|MYLK2_ENST00000468730.1_3'UTR Q9H1R3 MYLK2_HUMAN myosin light chain kinase 2 33 Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347) CATCGAGGGCGGAGAGCTCTT 0.587000 0 SO:0001583 missense ENST00000375994.2 0 1 hg19 CCDS13191.1 . . . . . . . . . . G 23.1 4.370531 0.82573 . . ENSG00000101306 ENST00000375994;ENST00000375985 T;T 0.57273 0.41;0.41 3.66 3.66 0.41972 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); . . . . T 0.70168 0.3193 M 0.83012 2.62 0.58432 D 0.999999 D 0.67145 0.996 P 0.59595 0.86 T 0.77606 -0.2525 9 0.87932 D 0 . 14.5797 0.68278 0.0:0.0:1.0:0.0 . 365 Q9H1R3 MYLK2_HUMAN R 365 ENSP00000365162:G365R;ENSP00000365152:G365R ENSP00000365152:G365R G + 1 0 MYLK2 29878271 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 9.494000 0.97962 1.882000 0.54519 0.435000 0.28638 GGA TCGA-IB-A7M4-01A-11D-A36O-08 MYLK2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078583.2 0 0 0 6 171 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 0.961928 6 165 0 45 2 0 0 0 0 45 2 -8.282029 1 1 121412 1 29 1 1 3 4 2.488582 1 0.440000 1.980000 0.561541 0.240000 0.080000 1.000000 0.200000 0.400511 0.240000 0 0.150000 1.000000 TOP1 7150 broad.mit.edu 37 20 39750710 39750710 + Missense_Mutation SNP C C A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr20:39750710C>A ENST00000361337.2 + 20 2360 c.2110C>A c.(2110-2112)Caa>Aaa p.Q704K RP1-1J6.2_ENST00000454626.1_RNA NM_003286.2 NP_003277.1 P11387 TOP1_HUMAN topoisomerase (DNA) I 37 Myeloproliferative disorder(115;0.00878) Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030) GCTGGAAGTTCAAGCCACAGA 0.478000 T NUP98 AML* Dom yes 20 20q12-q13.1 7150 topoisomerase (DNA) I L 0 SO:0001583 missense ENST00000361337.2 0 1 hg19 CCDS13312.1 . . . . . . . . . . C 18.31 3.595991 0.66332 . . ENSG00000198900 ENST00000361337 T 0.47869 0.83 5.91 4.93 0.64822 DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (1);DNA topoisomerases I, dispensable insert, eukaryotic-type (1); 0.101665 0.64402 D 0.000001 T 0.50531 0.1621 M 0.67569 2.06 0.80722 D 1 B 0.20261 0.043 B 0.26969 0.075 T 0.50825 -0.8782 10 0.52906 T 0.07 -14.8363 16.5333 0.84366 0.131:0.869:0.0:0.0 . 704 P11387 TOP1_HUMAN K 704 ENSP00000354522:Q704K ENSP00000354522:Q704K Q + 1 0 TOP1 39184124 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 4.802000 0.62539 2.793000 0.96121 0.655000 0.94253 CAA TCGA-IB-A7M4-01A-11D-A36O-08 TOP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080397.2 0 0 0 19 610 0 125 1 9.995536e-01 4 394 0 125 2 0 0 0 0 0 2 1 0.999988 18 594 0 122 2 0 0 0 0 125 2 -2.149438 0 1 0 0 1 0 6 6 2.522433 1 0.440000 1.980000 0.547511 0.180000 0.100000 1.000000 0.180000 0.333476 0.180000 0 0.130000 1.000000 BMP2 650 broad.mit.edu 37 20 6759506 6759506 + Missense_Mutation SNP C C G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr20:6759506C>G ENST00000378827.4 + 3 2180 c.961C>G c.(961-963)Cac>Gac p.H321D NM_001200.2 NP_001191.1 P12643 BMP2_HUMAN bone morphogenetic protein 2 13 CCCGGGGTATCACGCCTTTTA 0.512000 0 SO:0001583 missense ENST00000378827.4 1 1 hg19 CCDS13099.1 . . . . . . . . . . C 8.617 0.890572 0.17613 . . ENSG00000125845 ENST00000378827 D 0.83673 -1.75 5.57 5.57 0.84162 Transforming growth factor beta, conserved site (1);Transforming growth factor-beta, C-terminal (3); 0.132179 0.64402 D 0.000002 T 0.69378 0.3104 N 0.10664 0.02 0.53005 D 0.999968 B 0.14012 0.009 B 0.15052 0.012 T 0.65944 -0.6045 10 0.52906 T 0.07 . 14.6309 0.68655 0.1798:0.8202:0.0:0.0 . 321 P12643 BMP2_HUMAN D 321 ENSP00000368104:H321D ENSP00000368104:H321D H + 1 0 BMP2 6707506 1.000000 0.71417 1.000000 0.80357 0.964000 0.63967 2.436000 0.44819 2.775000 0.95449 0.650000 0.86243 CAC TCGA-IB-A7M4-01A-11D-A36O-08 BMP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077918.3 1 0 0 19 224 0 77 1 7.420389e-01 9 24 0 77 2 0 0 0 0 0 2 1 0.999992 19 222 0 76 2 0 0 0 0 77 2 -7.380157 1 1 0 0 1 0 1 1 1.537272 1 0.440000 1.980000 0.286079 0.270000 0.170000 0.410000 0.280000 0.288081 0.270000 0 0.220000 0.350000 ADAMTS5 11096 broad.mit.edu 37 21 28315795 28315795 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr21:28315795G>A ENST00000284987.5 - 3 1430 c.1309C>T c.(1309-1311)Cgc>Tgc p.R437C NM_007038.3 NP_008969.2 Q9UNA0 ATS5_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 5 72 GACATTAAGCGCTTATCTTCT 0.453000 Esophageal Squamous(53;683 1080 10100 14424 45938) 0 SO:0001583 missense ENST00000284987.5 1 1 hg19 CCDS13579.1 . . . . . . . . . . G 23.7 4.445910 0.84101 . . ENSG00000154736 ENST00000284987 T 0.21543 2.0 5.4 5.4 0.78164 Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2); 0.000000 0.85682 D 0.000000 T 0.16514 0.0397 N 0.00405 -1.535 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 T 0.60556 -0.7240 10 0.87932 D 0 . 15.0918 0.72201 0.0:0.0:0.858:0.142 . 437 Q9UNA0 ATS5_HUMAN C 437 ENSP00000284987:R437C ENSP00000284987:R437C R - 1 0 ADAMTS5 27237666 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 4.848000 0.62874 2.828000 0.97474 0.650000 0.86243 CGC TCGA-IB-A7M4-01A-11D-A36O-08 ADAMTS5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171648.1 0 0 0 9 236 0 65 0 1.795742e-03 0 2 0 65 2 0 0 0 0 0 2 1 0.994467 9 236 0 65 2 0 0 0 0 65 2 -3.826209 1 1 121406 7 38 1 1 2 3 2.048140 0 0.440000 1.980000 0.446093 0.170000 0.080000 1.000000 0.170000 0.216056 0.170000 0 0.120000 0.250000 CNTNAP5 129684 broad.mit.edu 37 2 125671709 125671709 + Silent SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr2:125671709C>T ENST00000431078.1 + 24 4129 c.3765C>T c.(3763-3765)atC>atT p.I1255I NM_130773.2 NP_570129.1 Q8WYK1 CNTP5_HUMAN contactin associated protein-like 5 p.I1255I(1) 176 TCTGTATCATCGGCATCATGA 0.468000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000431078.1 1 1 hg19 CCDS46401.1 TCGA-IB-A7M4-01A-11D-A36O-08 CNTNAP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330864.3 1 0 0 25 477 1 138 0 0 0 1 138 2 0 0 0 0 0 2 1 0.973005 25 471 1 136 14 0 0 0 1 138 2 -3.295186 1 1 120902 4 44 1 1 2 3 2.033132 0 0.440000 1.980000 0.446093 0.230000 0.140000 1.000000 0.230000 0.265476 0.230000 0 0.180000 0.290000 MYO7B 4648 broad.mit.edu 37 2 128335762 128335762 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr2:128335762C>T ENST00000409816.2 + 8 936 c.904C>T c.(904-906)Cgc>Tgc p.R302C MYO7B_ENST00000428314.1_Missense_Mutation_p.R302C|MYO7B_ENST00000389524.4_Missense_Mutation_p.R302C Q6PIF6 MYO7B_HUMAN myosin VIIB 75 Colorectal(110;0.1) CGCCCACATCCGCTCGGCCAT 0.622000 0 SO:0001583 missense ENST00000409816.2 1 1 hg19 CCDS46405.1 . . . . . . . . . . C 18.99 3.740794 0.69304 0.0 1.18E-4 ENSG00000169994 ENST00000389524;ENST00000428314;ENST00000409816 D;D;D 0.88431 -2.38;-2.38;-2.38 4.25 3.36 0.38483 Myosin head, motor domain (2); 0.061993 0.64402 D 0.000003 D 0.87569 0.6210 M 0.79475 2.455 0.80722 D 1 P 0.40250 0.709 B 0.36289 0.221 D 0.88167 0.2861 10 0.87932 D 0 . 12.4074 0.55447 0.0:0.9171:0.0:0.0828 . 302 Q6PIF6 MYO7B_HUMAN C 302 ENSP00000374175:R302C;ENSP00000415090:R302C;ENSP00000386461:R302C ENSP00000374175:R302C R + 1 0 MYO7B 128052232 0.998000 0.40836 0.872000 0.34217 0.964000 0.63967 3.741000 0.55090 1.136000 0.42199 0.563000 0.77884 CGC TCGA-IB-A7M4-01A-11D-A36O-08 MYO7B-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000331124.3 1 0 1 33 171 0 45 1 3.890862e-01 3 5 0 45 2 0 0 0 0 0 2 1 1.000000 32 168 0 44 2 0 0 0 0 45 2 -20.000000 1 1 121120 2 35 1 1 2 3 2.033132 0 0.440000 1.980000 0.446093 0.740000 0.530000 1.000000 0.740000 0.761996 0.740000 0 0.630000 0.890000 SCN9A 6335 broad.mit.edu 37 2 167141148 167141148 + Nonsense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr2:167141148G>A ENST00000409435.1 - 11 1788 c.1789C>T c.(1789-1791)Cga>Tga p.R597* AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Nonsense_Mutation_p.R597*|SCN9A_ENST00000303354.6_Nonsense_Mutation_p.R598*|SCN9A_ENST00000375387.4_Nonsense_Mutation_p.R598* Q15858 SCN9A_HUMAN sodium channel, voltage-gated, type IX, alpha subunit 108 Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909) CTGCTGCGTCGCTCCTGGGGT 0.542000 0 SO:0001587 stop_gained ENST00000409435.1 0 1 hg19 CCDS46441.1 . . . . . . . . . . G 19.93 3.918909 0.73098 . . ENSG00000169432 ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182 . . . 5.64 3.8 0.43715 . 0.000000 0.53938 D 0.000041 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 15.1065 0.72324 0.0:0.0:0.7411:0.2589 . . . . X 597;598;598;597;462;462 . ENSP00000304748:R598X R - 1 2 SCN9A 166849394 0.826000 0.29277 1.000000 0.80357 0.365000 0.29674 1.783000 0.38664 0.812000 0.34326 -0.270000 0.10280 CGA TCGA-IB-A7M4-01A-11D-A36O-08 SCN9A-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000333639.1 1 0 0 26 363 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 1.000000 26 351 0 120 2 0 0 0 0 121 2 -3.221912 1 1 0 0 1 1 2 3 2.033132 0 0.440000 1.980000 0.446093 0.310000 0.200000 1.000000 0.310000 0.342287 0.310000 0 0.250000 0.380000 ITGA6 3655 broad.mit.edu 37 2 173356152 173356152 + Splice_Site SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr2:173356152G>A ENST00000264106.6 + 24 3209 c.e24-1 AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Splice_Site|ITGA6_ENST00000264107.7_Splice_Site|ITGA6_ENST00000409080.1_Splice_Site|ITGA6_ENST00000375221.2_Splice_Site|ITGA6_ENST00000343713.4_Splice_Site P23229 ITA6_HUMAN integrin, alpha 6 p.?(2) 44 OV - Ovarian serous cystadenocarcinoma(117;0.0979) TCTCCAAACAGGAATATTCCA 0.463000 2 Unknown(2) SO:0001630 splice_region_variant ENST00000264106.6 1 1 hg19 . . . . . . . . . . G 17.51 3.408478 0.62399 . . ENSG00000091409 ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789 . . . 5.21 5.21 0.72293 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 18.7456 0.91791 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . ITGA6 173064398 1.000000 0.71417 0.998000 0.56505 0.705000 0.40729 8.573000 0.90759 2.432000 0.82394 0.467000 0.42956 . TCGA-IB-A7M4-01A-11D-A36O-08 ITGA6-201 KNOWN basic protein_coding protein_coding 1 0 0 15 322 0 83 0 0 0 1 0 83 2 0 0 0 0 0 2 1 0.999872 15 319 0 83 2 0 0 0 0 83 2 -2.989364 1 1 0 0 1 1 2 3 2.033132 0 0.440000 1.980000 0.446093 0.200000 0.110000 1.000000 0.200000 0.245865 0.200000 0 0.150000 0.280000 WIPF1 7456 broad.mit.edu 37 2 175436585 175436585 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr2:175436585G>A ENST00000392547.2 - 5 1047 c.948C>T c.(946-948)ccC>ccT p.P316P WIPF1_ENST00000409415.3_Silent_p.P316P|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000467149.1_5'Flank|WIPF1_ENST00000272746.5_Silent_p.P316P|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000392546.2_Silent_p.P316P|WIPF1_ENST00000409891.1_Silent_p.P316P|WIPF1_ENST00000359761.3_Silent_p.P316P NM_003387.4 NP_003378.3 O43516 WIPF1_HUMAN WAS/WASL interacting protein family, member 1 32 GAGGCGGCCCGGGCCTGCTGG 0.662000 0 SO:0001819 synonymous_variant ENST00000392547.2 1 1 hg19 CCDS2260.1 TCGA-IB-A7M4-01A-11D-A36O-08 WIPF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255453.1 1 0 1 34 148 0 57 1 9.991404e-01 2 49 0 57 2 0 0 0 0 0 2 1 1.000000 33 145 0 57 2 0 0 0 0 57 2 -3.208148 1 1 121396 1 32 1 1 2 3 2.033132 0 0.440000 1.980000 0.446093 0.860000 0.620000 1.000000 1.000000 0.861510 0.860000 1 0.730000 1.000000 COL6A3 1293 broad.mit.edu 37 2 238280504 238280504 + Missense_Mutation SNP C C T rs146092501 byFrequency TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr2:238280504C>T ENST00000295550.4 - 9 4608 c.4156G>A c.(4156-4158)Gaa>Aaa p.E1386K COL6A3_ENST00000472056.1_Missense_Mutation_p.E779K|COL6A3_ENST00000409809.1_Missense_Mutation_p.E1180K|COL6A3_ENST00000392004.3_Missense_Mutation_p.E1180K|COL6A3_ENST00000353578.4_Missense_Mutation_p.E1180K|COL6A3_ENST00000346358.4_Missense_Mutation_p.E1186K|COL6A3_ENST00000392003.2_Missense_Mutation_p.E979K|COL6A3_ENST00000347401.3_Missense_Mutation_p.E1185K NM_004369.3 NP_004360.2 P12111 CO6A3_HUMAN collagen, type VI, alpha 3 217 Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203) AACACATATTCGGGGCTCAGC 0.617000 0 GRCh37 CM050230 COL6A3 M rs146092501 SO:0001583 missense ENST00000295550.4 1 0 hg19 CCDS33412.1 6 0.0027472527472527475 0 0.0 0 0.0 0 0.0 6 0.0079155672823219 C 17.41 3.383806 0.61845 9.08E-4 0.004884 ENSG00000163359 ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003 D;D;D;D;D;D;D;D 0.82984 -1.67;-1.67;-1.67;-1.67;-1.67;-1.67;-1.67;-1.67 5.64 5.64 0.86602 von Willebrand factor, type A (3); 0.108957 0.40144 N 0.001174 T 0.77438 0.4130 L 0.33293 1 0.09310 N 0.999993 D;D;D;D;D 0.64830 0.99;0.981;0.961;0.994;0.986 P;P;P;P;P 0.60415 0.874;0.745;0.658;0.746;0.588 T 0.70425 -0.4875 10 0.23302 T 0.38 . 9.5113 0.39078 0.0:0.7818:0.1441:0.0741 . 779;979;1180;1180;1386 E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111 .;.;.;.;CO6A3_HUMAN K 1386;1185;1180;779;1180;1186;1180;979 ENSP00000295550:E1386K;ENSP00000315609:E1185K;ENSP00000315873:E1180K;ENSP00000418285:E779K;ENSP00000386844:E1180K;ENSP00000295546:E1186K;ENSP00000375861:E1180K;ENSP00000375860:E979K ENSP00000295550:E1386K E - 1 0 COL6A3 237945243 0.862000 0.29867 0.876000 0.34364 0.398000 0.30690 1.784000 0.38674 2.659000 0.90383 0.650000 0.86243 GAA TCGA-IB-A7M4-01A-11D-A36O-08 COL6A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315790.2 0 0 1 69 286 0 99 1 1 2 109 0 99 2 0 0 0 0 0 2 1 1.000000 68 282 0 99 2 0 0 0 0 99 2 -2.172057 0 1 121412 726 61 1 1 2 3 2.033132 0 0.440000 1.980000 0.446093 0.890000 0.710000 1.000000 1.000000 0.894332 0.890000 1 0.790000 1.000000 IQCB1 9657 broad.mit.edu 37 3 121526279 121526279 + Missense_Mutation SNP C C A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr3:121526279C>A ENST00000310864.6 - 7 713 c.499G>T c.(499-501)Gat>Tat p.D167Y IQCB1_ENST00000349820.6_Missense_Mutation_p.D167Y NM_001023570.2 NP_001018864.2 Q15051 IQCB1_HUMAN IQ motif containing B1 30 AAGAAATGATCACTTTGTAGT 0.308000 0 SO:0001583 missense ENST00000310864.6 0 1 hg19 CCDS33837.1 . . . . . . . . . . C 15.49 2.849869 0.51270 . . ENSG00000173226 ENST00000310864;ENST00000349820 T;T 0.36520 1.25;2.89 5.2 5.2 0.72013 . 0.355758 0.34156 N 0.004215 T 0.41282 0.1152 L 0.27053 0.805 0.31110 N 0.710065 P;D 0.63046 0.91;0.992 B;P 0.56960 0.424;0.81 T 0.44605 -0.9317 10 0.72032 D 0.01 -6.9459 14.1128 0.65134 0.0:1.0:0.0:0.0 . 167;167 Q15051;Q15051-2 IQCB1_HUMAN;. Y 167 ENSP00000311505:D167Y;ENSP00000323756:D167Y ENSP00000311505:D167Y D - 1 0 IQCB1 123008969 1.000000 0.71417 1.000000 0.80357 0.743000 0.42351 1.598000 0.36740 2.706000 0.92434 0.557000 0.71058 GAT TCGA-IB-A7M4-01A-11D-A36O-08 IQCB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250573.1 0 0 0 19 909 1 198 0 1.373876e-01 0 30 1 198 2 0 0 0 0 0 2 1 0.682396 19 901 1 197 17 0 0 0 1 198 2 -2.527107 1 1 0 0 1 2 2 4 2.113889 0 0.440000 1.980000 0.468085 0.090000 0.050000 1.000000 0.090000 0.189501 0.090000 0 0.070000 0.140000 NPHP3 27031 broad.mit.edu 37 3 132407536 132407536 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr3:132407536C>T ENST00000337331.5 - 21 3169 c.3083G>A c.(3082-3084)cGt>cAt p.R1028H NPHP3_ENST00000326682.8_3'UTR NM_153240.4 NP_694972.3 Q7Z494 NPHP3_HUMAN nephronophthisis 3 (adolescent) 42 TTCAAGTTCACGAGCAGTATA 0.388000 0 SO:0001583 missense ENST00000337331.5 1 1 hg19 CCDS3078.1 . . . . . . . . . . C 25.9 4.683896 0.88639 . . ENSG00000113971 ENST00000393144;ENST00000393156;ENST00000337331 T 0.64085 -0.08 5.57 5.57 0.84162 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1); 0.000000 0.85682 D 0.000000 T 0.71813 0.3384 L 0.32530 0.975 0.80722 D 1 D 0.89917 1.0 D 0.71414 0.973 T 0.72481 -0.4280 10 0.52906 T 0.07 -17.9717 19.5469 0.95302 0.0:1.0:0.0:0.0 . 1028 Q7Z494 NPHP3_HUMAN H 308;90;1028 ENSP00000338766:R1028H ENSP00000338766:R1028H R - 2 0 NPHP3 133890226 1.000000 0.71417 0.896000 0.35187 0.560000 0.35617 5.823000 0.69272 2.632000 0.89209 0.491000 0.48974 CGT TCGA-IB-A7M4-01A-11D-A36O-08 NPHP3-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357020.2 1 0 0 76 804 0 213 1 3.802078e-01 4 11 0 213 2 0 0 0 0 0 2 1 1.000000 73 792 0 213 2 0 0 0 0 213 2 -18.324050 1 1 121412 3 41 1 2 2 4 2.113889 0 0.440000 1.980000 0.468085 0.410000 0.320000 1.000000 0.410000 0.473565 0.410000 0 0.360000 0.490000 EIF4G1 1981 broad.mit.edu 37 3 184043334 184043334 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr3:184043334G>A ENST00000346169.2 + 20 3299 c.3028G>A c.(3028-3030)Gag>Aag p.E1010K EIF4G1_ENST00000411531.1_Missense_Mutation_p.E971K|EIF4G1_ENST00000352767.3_Missense_Mutation_p.E1017K|EIF4G1_ENST00000392537.2_Missense_Mutation_p.E923K|EIF4G1_ENST00000382330.3_Missense_Mutation_p.E1017K|EIF4G1_ENST00000427845.1_Missense_Mutation_p.E924K|EIF4G1_ENST00000350481.5_Missense_Mutation_p.E846K|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000434061.2_Missense_Mutation_p.E815K|EIF4G1_ENST00000435046.2_Missense_Mutation_p.E814K|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Missense_Mutation_p.E847K|EIF4G1_ENST00000342981.4_Missense_Mutation_p.E1011K|EIF4G1_ENST00000414031.1_Missense_Mutation_p.E970K|EIF4G1_ENST00000319274.6_Missense_Mutation_p.E1010K|EIF4G1_ENST00000424196.1_Missense_Mutation_p.E1017K NM_198241.2 NP_937884 Q04637 IF4G1_HUMAN eukaryotic translation initiation factor 4 gamma, 1 75 all_cancers(143;1.06e-10)|Ovarian(172;0.0339) Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22) TAAGGAGGCTGAGATGGAAGA 0.577000 0 SO:0001583 missense ENST00000346169.2 0 1 hg19 CCDS3259.1 . . . . . . . . . . G 10.23 1.293252 0.23564 . . ENSG00000114867 ENST00000346169;ENST00000414031;ENST00000392537;ENST00000382330;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000441154;ENST00000434061;ENST00000435046 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.04706 3.82;3.81;3.73;3.81;3.6;3.81;3.74;3.82;3.82;3.81;3.81;3.6;3.57;3.57 5.53 5.53 0.82687 . 0.000000 0.85682 D 0.000000 T 0.06050 0.0157 L 0.44542 1.39 0.80722 D 1 B;B;B 0.25312 0.123;0.063;0.059 B;B;B 0.25506 0.061;0.019;0.019 T 0.20571 -1.0271 10 0.05833 T 0.94 -17.1574 19.4726 0.94969 0.0:0.0:1.0:0.0 . 1017;1011;1010 E9PFM1;D3DNT2;Q04637 .;.;IF4G1_HUMAN K 1010;970;923;1017;846;1017;924;1011;1010;1017;971;847;815;814 ENSP00000316879:E1010K;ENSP00000391935:E970K;ENSP00000376320:E923K;ENSP00000371767:E1017K;ENSP00000317600:E846K;ENSP00000338020:E1017K;ENSP00000407682:E924K;ENSP00000343450:E1011K;ENSP00000323737:E1010K;ENSP00000416255:E1017K;ENSP00000395974:E971K;ENSP00000399858:E847K;ENSP00000411826:E815K;ENSP00000404754:E814K ENSP00000323737:E1010K E + 1 0 EIF4G1 185526028 1.000000 0.71417 0.972000 0.41901 0.947000 0.59692 6.342000 0.72982 2.618000 0.88619 0.561000 0.74099 GAG TCGA-IB-A7M4-01A-11D-A36O-08 EIF4G1-007 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000345733.1 0 0 0 8 624 0 163 1 9.316506e-01 2 369 0 163 2 0 0 0 0 0 2 1 0.988941 8 618 0 163 2 0 0 0 0 163 2 -3.075490 1 1 0 0 1 2 2 4 2.113889 0 0.440000 1.980000 0.468085 0.060000 0.020000 1.000000 0.070000 0.157969 0.060000 0 0.040000 0.110000 RPL14 9045 broad.mit.edu 37 3 40503613 40503613 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr3:40503613G>A ENST00000396203.2 + 6 670 c.538G>A c.(538-540)Gcc>Acc p.A180T RPL14_ENST00000416518.1_3'UTR|RPL14_ENST00000338970.6_Missense_Mutation_p.A180T NM_001034996.2 NP_001030168.1 P50914 RL14_HUMAN ribosomal protein L14 GAAGGTTCCTGCCCAGAAAGC 0.552000 0 SO:0001583 missense ENST00000396203.2 1 1 hg19 CCDS43070.1 . . . . . . . . . . G 11.44 1.638177 0.29157 . . ENSG00000188846 ENST00000338970;ENST00000396203 T;T 0.51071 0.72;0.72 4.03 3.15 0.36227 . 0.000000 0.42821 U 0.000651 T 0.32194 0.0821 L 0.27053 0.805 0.22479 N 0.999065 B 0.02656 0.0 B 0.04013 0.001 T 0.27938 -1.0059 10 0.66056 D 0.02 . 8.253 0.31737 0.1159:0.0:0.8841:0.0 . 180 P50914 RL14_HUMAN T 180 ENSP00000345156:A180T;ENSP00000379506:A180T ENSP00000345156:A180T A + 1 0 RPL14 40478617 0.082000 0.21442 0.047000 0.18901 0.779000 0.44077 2.579000 0.46059 0.989000 0.38761 -0.154000 0.13518 GCC TCGA-IB-A7M4-01A-11D-A36O-08 RPL14-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342889.2 1 0 1 50 162 0 47 1 1 3186 3804 0 47 2 0 0 0 0 0 2 1 1.000000 49 160 0 47 2 0 0 0 0 47 2 -20.000000 1 1 0 0 1 2 2 4 2.113889 0 0.440000 1.980000 0.468085 0.990000 0.870000 1.000000 1.000000 0.989844 0.990000 1 0.990000 1.000000 PCDH10 57575 broad.mit.edu 37 4 134084224 134084224 + Missense_Mutation SNP C C G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr4:134084224C>G ENST00000264360.5 + 4 3716 c.2890C>G c.(2890-2892)Cgc>Ggc p.R964G NM_032961.1 NP_116586.1 Q9P2E7 PCD10_HUMAN protocadherin 10 136 TTCTGATGGACGCCAGGCTGC 0.522000 0 SO:0001583 missense ENST00000264360.5 0 1 hg19 CCDS34063.1 . . . . . . . . . . C 19.04 3.749340 0.69533 . . ENSG00000138650 ENST00000264360;ENST00000394248 T 0.53857 0.6 5.24 5.24 0.73138 . 0.000000 0.40302 N 0.001138 T 0.54854 0.1884 N 0.08118 0 0.80722 D 1 D 0.69078 0.997 D 0.76071 0.987 T 0.61232 -0.7104 10 0.40728 T 0.16 . 18.6158 0.91302 0.0:1.0:0.0:0.0 . 964 Q9P2E7 PCD10_HUMAN G 964 ENSP00000264360:R964G ENSP00000264360:R964G R + 1 0 PCDH10 134303674 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.320000 0.79064 2.717000 0.92951 0.650000 0.86243 CGC TCGA-IB-A7M4-01A-11D-A36O-08 PCDH10-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000364457.2 0 0 0 10 392 0 125 0 0 0 1 0 125 2 0 0 0 0 0 2 1 0.996847 10 389 0 124 2 0 0 0 0 125 2 -9.434484 1 1 0 0 1 0 0 0 1.953199 0 0.440000 1.980000 0.422204 0.110000 0.050000 0.190000 0.110000 0.119541 0.110000 0 0.070000 0.150000 LRBA 987 broad.mit.edu 37 4 151199141 151199141 + Nonsense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr4:151199141G>A ENST00000357115.3 - 57 8608 c.8365C>T c.(8365-8367)Cga>Tga p.R2789* LRBA_ENST00000510413.1_Nonsense_Mutation_p.R2777*|LRBA_ENST00000535741.1_Nonsense_Mutation_p.R2778*|LRBA_ENST00000503716.1_5'UTR NM_006726.4 NP_006717.2 P50851 LRBA_HUMAN LPS-responsive vesicle trafficking, beach and anchor containing 91 all_hematologic(180;0.151) TGCCCATCTCGGCTCAGCTGG 0.547000 0 SO:0001587 stop_gained ENST00000357115.3 0 1 hg19 CCDS3773.1 . . . . . . . . . . G 51 18.130073 0.99899 . . ENSG00000198589 ENST00000535741;ENST00000510413;ENST00000357115 . . . 5.23 4.38 0.52667 . 0.062472 0.64402 D 0.000007 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 14.4711 0.67517 0.0:0.0:0.7348:0.2652 . . . . X 2778;2777;2789 . ENSP00000349629:R2789X R - 1 2 LRBA 151418591 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 2.422000 0.44696 1.176000 0.42840 0.655000 0.94253 CGA TCGA-IB-A7M4-01A-11D-A36O-08 LRBA-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000364939.1 1 0 0 15 276 0 77 0 7.974074e-01 1 56 0 77 2 0 0 0 0 0 2 1 0.999866 14 272 0 74 2 0 0 0 0 77 2 -2.848768 1 1 0 0 1 0 0 0 1.953199 0 0.440000 1.980000 0.422204 0.220000 0.130000 0.360000 0.230000 0.239443 0.220000 0 0.170000 0.300000 SEMA6A 57556 broad.mit.edu 37 5 115782948 115782948 + Silent SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:115782948C>T ENST00000343348.6 - 19 3241 c.2454G>A c.(2452-2454)ctG>ctA p.L818L CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000513137.1_Silent_p.L245L|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000282394.6_Silent_p.L295L|SEMA6A_ENST00000257414.8_Silent_p.L835L|SEMA6A_ENST00000510263.1_Silent_p.L818L|SEMA6A_ENST00000503865.1_Silent_p.L197L|CTB-118N6.3_ENST00000512128.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA NM_020796.3 NP_065847 Q9H2E6 SEM6A_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A 31 all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203) GCGTGATGGGCAGGACCACCA 0.662000 0 SO:0001819 synonymous_variant ENST00000343348.6 1 1 hg19 CCDS47256.1 . . . . . . . . . . C 2.211 -0.380738 0.05000 . . ENSG00000092421 ENST00000515129 . . . 5.11 2.34 0.29019 . . . . . T 0.58438 0.2122 . . . 0.80722 D 1 . . . . . . T 0.49273 -0.8957 4 . . . . 9.5769 0.39463 0.3536:0.5783:0.0:0.0681 . . . . Y 333 . . C - 2 0 SEMA6A 115810847 0.999000 0.42202 0.997000 0.53966 0.854000 0.48673 0.742000 0.26216 -0.041000 0.13558 -2.997000 0.00077 TGC TCGA-IB-A7M4-01A-11D-A36O-08 SEMA6A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371270.1 1 0 0 37 471 0 151 0 3.067231e-02 0 4 0 151 2 0 0 0 0 0 2 1 1.000000 37 467 0 150 2 0 0 0 0 151 2 -20.000000 1 1 0 0 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.310000 0.220000 0.420000 0.320000 0.321383 0.310000 0 0.260000 0.370000 DMXL1 1657 broad.mit.edu 37 5 118506551 118506551 + Missense_Mutation SNP A A C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:118506551A>C ENST00000311085.8 + 24 6145 c.6065A>C c.(6064-6066)gAt>gCt p.D2022A DMXL1_ENST00000539542.1_Missense_Mutation_p.D2022A NM_005509.4 NP_005500.4 Q9Y485 DMXL1_HUMAN Dmx-like 1 86 all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231) CCATCAGAAGATATAATTGCA 0.313000 0 SO:0001583 missense ENST00000311085.8 1 1 hg19 CCDS4125.1 . . . . . . . . . . A 19.04 3.749710 0.69533 . . ENSG00000172869 ENST00000311085;ENST00000539542 T;T 0.77750 -1.12;-1.12 5.49 5.49 0.81192 . 0.000000 0.85682 D 0.000000 D 0.89444 0.6717 M 0.86651 2.83 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.91353 0.5106 10 0.87932 D 0 -19.8717 15.606 0.76672 1.0:0.0:0.0:0.0 . 2022;2022 F5H269;Q9Y485 .;DMXL1_HUMAN A 2022 ENSP00000309690:D2022A;ENSP00000439479:D2022A ENSP00000309690:D2022A D + 2 0 DMXL1 118534450 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 8.962000 0.93254 2.083000 0.62718 0.455000 0.32223 GAT TCGA-IB-A7M4-01A-11D-A36O-08 DMXL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250862.1 1 0 1 63 276 0 71 0 1.631252e-01 1 3 0 71 2 0 0 0 0 0 2 1 1.000000 63 273 0 71 2 0 0 0 0 71 2 -20.000000 1 1 0 0 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.790000 0.630000 0.980000 0.800000 0.807570 0.790000 0 0.710000 0.900000 FTMT 94033 broad.mit.edu 37 5 121188177 121188177 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:121188177G>A ENST00000321339.1 + 1 528 c.519G>A c.(517-519)tcG>tcA p.S173S NM_177478.1 NP_803431.1 Q8N4E7 FTMT_HUMAN ferritin mitochondrial 33 all_cancers(142;0.0124)|Prostate(80;0.0322) KIRC - Kidney renal clear cell carcinoma(527;0.206) TGAACCAGTCGTTGCTGGAAT 0.517000 0 SO:0001819 synonymous_variant ENST00000321339.1 1 1 hg19 CCDS4128.1 TCGA-IB-A7M4-01A-11D-A36O-08 FTMT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250884.1 1 0 0 32 514 0 151 0 0 0 0 151 2 0 0 0 0 0 2 1 1.000000 32 507 0 147 2 0 0 0 0 151 2 -6.820153 1 1 121412 2 38 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.250000 0.170000 0.350000 0.250000 0.259793 0.250000 0 0.210000 0.300000 LOX 4015 broad.mit.edu 37 5 121409724 121409724 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:121409724C>T ENST00000231004.4 - 4 1318 c.1019G>A c.(1018-1020)tGt>tAt p.C340Y SRFBP1_ENST00000504881.1_Intron|LOX_ENST00000513319.1_5'UTR NM_001178102.1|NM_002317.5 NP_001171573.1|NP_002308.2 P28300 LYOX_HUMAN lysyl oxidase 8 all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143) KIRC - Kidney renal clear cell carcinoma(527;0.206) GTGTGCAGTACATGCAAATCG 0.478000 0 SO:0001583 missense ENST00000231004.4 1 1 hg19 CCDS4129.1 . . . . . . . . . . C 27.2 4.811350 0.90707 . . ENSG00000113083 ENST00000231004;ENST00000543620 T 0.45668 0.89 5.98 5.98 0.97165 . 0.000000 0.85682 D 0.000000 T 0.75803 0.3899 M 0.93594 3.435 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.81088 -0.1091 10 0.87932 D 0 . 20.4581 0.99154 0.0:1.0:0.0:0.0 . 340 P28300 LYOX_HUMAN Y 340;300 ENSP00000231004:C340Y ENSP00000231004:C340Y C - 2 0 LOX 121437623 1.000000 0.71417 0.982000 0.44146 0.965000 0.64279 7.487000 0.81328 2.835000 0.97688 0.650000 0.86243 TGT TCGA-IB-A7M4-01A-11D-A36O-08 LOX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250887.2 0 0 0 58 889 0 255 0 5.422736e-01 1 28 0 255 2 0 0 0 0 0 2 1 1.000000 58 881 0 252 2 0 0 0 0 255 2 -9.466318 1 1 0 0 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.260000 0.190000 0.330000 0.270000 0.268513 0.260000 0 0.220000 0.300000 PCDHGA2 56113 broad.mit.edu 37 5 140720214 140720214 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:140720214C>T ENST00000394576.2 + 1 1676 c.1676C>T c.(1675-1677)gCg>gTg p.A559V PCDHGA1_ENST00000517417.1_Intron NM_018915.2 NP_061738.1 Q9Y5H1 PCDG2_HUMAN protocadherin gamma subfamily A, 2 77 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AACGACAACGCGCCCGAGATC 0.622000 0 SO:0001583 missense ENST00000394576.2 1 1 hg19 CCDS47289.1 . . . . . . . . . . . 7.268 0.606631 0.14002 . . ENSG00000081853 ENST00000394576 T 0.03181 4.02 5.02 1.19 0.21007 Cadherin (4);Cadherin conserved site (1);Cadherin-like (1); 1.143520 0.06915 U 0.808345 T 0.07007 0.0178 M 0.69185 2.1 0.09310 N 1 B;B 0.22541 0.005;0.071 B;B 0.24394 0.053;0.033 T 0.41016 -0.9532 10 0.44086 T 0.13 . 10.0865 0.42421 0.0:0.7185:0.0:0.2815 . 559;559 Q9Y5H1-2;Q9Y5H1 .;PCDG2_HUMAN V 559 ENSP00000378077:A559V ENSP00000378077:A559V A + 2 0 PCDHGA2 140700398 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 0.115000 0.15540 0.005000 0.14708 -0.225000 0.12378 GCG TCGA-IB-A7M4-01A-11D-A36O-08 PCDHGA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374738.1 1 0 0 45 823 0 264 0 2.853108e-03 0 2 0 264 2 0 0 0 0 0 2 1 1.000000 45 810 0 262 2 0 0 0 0 264 2 -6.525954 1 0 121412 1 35 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.220000 0.160000 0.290000 0.230000 0.228323 0.220000 0 0.180000 0.260000 RASGRF2 5924 broad.mit.edu 37 5 80376464 80376464 + Missense_Mutation SNP T T G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:80376464T>G ENST00000265080.4 + 7 1084 c.1017T>G c.(1015-1017)ttT>ttG p.F339L RASGRF2_ENST00000502677.1_3'UTR NM_006909.2 NP_008840.1 O14827 RGRF2_HUMAN Ras protein-specific guanine nucleotide-releasing factor 2 75 Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357) ATCAAGAATTTGTGCGTAATC 0.403000 0 SO:0001583 missense ENST00000265080.4 1 1 hg19 CCDS4052.1 . . . . . . . . . . T 31 5.090469 0.94149 . . ENSG00000113319 ENST00000265080 T 0.68181 -0.31 5.7 4.55 0.56014 Dbl homology (DH) domain (5); 0.095640 0.85682 D 0.000000 T 0.75072 0.3800 L 0.50333 1.59 0.58432 D 0.999995 D;D 0.76494 0.999;0.994 D;D 0.69307 0.963;0.933 T 0.76160 -0.3061 10 0.72032 D 0.01 . 11.4093 0.49917 0.0:0.0702:0.0:0.9298 . 339;339 D6RAS9;O14827 .;RGRF2_HUMAN L 339 ENSP00000265080:F339L ENSP00000265080:F339L F + 3 2 RASGRF2 80412220 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.483000 0.53194 1.006000 0.39211 0.459000 0.35465 TTT TCGA-IB-A7M4-01A-11D-A36O-08 RASGRF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239215.2 1 0 0 49 707 0 222 0 3.847422e-02 1 4 0 222 2 0 0 0 0 0 2 1 1.000000 49 702 0 222 2 0 0 0 0 222 2 -20.000000 1 0 0 0 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.270000 0.200000 0.360000 0.280000 0.284783 0.270000 0 0.240000 0.320000 ACOT12 134526 broad.mit.edu 37 5 80640798 80640798 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr5:80640798C>T ENST00000307624.3 - 8 864 c.836G>A c.(835-837)cGt>cAt p.R279H ACOT12_ENST00000508234.1_5'Flank NM_130767.2 NP_570123.1 Q8WYK0 ACO12_HUMAN acyl-CoA thioesterase 12 23 Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135) GTTGATGTGACGCCCTCGGCC 0.493000 0 SO:0001583 missense ENST00000307624.3 1 1 hg19 CCDS4055.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 C 23.7 4.451499 0.84209 . . ENSG00000172497 ENST00000307624 T 0.32753 1.44 5.53 4.64 0.57946 . 0.131978 0.52532 D 0.000073 T 0.57932 0.2087 M 0.80746 2.51 0.80722 D 1 D 0.89917 1.0 D 0.76071 0.987 T 0.65067 -0.6258 10 0.87932 D 0 -19.3255 15.1428 0.72623 0.0:0.8576:0.1424:0.0 . 279 Q8WYK0 ACO12_HUMAN H 279 ENSP00000303246:R279H ENSP00000303246:R279H R - 2 0 ACOT12 80676554 1.000000 0.71417 0.454000 0.27019 0.882000 0.50991 6.380000 0.73158 1.301000 0.44836 0.561000 0.74099 CGT TCGA-IB-A7M4-01A-11D-A36O-08 ACOT12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254074.1 0 0 1 65 266 0 116 0 0 0 0 116 2 0 0 0 0 0 2 1 1.000000 64 265 0 116 2 0 0 0 0 116 2 -20.000000 1 1 121412 12 43 1 0 0 0 1.910850 0 0.440000 1.980000 0.411517 0.840000 0.670000 1.000000 1.000000 0.850711 0.840000 0 0.750000 0.940000 PHACTR1 221692 broad.mit.edu 37 6 13273094 13273094 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr6:13273094G>A ENST00000379350.1 + 10 1523 c.1394G>A c.(1393-1395)cGg>cAg p.R465Q PHACTR1_ENST00000379329.1_Missense_Mutation_p.R29Q|PHACTR1_ENST00000332995.7_Missense_Mutation_p.R465Q|RP1-257A7.4_ENST00000399446.2_RNA|PHACTR1_ENST00000379335.3_Missense_Mutation_p.R29Q|PHACTR1_ENST00000457702.2_Missense_Mutation_p.R320Q|RP1-257A7.4_ENST00000606627.1_RNA Q9C0D0 PHAR1_HUMAN phosphatase and actin regulator 1 26 Breast(50;0.0427)|Ovarian(93;0.12) all_hematologic(90;0.122)|Lung SC(78;0.195) Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239) TTCCGTAGGCGGCTGAGCCAG 0.483000 0 SO:0001583 missense ENST00000379350.1 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 37|37 6.030241|6.030241 0.97216|0.97216 .|. .|. ENSG00000112137|ENSG00000112137 ENST00000415087|ENST00000379350;ENST00000332995;ENST00000457702;ENST00000379335;ENST00000379329 .|T;T;T .|0.56941 .|0.43;1.11;1.18 5.91|5.91 5.91|5.91 0.95273|0.95273 .|. .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.72851|0.72851 0.3512|0.3512 M|M 0.84326|0.84326 2.69|2.69 0.80722|0.80722 D|D 1|1 .|D;D .|0.89917 .|1.0;0.997 .|D;D .|0.91635 .|0.999;0.947 T|T 0.75536|0.75536 -0.3283|-0.3283 5|10 .|0.87932 .|D .|0 -14.4638|-14.4638 19.29|19.29 0.94095|0.94095 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|465;465 .|Q9C0D0;Q9C0D0-2 .|PHAR1_HUMAN;. S|Q 300|465;465;320;29;29 .|ENSP00000368655:R465Q;ENSP00000329880:R465Q;ENSP00000397669:R320Q .|ENSP00000329880:R465Q G|R +|+ 1|2 0|0 PHACTR1|PHACTR1 13381073|13381073 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 1.000000|1.000000 0.99986|0.99986 8.473000|8.473000 0.90410|0.90410 2.799000|2.799000 0.96334|0.96334 0.650000|0.650000 0.86243|0.86243 GGC|CGG TCGA-IB-A7M4-01A-11D-A36O-08 PHACTR1-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000039876.1 1 0 0 38 785 0 183 0 0 0 1 0 183 2 0 0 0 0 0 2 1 1.000000 37 776 0 182 2 0 0 0 0 183 2 -4.625984 1 1 120826 2 37 1 1 2 3 2.032223 0 0.440000 1.980000 0.442453 0.200000 0.140000 0.300000 0.210000 0.223178 0.200000 0 0.170000 0.250000 CPNE5 57699 broad.mit.edu 37 6 36710085 36710085 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr6:36710085G>A ENST00000244751.2 - 21 2366 c.1742C>T c.(1741-1743)gCc>gTc p.A581V CPNE5_ENST00000459703.1_5'UTR|CPNE5_ENST00000393189.2_Missense_Mutation_p.A289V NM_020939.1 NP_065990.1 Q9HCH3 CPNE5_HUMAN copine V 25 GGGCGTGCGGGCTGGGGACTG 0.682000 0 SO:0001583 missense ENST00000244751.2 1 1 hg19 CCDS4825.1 . . . . . . . . . . G 14.13 2.444369 0.43429 . . ENSG00000124772 ENST00000244751;ENST00000393189 T;T 0.12039 3.51;2.72 4.6 2.8 0.32819 . 0.243896 0.41823 D 0.000812 T 0.02970 0.0088 L 0.36672 1.1 0.27941 N 0.937519 B 0.06786 0.001 B 0.04013 0.001 T 0.42481 -0.9449 10 0.29301 T 0.29 . 6.038 0.19718 0.1033:0.1925:0.7042:0.0 . 581 Q9HCH3 CPNE5_HUMAN V 581;289 ENSP00000244751:A581V;ENSP00000376885:A289V ENSP00000244751:A581V A - 2 0 CPNE5 36818063 0.057000 0.20700 0.864000 0.33941 0.739000 0.42172 0.598000 0.24074 0.551000 0.29008 0.561000 0.74099 GCC TCGA-IB-A7M4-01A-11D-A36O-08 CPNE5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040351.1 1 0 1 46 283 0 73 0 2.058567e-01 0 6 0 73 2 0 0 0 0 0 2 1 1.000000 46 279 0 72 2 0 0 0 0 73 2 -19.957780 1 1 0 0 1 1 2 3 2.033469 0 0.440000 1.980000 0.442453 0.630000 0.470000 0.850000 0.630000 0.649257 0.630000 0 0.550000 0.740000 KLHDC3 116138 broad.mit.edu 37 6 42985680 42985680 + Missense_Mutation SNP T T C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr6:42985680T>C ENST00000326974.4 + 4 616 c.421T>C c.(421-423)Tac>Cac p.Y141H KLHDC3_ENST00000332245.8_Missense_Mutation_p.Y82H|KLHDC3_ENST00000244670.8_Intron NM_057161.3 NP_476502.1 Q9BQ90 KLDC3_HUMAN kelch domain containing 3 9 Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188) CAAGATCATGTACATTTTTGG 0.512000 0 SO:0001583 missense ENST00000326974.4 0 1 hg19 CCDS4880.1 . . . . . . . . . . T 20.7 4.033569 0.75504 . . ENSG00000124702 ENST00000326974;ENST00000432243;ENST00000394096;ENST00000426116;ENST00000332245 T;T 0.24350 1.86;1.86 5.15 5.15 0.70609 Kelch-type beta propeller (1); 0.065520 0.64402 D 0.000006 T 0.61590 0.2359 H 0.98276 4.19 0.80722 D 1 D;D;D 0.71674 0.998;0.998;0.998 D;D;D 0.73708 0.981;0.981;0.981 T 0.78833 -0.2048 10 0.87932 D 0 . 14.9695 0.71223 0.0:0.0:0.0:1.0 . 141;82;141 E7ENU0;E7ERR0;Q9BQ90 .;.;KLDC3_HUMAN H 141;141;141;114;82 ENSP00000313995:Y141H;ENSP00000331562:Y82H ENSP00000313995:Y141H Y + 1 0 KLHDC3 43093658 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.693000 0.84214 1.950000 0.56595 0.459000 0.35465 TAC TCGA-IB-A7M4-01A-11D-A36O-08 KLHDC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040570.1 0 0 0 8 562 0 118 1 7.288690e-01 6 172 0 118 2 0 0 0 0 0 2 1 0.988742 8 553 0 117 2 0 0 0 0 118 2 -6.596216 1 1 0 0 1 1 2 3 2.033469 0 0.440000 1.980000 0.442453 0.060000 0.020000 0.130000 0.060000 0.080781 0.060000 0 0.040000 0.100000 DST 667 broad.mit.edu 37 6 56325048 56325048 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr6:56325048G>A ENST00000361203.3 - 97 22011 c.22004C>T c.(22003-22005)aCg>aTg p.T7335M DST_ENST00000370788.2_Missense_Mutation_p.T5249M|DST_ENST00000421834.2_Missense_Mutation_p.T5331M|DST_ENST00000370754.5_Missense_Mutation_p.T7624M|DST_ENST00000446842.2_Missense_Mutation_p.T7120M|DST_ENST00000312431.6_3'UTR|DST_ENST00000244364.6_Missense_Mutation_p.T5045M|DST_ENST00000370769.4_Missense_Mutation_p.T7446M Q03001 DYST_HUMAN dystonin 105 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) TTGTATTGGCGTTCCCTGTAT 0.443000 0 SO:0001583 missense ENST00000361203.3 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.9|22.9 4.352831|4.352831 0.82132|0.82132 .|. .|. ENSG00000151914|ENSG00000151914 ENST00000523292|ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203 .|T;T;T;T;T;T;T .|0.65732 .|0.71;-0.16;-0.17;-0.07;0.78;-0.04;-0.11 6.17|6.17 6.17|6.17 0.99709|0.99709 .|. .|0.000000 .|0.56097 .|D .|0.000029 T|T 0.73590|0.73590 0.3606|0.3606 L|L 0.55481|0.55481 1.735|1.735 .|. .|. .|. .|D;D;D;D;D;D;D;D .|0.89917 .|1.0;1.0;1.0;1.0;0.972;0.999;0.999;0.993 .|D;D;D;D;P;P;P;P .|0.87578 .|0.998;0.996;0.994;0.998;0.503;0.802;0.891;0.73 T|T 0.70085|0.70085 -0.4969|-0.4969 4|9 .|0.49607 .|T .|0.09 .|. 20.8794|20.8794 0.99867|0.99867 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|5331;7446;7624;7444;5045;132;132;5249 .|Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8;Q9BSP9;Q86T18;E7ERU0 .|.;.;.;DYST_HUMAN;.;.;.;. C|M 133|5045;7624;7446;5331;7120;5249;7335 .|ENSP00000244364:T5045M;ENSP00000359790:T7624M;ENSP00000359805:T7446M;ENSP00000400883:T5331M;ENSP00000393645:T7120M;ENSP00000359824:T5249M;ENSP00000354508:T7335M .|ENSP00000244364:T5045M R|T -|- 1|2 0|0 DST|DST 56433007|56433007 1.000000|1.000000 0.71417|0.71417 0.899000|0.899000 0.35326|0.35326 0.996000|0.996000 0.88848|0.88848 7.542000|7.542000 0.82095|0.82095 2.941000|2.941000 0.99782|0.99782 0.655000|0.655000 0.94253|0.94253 CGC|ACG TCGA-IB-A7M4-01A-11D-A36O-08 DST-004 NOVEL not_organism_supported|basic|appris_candidate protein_coding protein_coding OTTHUMT00000041021.3 1 0 1 83 245 0 63 1 1 26 65 0 63 2 0 0 0 0 0 2 1 1.000000 82 245 0 63 2 0 0 0 0 63 2 -20.000000 1 1 120852 11 41 1 1 2 3 2.033469 0 0.440000 1.980000 0.442453 0.990000 0.940000 1.000000 1.000000 0.996880 0.990000 1 0.990000 1.000000 KCNQ5 56479 broad.mit.edu 37 6 73904417 73904417 + Silent SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr6:73904417G>A ENST00000370398.1 + 14 2188 c.2079G>A c.(2077-2079)acG>acA p.T693T KCNQ5_ENST00000355635.3_Silent_p.T694T|KCNQ5_ENST00000355194.4_Silent_p.T693T|KCNQ5_ENST00000414165.2_Silent_p.T583T|KCNQ5_ENST00000342056.2_Silent_p.T712T|KCNQ5_ENST00000403813.2_Silent_p.T684T|KCNQ5_ENST00000402622.2_Silent_p.T703T NM_019842.3 NP_062816.2 Q9NR82 KCNQ5_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 5 57 all_epithelial(107;0.116)|Lung NSC(302;0.219) Ezogabine(DB04953) TCATTCTGACGCCAAATGAGT 0.502000 GBM(142;1375 1859 14391 23261 44706) 0 SO:0001819 synonymous_variant ENST00000370398.1 1 1 hg19 CCDS4976.1 TCGA-IB-A7M4-01A-11D-A36O-08 KCNQ5-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000041198.3 1 0 1 117 422 0 160 0 0 0 1 0 160 2 0 0 0 0 0 2 1 1.000000 113 416 0 160 2 0 0 0 0 160 2 -4.035921 1 1 121412 9 44 1 1 2 3 2.033469 0 0.440000 1.980000 0.442453 0.980000 0.830000 1.000000 1.000000 0.964557 0.980000 1 0.900000 1.000000 CUL1 8454 broad.mit.edu 37 7 148484186 148484186 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr7:148484186G>A ENST00000325222.4 + 13 1732 c.1453G>A c.(1453-1455)Gaa>Aaa p.E485K CUL1_ENST00000602748.1_Missense_Mutation_p.E485K|CUL1_ENST00000409469.1_Missense_Mutation_p.E485K NM_003592.2 NP_003583.2 Q13616 CUL1_HUMAN cullin 1 p.E485K(4) 40 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00291) TGACGATGCCGAAGCCAGCAT 0.458000 4 Substitution - Missense(4) SO:0001583 missense ENST00000325222.4 1 1 hg19 CCDS34772.1 . . . . . . . . . . G 33 5.288263 0.95517 . . ENSG00000055130 ENST00000409469;ENST00000325222;ENST00000543583;ENST00000433865 D;D 0.86865 -2.18;-2.18 5.5 5.5 0.81552 Cullin, N-terminal (1);Cullin homology (3); 0.047140 0.85682 D 0.000000 D 0.95847 0.8648 H 0.95745 3.715 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.98 D 0.96814 0.9599 10 0.87932 D 0 -0.8542 19.4118 0.94677 0.0:0.0:1.0:0.0 . 412;485 E7EWR0;Q13616 .;CUL1_HUMAN K 485;485;443;412 ENSP00000387160:E485K;ENSP00000326804:E485K ENSP00000326804:E485K E + 1 0 CUL1 148115119 1.000000 0.71417 0.913000 0.36048 0.576000 0.36127 9.497000 0.97970 2.595000 0.87683 0.655000 0.94253 GAA TCGA-IB-A7M4-01A-11D-A36O-08 CUL1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000467785.1 1 0 0 19 309 1 82 1 5.099373e-01 7 89 1 82 6 0 0 0 0 0 2 1 0.841242 18 303 1 82 14 0 0 0 1 82 2 -2.842321 1 1 0 0 1 1 2 3 2.014673 0 0.440000 1.980000 0.446093 0.270000 0.160000 1.000000 0.270000 0.304901 0.270000 0 0.210000 0.350000 CSMD3 114788 broad.mit.edu 37 8 113349048 113349048 + Silent SNP A A T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr8:113349048A>T ENST00000297405.5 - 44 7096 c.6852T>A c.(6850-6852)ggT>ggA p.G2284G CSMD3_ENST00000352409.3_Silent_p.G2214G|CSMD3_ENST00000455883.2_Silent_p.G2180G|CSMD3_ENST00000343508.3_Silent_p.G2244G NM_198123.1 NP_937756.1 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 646 TTATATTCCCACCACAAAGAG 0.348000 HNSCC(6;0.00088)|TCGA Ovarian(7;0.080) 0 SO:0001819 synonymous_variant ENST00000297405.5 1 1 hg19 CCDS6315.1 TCGA-IB-A7M4-01A-11D-A36O-08 CSMD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347141.1 1 0 1 164 314 0 114 0 0 0 0 114 2 0 0 0 0 0 2 1 1.000000 162 310 0 114 2 0 0 0 0 114 2 -20.000000 1 1 0 0 1 1 3 4 2.513552 1 0.440000 1.980000 0.553856 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SCRIB 23513 broad.mit.edu 37 8 144891159 144891159 + Missense_Mutation SNP C C T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr8:144891159C>T ENST00000320476.3 - 15 1741 c.1735G>A c.(1735-1737)Ggg>Agg p.G579R SCRIB_ENST00000356994.2_Missense_Mutation_p.G579R|SCRIB_ENST00000377533.3_Missense_Mutation_p.G498R NM_015356.4 NP_056171 Q14160 SCRIB_HUMAN scribbled planar cell polarity protein 42 all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18) CTGTCATCCCCGGGCAGCAGT 0.642000 Pancreas(51;966 1133 10533 14576 29674) 0 SO:0001583 missense ENST00000320476.3 1 1 hg19 CCDS6411.1 . . . . . . . . . . c 7.938 0.742196 0.15642 0.0 1.16E-4 ENSG00000180900 ENST00000356994;ENST00000320476;ENST00000377533 T;T;T 0.36340 1.49;1.45;1.26 4.79 -7.88 0.01178 . . . . . T 0.13543 0.0328 N 0.11756 0.17 0.09310 N 1 B;B 0.11235 0.002;0.004 B;B 0.09377 0.001;0.004 T 0.25502 -1.0130 9 0.13853 T 0.58 . 5.0756 0.14630 0.0935:0.0875:0.2007:0.6183 . 579;579 Q14160;Q14160-3 SCRIB_HUMAN;. R 579;579;498 ENSP00000349486:G579R;ENSP00000322938:G579R;ENSP00000366756:G498R ENSP00000322938:G579R G - 1 0 SCRIB 144963147 0.000000 0.05858 0.000000 0.03702 0.011000 0.07611 0.067000 0.14510 -1.579000 0.01646 0.401000 0.26515 GGG TCGA-IB-A7M4-01A-11D-A36O-08 SCRIB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000382215.1 1 0 0 26 446 0 58 1 9.955213e-01 9 136 0 58 2 0 0 0 0 0 2 1 1.000000 26 441 0 55 2 0 0 0 0 58 2 -2.690843 1 1 121410 2 34 1 1 4 5 3.074370 1 0.440000 1.980000 0.633508 0.400000 0.250000 1.000000 0.390000 0.486838 0.400000 0 0.320000 0.590000 PLEC 5339 broad.mit.edu 37 8 144991972 144991972 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr8:144991972G>A ENST00000322810.4 - 32 12597 c.12428C>T c.(12427-12429)tCg>tTg p.S4143L PLEC_ENST00000436759.2_Missense_Mutation_p.S4033L|PLEC_ENST00000354589.3_Missense_Mutation_p.S4006L|PLEC_ENST00000527096.1_Missense_Mutation_p.S4029L|PLEC_ENST00000357649.2_Missense_Mutation_p.S4010L|PLEC_ENST00000354958.2_Missense_Mutation_p.S3984L|PLEC_ENST00000345136.3_Missense_Mutation_p.S4006L|PLEC_ENST00000356346.3_Missense_Mutation_p.S3992L|PLEC_ENST00000398774.2_Missense_Mutation_p.S3974L NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 137 GCGCTCGGCCGACAGCAGCTT 0.607000 0 SO:0001583 missense ENST00000322810.4 0 1 hg19 CCDS43772.1 . . . . . . . . . . G 10.18 1.279669 0.23307 4.61E-4 0.0 ENSG00000178209 ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096 T;T;T;T;T;T;T;T;T 0.74737 -0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87 5.08 5.08 0.68730 . 0.000000 0.64402 U 0.000014 D 0.84511 0.5488 L 0.58302 1.8 0.80722 D 1 D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D 0.91635 0.998;0.998;0.998;0.999;0.998;0.998;0.998;0.998 D 0.85805 0.1376 10 0.87932 D 0 . 18.2755 0.90081 0.0:0.0:1.0:0.0 . 4033;3992;3984;4143;3974;4006;4010;4006 Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4 .;.;.;PLEC_HUMAN;.;.;.;. L 4006;4010;4006;3974;4143;3984;3992;4033;4029 ENSP00000344848:S4006L;ENSP00000350277:S4010L;ENSP00000346602:S4006L;ENSP00000381756:S3974L;ENSP00000323856:S4143L;ENSP00000347044:S3984L;ENSP00000348702:S3992L;ENSP00000388180:S4033L;ENSP00000434583:S4029L ENSP00000323856:S4143L S - 2 0 PLEC 145063960 1.000000 0.71417 0.996000 0.52242 0.232000 0.25224 9.595000 0.98260 2.654000 0.90174 0.549000 0.68633 TCG TCGA-IB-A7M4-01A-11D-A36O-08 PLEC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383281.1 0 0 0 12 345 0 60 1 1 45 1189 0 60 2 0 0 0 0 0 2 1 0.999077 12 341 0 58 2 0 0 0 0 60 2 -3.462155 1 0 121208 3 36 1 1 4 5 3.074370 1 0.440000 1.980000 0.633508 0.250000 0.120000 1.000000 0.230000 0.364634 0.250000 0 0.180000 0.440000 BMP1 649 broad.mit.edu 37 8 22037971 22037971 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr8:22037971G>A ENST00000306385.5 + 8 1722 c.1052G>A c.(1051-1053)cGc>cAc p.R351H BMP1_ENST00000397816.3_Missense_Mutation_p.R351H|BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000306349.8_Missense_Mutation_p.R351H|BMP1_ENST00000397814.3_Missense_Mutation_p.R351H NM_006129.4 NP_006120.1 P13497 BMP1_HUMAN bone morphogenetic protein 1 30 TGCGTGTGGCGCATCTCTGTC 0.612000 0 SO:0001583 missense ENST00000306385.5 0 1 hg19 CCDS6026.1 . . . . . . . . . . G 27.0 4.795501 0.90453 . . ENSG00000168487 ENST00000306385;ENST00000397816;ENST00000306349;ENST00000397814 T;T;T;T 0.34275 1.37;1.37;1.37;1.37 5.66 5.66 0.87406 CUB (5); 0.000000 0.39274 U 0.001412 T 0.53722 0.1814 L 0.44542 1.39 0.80722 D 1 D;D;D;D 0.89917 0.99;1.0;0.998;0.994 P;D;P;P 0.91635 0.818;0.999;0.886;0.629 T 0.42241 -0.9463 10 0.35671 T 0.21 . 18.5112 0.90917 0.0:0.0:1.0:0.0 . 351;424;351;351 P13497;Q59F71;P13497-2;P13497-6 BMP1_HUMAN;.;.;. H 351 ENSP00000305714:R351H;ENSP00000380917:R351H;ENSP00000306121:R351H;ENSP00000380915:R351H ENSP00000306121:R351H R + 2 0 BMP1 22093916 1.000000 0.71417 1.000000 0.80357 0.873000 0.50193 6.755000 0.74914 2.665000 0.90641 0.561000 0.74099 CGC TCGA-IB-A7M4-01A-11D-A36O-08 BMP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214995.2 0 0 0 5 406 0 152 0 1.254665e-01 0 41 0 152 2 0 0 0 0 0 2 1 0.935044 5 399 0 149 2 0 0 0 0 152 2 -2.051240 0 1 121412 2 41 1 0 1 1 1.634903 1 0.440000 1.980000 0.284071 0.040000 0.010000 0.100000 0.040000 0.051342 0.040000 0 0.020000 0.070000 SLCO5A1 81796 broad.mit.edu 37 8 70591817 70591817 + Missense_Mutation SNP C C T rs151145765 byFrequency TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr8:70591817C>T ENST00000260126.4 - 8 2526 c.1820G>A c.(1819-1821)cGc>cAc p.R607H SLCO5A1_ENST00000524945.1_Missense_Mutation_p.R607H|SLCO5A1_ENST00000530307.1_Missense_Mutation_p.R552H NM_030958.2 NP_112220.2 Q9H2Y9 SO5A1_HUMAN solute carrier organic anion transporter family, member 5A1 53 Breast(64;0.0654) Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594) GATCACTTGGCGACTTTGGAC 0.453000 0 SO:0001583 missense ENST00000260126.4 0 1 hg19 CCDS6205.1 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 C 22.7 4.328881 0.81690 0.002724 0.0 ENSG00000137571 ENST00000260126;ENST00000524945;ENST00000530307 T;T;T 0.41758 1.1;1.47;0.99 5.62 5.62 0.85841 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.000000 0.64402 D 0.000005 T 0.53222 0.1783 N 0.25890 0.77 0.49798 D 0.99982 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.77557 0.99;0.987;0.986 T 0.46331 -0.9199 10 0.30854 T 0.27 . 19.6614 0.95875 0.0:1.0:0.0:0.0 . 552;607;607 E9PKK5;Q9H2Y9;G3V1C0 .;SO5A1_HUMAN;. H 607;607;552 ENSP00000260126:R607H;ENSP00000434422:R607H;ENSP00000431611:R552H ENSP00000260126:R607H R - 2 0 SLCO5A1 70754371 1.000000 0.71417 0.989000 0.46669 0.645000 0.38454 6.038000 0.70964 2.633000 0.89246 0.655000 0.94253 CGC TCGA-IB-A7M4-01A-11D-A36O-08 SLCO5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381990.3 0 0 0 15 561 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 0.999855 15 552 0 148 2 0 0 0 0 148 2 -2.670482 1 1 121412 39 50 1 1 2 3 2.053415 0 0.440000 1.980000 0.447296 0.120000 0.060000 1.000000 0.120000 0.168200 0.120000 0 0.090000 0.170000 STK3 6788 broad.mit.edu 37 8 99468195 99468195 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr8:99468195G>A ENST00000419617.2 - 11 1491 c.1351C>T c.(1351-1353)Cgg>Tgg p.R451W STK3_ENST00000523601.1_Missense_Mutation_p.R479W NM_006281.3 NP_006272.2 Q13188 STK3_HUMAN serine/threonine kinase 3 17 Breast(36;2.4e-06) Breast(495;0.106) OV - Ovarian serous cystadenocarcinoma(57;0.0382) GCTTTTAACCGCATCTGTAGT 0.383000 0 SO:0001583 missense ENST00000419617.2 0 1 hg19 CCDS47900.1 . . . . . . . . . . G 19.90 3.912410 0.72983 . . ENSG00000104375 ENST00000419617;ENST00000523601 T;T 0.75260 -0.91;-0.92 5.51 4.58 0.56647 SARAH domain (1);SARAH (1); 0.000000 0.85682 D 0.000000 D 0.83594 0.5288 M 0.70595 2.14 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.74023 0.977;0.982 D 0.84708 0.0732 10 0.87932 D 0 . 12.0474 0.53487 0.0:0.0:0.6717:0.3283 . 451;479 Q13188;B3KYA7 STK3_HUMAN;. W 451;479 ENSP00000390500:R451W;ENSP00000429744:R479W ENSP00000390500:R451W R - 1 2 STK3 99537371 1.000000 0.71417 1.000000 0.80357 0.950000 0.60333 1.638000 0.37165 2.746000 0.94184 0.591000 0.81541 CGG TCGA-IB-A7M4-01A-11D-A36O-08 STK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379635.1 0 0 0 6 173 0 37 1 6.368836e-01 4 56 0 37 2 0 0 0 0 0 2 1 0.963270 6 169 0 37 2 0 0 0 0 37 2 -3.846188 1 1 120776 1 24 1 1 3 4 2.513552 1 0.440000 1.980000 0.553856 0.230000 0.080000 1.000000 0.190000 0.403854 0.230000 0 0.140000 1.000000 DBH 1621 broad.mit.edu 37 9 136508616 136508616 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr9:136508616G>A ENST00000393056.2 + 4 838 c.826G>A c.(826-828)Gtc>Atc p.V276I NM_000787.3 NP_000778.3 P09172 DOPO_HUMAN dopamine beta-hydroxylase (dopamine beta-monooxygenase) p.V276I(1) 36 Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126) GATGGACAGCGTCCCCCACTT 0.657000 1 Substitution - Missense(1) SO:0001583 missense ENST00000393056.2 0 1 hg19 CCDS6977.2 . . . . . . . . . . G 0.011 -1.699360 0.00725 . . ENSG00000123454 ENST00000393056;ENST00000371880;ENST00000263611 T;T 0.29917 1.55;1.55 4.9 -8.25 0.01025 Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1); 0.610624 0.17687 N 0.165404 T 0.07954 0.0199 N 0.04373 -0.215 0.19775 N 0.99995 B 0.06786 0.001 B 0.11329 0.006 T 0.25502 -1.0130 10 0.02654 T 1 -15.1191 7.9737 0.30143 0.4294:0.0:0.3685:0.2021 . 276 P09172 DOPO_HUMAN I 276;213;213 ENSP00000376776:V276I;ENSP00000263611:V213I ENSP00000263611:V213I V + 1 0 DBH 135498437 0.000000 0.05858 0.001000 0.08648 0.003000 0.03518 -1.053000 0.03500 -1.933000 0.01052 -0.410000 0.06199 GTC TCGA-IB-A7M4-01A-11D-A36O-08 DBH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054929.2 0 0 0 10 348 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 0.996850 9 346 0 87 2 0 0 0 0 87 2 -3.607988 1 1 121410 1 36 1 1 2 3 2.023196 0 0.440000 1.980000 0.442453 0.130000 0.060000 0.240000 0.120000 0.147442 0.130000 0 0.090000 0.180000 PRUNE2 158471 broad.mit.edu 37 9 79323756 79323756 + Missense_Mutation SNP G G A TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr9:79323756G>A ENST00000376718.3 - 8 3557 c.3434C>T c.(3433-3435)gCg>gTg p.A1145V PRUNE2_ENST00000428286.1_Missense_Mutation_p.A786V NM_015225.2 NP_056040.2 Q8WUY3 PRUN2_HUMAN prune homolog 2 (Drosophila) 16 GGGGATTGCCGCACCCCCACT 0.522000 0 SO:0001583 missense ENST00000376718.3 0 1 hg19 CCDS47982.1 . . . . . . . . . . A 2.851 -0.238399 0.05944 . . ENSG00000106772 ENST00000376718;ENST00000428286;ENST00000422033 T;T 0.38401 1.15;1.14 6.08 6.08 0.98989 . 0.121361 0.37577 N 0.002034 T 0.12603 0.0306 N 0.01576 -0.805 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.16748 -1.0392 10 0.02654 T 1 -10.7943 11.0795 0.48051 0.9304:0.0:0.0696:0.0 . 1145 Q8WUY3 PRUN2_HUMAN V 1145;786;1144 ENSP00000365908:A1145V;ENSP00000397425:A786V ENSP00000365908:A1145V A - 2 0 PRUNE2 78513576 0.218000 0.23608 0.794000 0.32065 0.308000 0.27856 0.910000 0.28571 1.126000 0.42016 -0.254000 0.11334 GCG TCGA-IB-A7M4-01A-11D-A36O-08 PRUNE2-003 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052730.2 0 0 0 7 589 0 164 0 0 0 0 164 2 0 0 0 0 0 2 1 0.979119 7 576 0 164 2 0 0 0 0 164 2 -1.925693 0 1 120486 4 37 1 1 2 3 2.026129 0 0.440000 1.980000 0.442453 0.050000 0.010000 0.120000 0.060000 0.070200 0.050000 0 0.030000 0.080000 PTPDC1 138639 broad.mit.edu 37 9 96847575 96847575 + Missense_Mutation SNP A A G TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chr9:96847575A>G ENST00000375360.3 + 3 465 c.125A>G c.(124-126)gAg>gGg p.E42G PTPDC1_ENST00000288976.3_Missense_Mutation_p.E94G NM_001253830.1|NM_177995.2 NP_001240759.1|NP_818931.1 A2A3K4 PTPC1_HUMAN protein tyrosine phosphatase domain containing 1 32 AAAGTAGGGGAGCGTTTACGG 0.453000 0 SO:0001583 missense ENST00000375360.3 1 1 hg19 CCDS6707.1 . . . . . . . . . . . 24.7 4.564213 0.86335 . . ENSG00000158079 ENST00000375360;ENST00000288976 T;T 0.75589 -0.95;-0.95 5.51 5.51 0.81932 . 0.000000 0.85682 D 0.000000 D 0.86818 0.6024 M 0.83953 2.67 0.54753 D 0.999987 D;D;D;D 0.89917 0.999;1.0;0.999;1.0 D;D;D;D 0.81914 0.981;0.992;0.971;0.995 D 0.88807 0.3289 10 0.87932 D 0 -27.4699 15.0953 0.72229 1.0:0.0:0.0:0.0 . 96;94;96;42 E7EN59;A2A3K4-2;A8K0X7;A2A3K4 .;.;.;PTPC1_HUMAN G 42;94 ENSP00000364509:E42G;ENSP00000288976:E94G ENSP00000288976:E94G E + 2 0 PTPDC1 95887396 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 8.771000 0.91751 2.226000 0.72624 0.482000 0.46254 GAG TCGA-IB-A7M4-01A-11D-A36O-08 PTPDC1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000215007.1 0 0 1 149 521 0 158 1 5.008225e-02 2 0 0 158 2 0 0 0 0 0 2 1 1.000000 146 515 0 156 2 0 0 0 0 158 2 -20.000000 1 1 0 0 1 1 2 3 2.026129 0 0.440000 1.980000 0.442453 0.990000 0.870000 1.000000 1.000000 0.978770 0.990000 1 0.930000 1.000000 USP26 83844 broad.mit.edu 37 X 132160691 132160691 + Missense_Mutation SNP G G T TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chrX:132160691G>T ENST00000511190.1 - 6 2027 c.1558C>A c.(1558-1560)Cac>Aac p.H520N USP26_ENST00000406273.1_Missense_Mutation_p.H520N|USP26_ENST00000370832.1_Missense_Mutation_p.H520N NM_031907.1 NP_114113.1 Q9BXU7 UBP26_HUMAN ubiquitin specific peptidase 26 60 Acute lymphoblastic leukemia(192;0.000127) CGTTTGAGGTGAACAATAAGG 0.383000 NSCLC(104;342 1621 36940 47097 52632) 0 SO:0001583 missense ENST00000511190.1 1 0 hg19 CCDS14635.1 . . . . . . . . . . G 12.80 2.047339 0.36085 . . ENSG00000134588 ENST00000370832;ENST00000511190;ENST00000406273 T;T;T 0.77877 -1.13;-1.13;-1.13 3.8 3.8 0.43715 Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2); 0.115910 0.35378 N 0.003241 D 0.85687 0.5754 M 0.76574 2.34 0.32585 N 0.527976 D 0.89917 1.0 D 0.97110 1.0 D 0.87940 0.2716 10 0.87932 D 0 -18.1599 10.167 0.42886 0.0:0.0:1.0:0.0 . 520 Q9BXU7 UBP26_HUMAN N 520 ENSP00000359869:H520N;ENSP00000423390:H520N;ENSP00000384360:H520N ENSP00000359869:H520N H - 1 0 USP26 131988357 1.000000 0.71417 0.751000 0.31187 0.034000 0.12701 6.092000 0.71414 2.153000 0.67306 0.529000 0.55759 CAC TCGA-IB-A7M4-01A-11D-A36O-08 USP26-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359441.1 1 0 0 21 524 0 167 0 0 0 0 167 2 0 0 0 0 0 2 1 0.999997 20 518 0 166 2 0 0 0 0 167 2 -3.416538 1 1 0 0 1 0 1 1 0.440000 1.980000 0.440000 0.080000 0.050000 0.130000 0.090000 0.091186 0.080000 0 0.060000 0.110000 NHS 4810 broad.mit.edu 37 X 17745920 17745920 + Missense_Mutation SNP G G C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chrX:17745920G>C ENST00000380060.3 + 6 3969 c.3631G>C c.(3631-3633)Gaa>Caa p.E1211Q NHS_ENST00000398097.3_Missense_Mutation_p.E1055Q NM_198270.2 NP_938011.1 Q6T4R5 NHS_HUMAN Nance-Horan syndrome (congenital cataracts and dental anomalies) 71 Hepatocellular(33;0.183) CTGCGATCCAGAAACCATAAC 0.408000 0 SO:0001583 missense ENST00000380060.3 1 1 hg19 CCDS14181.1 . . . . . . . . . . G 11.69 1.714361 0.30413 . . ENSG00000188158 ENST00000380060;ENST00000398097;ENST00000380057 T;T 0.50277 0.8;0.75 5.79 5.79 0.91817 . 0.270289 0.35970 N 0.002870 T 0.47544 0.1451 L 0.54323 1.7 0.24754 N 0.992961 P;P;P;P 0.51933 0.919;0.919;0.919;0.949 P;P;P;P 0.47346 0.51;0.51;0.51;0.544 T 0.45381 -0.9265 10 0.17832 T 0.49 -17.3353 13.2279 0.59924 0.0773:0.0:0.9227:0.0 . 1232;1053;1055;1211 B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5 .;.;.;NHS_HUMAN Q 1211;1055;1053 ENSP00000369400:E1211Q;ENSP00000381170:E1055Q ENSP00000369397:E1053Q E + 1 0 NHS 17655841 1.000000 0.71417 0.952000 0.39060 0.101000 0.19017 4.755000 0.62198 2.444000 0.82710 0.544000 0.68410 GAA TCGA-IB-A7M4-01A-11D-A36O-08 NHS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059120.1 0 0 0 13 357 0 107 0 2.013857e-02 0 6 0 107 2 0 0 0 0 0 2 1 0.999503 13 351 0 107 2 0 0 0 0 107 2 -3.717508 1 1 0 0 1 0 1 1 0.440000 1.980000 0.440000 0.070000 0.040000 0.130000 0.080000 0.085231 0.070000 0 0.050000 0.110000 FAM133A 286499 broad.mit.edu 37 X 92964973 92964973 + Silent SNP T T C TCGA-IB-A7M4-01A-11D-A36O-08 TCGA-IB-A7M4-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 69885b57-a521-4397-a1cc-a2580e98fda1 18d4d3f9-58cf-49c3-baa2-b4151bd1fa5a g.chrX:92964973T>C ENST00000355813.5 + 4 1081 c.555T>C c.(553-555)ccT>ccC p.P185P FAM133A_ENST00000538690.1_Silent_p.P185P|FAM133A_ENST00000322139.4_Silent_p.P185P|FAM133A_ENST00000332647.4_Silent_p.P185P NM_001171109.1|NM_173698.2 NP_001164580.1|NP_775969.1 Q8N9E0 F133A_HUMAN family with sequence similarity 133, member A 20 AAAGTTACCCTGATGATAAAC 0.368000 0 SO:0001819 synonymous_variant ENST00000355813.5 0 1 hg19 CCDS14466.1 TCGA-IB-A7M4-01A-11D-A36O-08 FAM133A-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057452.1 1 0 1 7 60 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 0.982577 7 60 0 16 2 0 0 0 0 16 2 -13.224930 1 1 0 0 1 0 1 1 0.440000 1.980000 0.440000 0.240000 0.110000 0.430000 0.230000 0.258568 0.240000 0 0.160000 0.340000