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 CDC73 79577 broad.mit.edu 37 1 193172923 193172949 + Splice_Site DEL AGGAGGGTGCATCTGCCCGGAAGACTC AGGAGGGTGCATCTGCCCGGAAGACTC - rs149875598 TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr1:193172923_193172949delAGGAGGGTGCATCTGCCCGGAAGACTC ENST00000367435.3 + 11 1156_1181 c.972_997delAGGAGGGTGCATCTGCCCGGAAGACTC c.(970-999)acaggagggtgcatctgcccggaagactca>acca p.GGCICPEDS325del NM_024529.4 NP_078805.3 Q6P1J9 CDC73_HUMAN cell division cycle 73 p.R330L(1)|p.R330R(1) 87 ATTCTTTTAAAGGAGGGTGCATCTGCCCGGAAGACTCAGACTCCTGC 0.352000 2 Substitution - Missense(1)|Substitution - coding silent(1) SO:0001630 splice_region_variant ENST00000367435.3 1 1 hg19 CCDS1382.1 TCGA-3E-AAAZ-01A-11D-A38G-08 CDC73-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086696.2 0 0 0 9 270 0 117 0 7.433416e-01 0 80 0 117 2 0 0 0 0 0 0 1 9.768436e-02 31 281 3 119 18 0 0 0 0 0 0 -3.142408 1 1 0 0 1 1 2 3 2.507409 1 0.380000 1.810000 0.478992 0.200000 0.090000 0.360000 0.210000 0.222017 0.200000 0 0.140000 0.290000 CDC20B 166979 broad.mit.edu 37 5 54423083 54423083 + Splice_Site DEL A A - TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr5:54423083delA ENST00000381375.2 - 8 1135 c.e8+1 CDC20B_ENST00000296733.1_Splice_Site|CDC20B_ENST00000334206.5_Splice_Site|CDC20B_ENST00000322374.6_Splice_Site Q86Y33 CD20B_HUMAN cell division cycle 20B 19 Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194) LUSC - Lung squamous cell carcinoma(15;0.225) GACGCTTCTTACCTGCTGAGG 0.383000 0 SO:0001630 splice_region_variant ENST00000381375.2 1 1 hg19 CCDS54852.1 TCGA-3E-AAAZ-01A-11D-A38G-08 CDC20B-004 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000369715.1 0 0 0 123 708 0 255 0 0 0 255 0 0 0 0 0 0 1 1 123 687 0 253 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.098585 0 0.380000 1.810000 0.384676 0.780000 0.650000 1.000000 0.780000 0.793991 0.780000 0 0.710000 0.860000 FRMD4A 55691 broad.mit.edu 37 10 13696478 13696478 + Silent SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr10:13696478C>T ENST00000357447.2 - 23 3356 c.2988G>A c.(2986-2988)ccG>ccA p.P996P FRMD4A_ENST00000378503.1_Silent_p.P996P|FRMD4A_ENST00000358621.4_Silent_p.P981P NM_018027.3 NP_060497.3 Q9P2Q2 FRM4A_HUMAN FERM domain containing 4A 41 TTTCACTTGACGGTGTCGAGC 0.547000 0 SO:0001819 synonymous_variant ENST00000357447.2 1 1 hg19 CCDS7101.1 TCGA-3E-AAAZ-01A-11D-A38G-08 FRMD4A-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000046889.1 0 0 0 7 226 1 80 0 1.286869e-01 0 18 1 80 2 0 0 0 0 0 2 0 2.187635e-01 7 221 1 80 11 0 0 0 1 80 2 -3.017760 1 1 121412 15 43 1 1 2 3 2.123923 0 0.380000 1.810000 0.388138 0.170000 0.070000 1.000000 0.160000 0.226029 0.170000 0 0.110000 0.260000 ATM 472 broad.mit.edu 37 11 108117798 108117798 + Missense_Mutation SNP C C T rs138398778 TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr11:108117798C>T ENST00000452508.2 + 9 1198 c.1009C>T c.(1009-1011)Cgt>Tgt p.R337C ATM_ENST00000278616.4_Missense_Mutation_p.R337C Q13315 ATM_HUMAN ATM serine/threonine kinase p.R337C(3)|p.R337S(2)|p.F336_A340del(1) 448 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Caffeine(DB00201) TTCAGGATTTCGTAATATTGC 0.323000 D, Mis, N, F, S T-PLL leukemia, lymphoma, medulloblastoma, glioma Genes defective in diseases associated with sensitivity to DNA damaging agents Ataxia Telangiectasia TSP Lung(14;0.12) yes Rec yes Ataxia-telangiectasia 11 11q22.3 472 ataxia telangiectasia mutated L, O 6 Substitution - Missense(5)|Deletion - In frame(1) SO:0001583 missense Familial Cancer Database AT, Louis-Bar syndrome ENST00000452508.2 1 1 hg19 CCDS31669.1 . . . . . . . . . . C 24.8 4.568847 0.86439 0.0 1.16E-4 ENSG00000149311 ENST00000527805;ENST00000278616;ENST00000452508 T;T;T 0.02369 4.32;4.62;4.62 5.72 5.72 0.89469 Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.15565 0.0375 M 0.68952 2.095 0.80722 D 1 D 0.89917 1.0 D 0.76575 0.988 T 0.00022 -1.2342 10 0.87932 D 0 . 19.8868 0.96915 0.0:1.0:0.0:0.0 . 337 Q13315 ATM_HUMAN C 337 ENSP00000435747:R337C;ENSP00000278616:R337C;ENSP00000388058:R337C ENSP00000278616:R337C R + 1 0 ATM 107623008 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 4.213000 0.58520 2.709000 0.92574 0.655000 0.94253 CGT TCGA-3E-AAAZ-01A-11D-A38G-08 ATM-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389938.1 1 0 1 58 279 0 97 0 3.507537e-01 0 7 0 97 2 1 1 30 175 0 203 2 1 1 57 272 0 96 2 0 0 0 0 97 2 -3.270775 1 1 121406 11 42 1 0 0 0 2.055980 0 0.380000 1.810000 0.375252 0.890000 0.690000 1.000000 1.000000 0.892887 0.890000 1 0.790000 1.000000 IGSF22 283284 broad.mit.edu 37 11 18738405 18738405 + Missense_Mutation SNP C C A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr11:18738405C>A ENST00000513874.1 - 10 1255 c.1116G>T c.(1114-1116)aaG>aaT p.K372N RP11-1081L13.4_ENST00000527285.1_RNA NM_173588.3 NP_775859 Q8N9C0 IGS22_HUMAN immunoglobulin superfamily, member 22 56 TGATTTCATACTTGTCATCCC 0.527000 0 SO:0001583 missense ENST00000513874.1 1 1 hg19 CCDS41625.2 . . . . . . . . . . C 19.21 3.783844 0.70222 . . ENSG00000179057 ENST00000513874 T 0.44083 0.93 4.94 -0.225 0.13111 . 0.000000 0.37857 U 0.001902 T 0.39091 0.1065 M 0.73319 2.225 0.27060 N 0.96358 P 0.40578 0.722 B 0.39738 0.308 T 0.34650 -0.9820 10 0.45353 T 0.12 . 9.8716 0.41177 0.0:0.6398:0.0:0.3602 . 372 D6RGV7 . N 372 ENSP00000421191:K372N ENSP00000322422:K372N K - 3 2 IGSF22 18694981 0.334000 0.24739 0.728000 0.30774 0.997000 0.91878 -0.495000 0.06443 0.050000 0.15949 0.655000 0.94253 AAG TCGA-3E-AAAZ-01A-11D-A38G-08 IGSF22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360850.2 1 0 1 148 579 0 242 0 0 0 0 242 2 0 0 0 0 0 2 1 1 147 571 0 238 2 0 0 0 0 242 2 -20.000000 1 1 0 0 1 0 0 0 2.063146 0 0.380000 1.810000 0.377635 0.990000 0.910000 1.000000 1.000000 0.992214 0.990000 1 0.980000 1.000000 OR5M3 219482 broad.mit.edu 37 11 56237502 56237502 + Missense_Mutation SNP T T C rs148100298 by1000genomes TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr11:56237502T>C ENST00000312240.2 - 1 512 c.472A>G c.(472-474)Aca>Gca p.T158A NM_001004742.2 NP_001004742.2 Q8NGP4 OR5M3_HUMAN olfactory receptor, family 5, subfamily M, member 3 p.T158A(1)|p.T158P(1) 37 Esophageal squamous(21;0.00448) GTCCATAATGTTGCTGCCAGA 0.428000 2 Substitution - Missense(2) SO:0001583 missense ENST00000312240.2 1 1 hg19 CCDS31532.1 . . . . . . . . . . T 12.21 1.870782 0.33069 . . ENSG00000174937 ENST00000312240 T 0.00256 8.42 5.22 4.07 0.47477 GPCR, rhodopsin-like superfamily (1); 0.000000 0.48767 D 0.000173 T 0.00412 0.0013 L 0.60904 1.88 0.09310 N 1 D 0.89917 1.0 D 0.91635 0.999 T 0.51411 -0.8709 10 0.48119 T 0.1 -6.2895 10.3656 0.44021 0.1471:0.0:0.0:0.8529 . 158 Q8NGP4 OR5M3_HUMAN A 158 ENSP00000312208:T158A ENSP00000312208:T158A T - 1 0 OR5M3 55994078 0.000000 0.05858 0.015000 0.15790 0.560000 0.35617 0.095000 0.15127 0.796000 0.33947 0.448000 0.29417 ACA TCGA-3E-AAAZ-01A-11D-A38G-08 OR5M3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391639.1 1 0 1 134 541 0 226 0 0 0 0 226 2 0 0 0 0 0 2 1 1 133 522 0 222 2 0 0 0 0 226 2 -2.941315 1 1 0 0 1 0 0 0 2.063146 0 0.380000 1.810000 0.377635 0.990000 0.880000 1.000000 1.000000 0.985164 0.990000 1 0.950000 1.000000 PRKRIR 5612 broad.mit.edu 37 11 76063580 76063580 + Missense_Mutation SNP A A G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr11:76063580A>G ENST00000260045.3 - 5 719 c.614T>C c.(613-615)cTg>cCg p.L205P PRKRIR_ENST00000531878.1_5'Flank NM_004705.2 NP_004696.2 O43422 P52K_HUMAN protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) 25 CCGACACTCCAGCAGTGCCTG 0.438000 0 SO:0001583 missense ENST00000260045.3 1 1 hg19 CCDS8243.1 . . . . . . . . . . A 18.40 3.615922 0.66672 . . ENSG00000137492 ENST00000529901;ENST00000260045 . . . 4.75 4.75 0.60458 . 0.061993 0.64402 D 0.000003 T 0.77452 0.4132 M 0.72894 2.215 0.80722 D 1 D 0.89917 1.0 D 0.79108 0.992 T 0.80759 -0.1239 9 0.87932 D 0 . 14.5953 0.68400 1.0:0.0:0.0:0.0 . 205 O43422 P52K_HUMAN P 30;205 . ENSP00000260045:L205P L - 2 0 PRKRIR 75741228 1.000000 0.71417 0.993000 0.49108 0.908000 0.53690 8.562000 0.90719 1.925000 0.55765 0.397000 0.26171 CTG TCGA-3E-AAAZ-01A-11D-A38G-08 PRKRIR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383188.1 1 0 1 68 264 0 123 1 9.993306e-01 14 31 0 123 2 0 0 0 0 0 2 1 1 67 253 0 127 2 0 0 0 0 123 2 -20.000000 1 1 0 0 1 0 0 0 2.055980 0 0.380000 1.810000 0.375252 0.990000 0.850000 1.000000 1.000000 0.982455 0.990000 1 0.950000 1.000000 ANAPC7 51434 broad.mit.edu 37 12 110815272 110815272 + Missense_Mutation SNP T T C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:110815272T>C ENST00000455511.3 - 9 1385 c.1385A>G c.(1384-1386)aAa>aGa p.K462R ANAPC7_ENST00000481473.1_5'UTR|ANAPC7_ENST00000450008.2_Missense_Mutation_p.K462R NM_016238.2 NP_057322.2 Q9UJX3 APC7_HUMAN anaphase promoting complex subunit 7 19 TAATAATGTTTTGGCTTTCTC 0.423000 0 SO:0001583 missense ENST00000455511.3 1 1 hg19 CCDS9145.2 . . . . . . . . . . T 25.4 4.634913 0.87760 . . ENSG00000196510 ENST00000455511;ENST00000481473;ENST00000486321;ENST00000450008;ENST00000471602 T;T 0.78126 -1.15;0.67 5.79 5.79 0.91817 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1); 0.000000 0.85682 D 0.000000 T 0.80752 0.4683 L 0.37800 1.135 0.58432 D 0.999998 D;P 0.56035 0.974;0.671 D;B 0.70487 0.969;0.202 T 0.75121 -0.3429 10 0.07482 T 0.82 -10.9948 16.1303 0.81428 0.0:0.0:0.0:1.0 . 462;462 Q9UJX3-2;Q9UJX3 .;APC7_HUMAN R 462;36;60;462;155 ENSP00000394394:K462R;ENSP00000402314:K462R ENSP00000402314:K462R K - 2 0 ANAPC7 109299655 1.000000 0.71417 0.999000 0.59377 0.995000 0.86356 7.698000 0.84413 2.218000 0.71995 0.533000 0.62120 AAA TCGA-3E-AAAZ-01A-11D-A38G-08 ANAPC7-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000347075.3 1 0 1 156 576 0 240 1 1 49 106 0 240 2 0 0 0 0 0 2 1 1 154 568 0 239 2 0 0 0 0 240 2 -20.000000 1 1 0 0 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.990000 0.930000 1.000000 1.000000 0.995523 0.990000 1 0.990000 1.000000 LHX5 64211 broad.mit.edu 37 12 113906184 113906184 + Missense_Mutation SNP C C G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:113906184C>G ENST00000261731.3 - 3 996 c.423G>C c.(421-423)ttG>ttC p.L141F NM_022363.2 NP_071758.1 Q9H2C1 LHX5_HUMAN LIM homeobox 5 10 GGTCCGGGGACAAACTGCGGT 0.642000 0 SO:0001583 missense ENST00000261731.3 1 1 hg19 CCDS9171.1 . . . . . . . . . . C 15.46 2.838936 0.51057 . . ENSG00000089116 ENST00000261731 D 0.91945 -2.94 4.85 2.98 0.34508 . 0.000000 0.43747 D 0.000537 D 0.89451 0.6719 L 0.59436 1.845 0.51767 D 0.999931 P 0.40332 0.713 B 0.44044 0.439 D 0.85201 0.1015 10 0.16896 T 0.51 . 9.9534 0.41653 0.0:0.7986:0.0:0.2014 . 141 Q9H2C1 LHX5_HUMAN F 141 ENSP00000261731:L141F ENSP00000261731:L141F L - 3 2 LHX5 112390567 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 1.206000 0.32321 2.213000 0.71641 0.491000 0.48974 TTG TCGA-3E-AAAZ-01A-11D-A38G-08 LHX5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404788.3 1 0 1 22 79 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 9.999993e-01 22 76 0 44 2 0 0 0 0 44 2 -20.000000 1 1 0 0 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.990000 0.740000 1.000000 1.000000 0.966564 0.990000 1 0.910000 1.000000 MLEC 9761 broad.mit.edu 37 12 121134267 121134267 + Silent SNP G G A rs144716658 TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:121134267G>A ENST00000228506.3 + 5 1226 c.798G>A c.(796-798)tcG>tcA p.S266S MLEC_ENST00000535413.1_3'UTR|RP11-173P15.3_ENST00000541383.1_RNA|MLEC_ENST00000412616.2_Missense_Mutation_p.R188Q|RP11-173P15.3_ENST00000535720.1_RNA NM_014730.2 NP_055545.1 Q14165 MLEC_HUMAN malectin 16 CCTATGCCTCGGACAACAGCA 0.502000 0 SO:0001819 synonymous_variant ENST00000228506.3 0 1 hg19 CCDS9206.1 . . . . . . . . . . G 11.21 1.572146 0.28092 2.27E-4 0.0 ENSG00000110917 ENST00000412616 . . . 5.43 -2.37 0.06643 . . . . . T 0.23926 0.0579 . . . 0.22156 N 0.999323 . . . . . . T 0.31668 -0.9935 5 0.45353 T 0.12 . 1.5104 0.02494 0.3009:0.0872:0.3554:0.2565 . . . . Q 188 . ENSP00000440746:R188Q R + 2 0 MLEC 119618650 0.974000 0.33945 0.996000 0.52242 0.982000 0.71751 0.103000 0.15292 -0.107000 0.12088 -1.008000 0.02478 CGG TCGA-3E-AAAZ-01A-11D-A38G-08 MLEC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402781.2 0 0 0 10 773 0 266 1 8.067091e-01 5 232 0 266 2 0 0 0 0 0 2 1 9.964880e-01 10 755 0 265 2 0 0 0 0 266 2 -1.807407 0 1 121412 2 40 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.060000 0.020000 0.120000 0.070000 0.071332 0.060000 0 0.040000 0.090000 DNAH10 196385 broad.mit.edu 37 12 124326011 124326011 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:124326011C>T ENST00000409039.3 + 29 4950 c.4925C>T c.(4924-4926)aCg>aTg p.T1642M NM_207437.3 NP_997320.2 Q8IVF4 DYH10_HUMAN dynein, axonemal, heavy chain 10 52 all_neural(191;0.101)|Medulloblastoma(191;0.163) GACTGGATGACGGCAGTTTTG 0.463000 0 SO:0001583 missense ENST00000409039.3 1 1 hg19 CCDS9255.2 . . . . . . . . . . C 14.89 2.671082 0.47781 0.0 3.61E-4 ENSG00000197653 ENST00000409039 T 0.61510 0.1 5.23 5.23 0.72850 Dynein heavy chain, domain-2 (1); 0.000000 0.64402 U 0.000001 T 0.77644 0.4161 M 0.81942 2.565 0.58432 D 0.999995 D 0.89917 1.0 D 0.75484 0.986 T 0.77550 -0.2546 10 0.39692 T 0.17 . 18.7853 0.91952 0.0:1.0:0.0:0.0 . 1642 Q8IVF4 DYH10_HUMAN M 1642 ENSP00000386770:T1642M ENSP00000386770:T1642M T + 2 0 DNAH10 122891964 1.000000 0.71417 0.945000 0.38365 0.206000 0.24218 4.564000 0.60830 2.457000 0.83068 0.561000 0.74099 ACG TCGA-3E-AAAZ-01A-11D-A38G-08 DNAH10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335420.3 1 0 1 75 346 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 1 72 337 0 138 2 0 0 0 0 138 2 -20.000000 1 1 120916 17 46 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.900000 0.720000 1.000000 1.000000 0.903182 0.900000 1 0.810000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-3E-AAAZ-01A-11D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 52 306 0 97 1 8.929242e-01 7 18 0 97 2 1 1 38 274 0 369 2 1 1 51 297 0 97 2 1 1 2010 6000 0 97 2 -19.999950 1 1 0 0 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.730000 0.560000 0.930000 0.740000 0.747354 0.730000 0 0.640000 0.840000 SLC16A7 9194 broad.mit.edu 37 12 60173406 60173406 + Silent SNP C C T rs3763979 byFrequency TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:60173406C>T ENST00000261187.4 + 5 1547 c.1383C>T c.(1381-1383)aaC>aaT p.N461N SLC16A7_ENST00000547379.1_Silent_p.N461N|SLC16A7_ENST00000552432.1_Silent_p.N461N|SLC16A7_ENST00000543448.1_Silent_p.N362N|SLC16A7_ENST00000552024.1_Silent_p.N461N NM_004731.4 NP_004722.2 O60669 MOT2_HUMAN solute carrier family 16 (monocarboxylate transporter), member 7 30 Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119) AAGATGTTAACGTCAAAGTTT 0.373000 0 SO:0001819 synonymous_variant ENST00000261187.4 1 0 hg19 CCDS8961.1 TCGA-3E-AAAZ-01A-11D-A38G-08 SLC16A7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406587.1 0 0 1 30 156 0 68 0 5.018894e-01 0 10 0 68 2 0 0 0 0 0 2 1 1 29 155 0 67 2 0 0 0 0 68 2 -1.741521 0 1 121356 10588 70 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.820000 0.570000 1.000000 1.000000 0.824857 0.820000 0 0.690000 0.960000 AVPR1A 552 broad.mit.edu 37 12 63543857 63543857 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr12:63543857G>A ENST00000299178.2 - 1 865 c.760C>T c.(760-762)Cgc>Tgc p.R254C NM_000706.4 NP_000697.1 P37288 V1AR_HUMAN arginine vasopressin receptor 1A p.R254C(1) 26 BRCA - Breast invasive adenocarcinoma(9;0.193) Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067) TTGCTCTGGCGCGACGCCGTC 0.617000 1 Substitution - Missense(1) SO:0001583 missense ENST00000299178.2 1 1 hg19 CCDS8965.1 . . . . . . . . . . G 12.38 1.921813 0.33908 . . ENSG00000166148 ENST00000550940;ENST00000299178 T;T 0.73469 -0.75;-0.75 5.29 1.6 0.23607 GPCR, rhodopsin-like superfamily (1); 0.000000 0.38959 N 0.001512 T 0.59115 0.2170 L 0.39514 1.22 0.21220 N 0.999759 B 0.19817 0.039 B 0.21546 0.035 T 0.40270 -0.9572 9 . . . -13.3074 5.8336 0.18594 0.1974:0.3561:0.4465:0.0 . 254 P37288 V1AR_HUMAN C 35;254 ENSP00000449822:R35C;ENSP00000299178:R254C . R - 1 0 AVPR1A 61830124 0.001000 0.12720 0.135000 0.22099 0.903000 0.53119 0.341000 0.19909 1.224000 0.43551 0.455000 0.32223 CGC TCGA-3E-AAAZ-01A-11D-A38G-08 AVPR1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406734.1 1 0 1 140 557 0 221 0 1.060643e-01 0 3 0 221 2 0 0 0 0 0 2 1 1 140 550 0 220 2 0 0 0 0 221 2 -20.000000 1 1 0 0 1 0 0 0 2.011306 0 0.380000 1.810000 0.360561 0.990000 0.870000 1.000000 1.000000 0.980840 0.990000 1 0.940000 1.000000 MYO16 23026 broad.mit.edu 37 13 109777647 109777647 + Silent SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr13:109777647C>T ENST00000357550.2 + 29 3698 c.3657C>T c.(3655-3657)aaC>aaT p.N1219N MYO16_ENST00000356711.2_Silent_p.N1219N|MYO16_ENST00000457511.2_Silent_p.N731N NM_001198950.1 NP_001185879.1 myosin XVI 121 all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104) BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201) GTGAAATGAACGCTCCCTACC 0.458000 0 SO:0001819 synonymous_variant ENST00000357550.2 1 1 hg19 CCDS32008.1 TCGA-3E-AAAZ-01A-11D-A38G-08 MYO16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045746.1 1 0 0 32 179 0 66 0 0 0 1 0 66 2 0 0 0 0 0 2 1 1 32 178 0 66 2 0 0 0 0 66 2 -20.000000 1 1 121412 3 35 1 0 0 0 2.029422 0 0.380000 1.810000 0.365534 0.770000 0.550000 1.000000 1.000000 0.786874 0.770000 0 0.650000 0.910000 BAHD1 22893 broad.mit.edu 37 15 40756141 40756141 + Missense_Mutation SNP C C G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr15:40756141C>G ENST00000416165.1 + 4 1968 c.1897C>G c.(1897-1899)Ctt>Gtt p.L633V BAHD1_ENST00000561234.1_Missense_Mutation_p.L632V|BAHD1_ENST00000560846.1_Missense_Mutation_p.L633V|RP11-64K12.8_ENST00000559730.1_RNA NM_014952.3 NP_055767.3 Q8TBE0 BAHD1_HUMAN bromo adjacent homology domain containing 1 28 all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GGACACCGTCCTTCTCAAATC 0.592000 0 SO:0001583 missense ENST00000416165.1 1 1 hg19 CCDS10058.1 . . . . . . . . . . C 27.9 4.871132 0.91587 . . ENSG00000140320 ENST00000416165 D 0.86865 -2.18 5.28 5.28 0.74379 Bromo adjacent homology (BAH) domain (3); 0.068049 0.64402 D 0.000012 D 0.92018 0.7471 L 0.55103 1.725 0.80722 D 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.87578 0.959;0.998;0.997 D 0.90870 0.4745 10 0.41790 T 0.15 -24.8954 19.0957 0.93249 0.0:1.0:0.0:0.0 . 633;633;632 Q8TBE0-3;Q8TBE0;Q8TBE0-2 .;BAHD1_HUMAN;. V 633 ENSP00000396976:L633V ENSP00000396976:L633V L + 1 0 BAHD1 38543433 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 5.606000 0.67641 2.755000 0.94549 0.655000 0.94253 CTT TCGA-3E-AAAZ-01A-11D-A38G-08 BAHD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252248.1 1 0 1 43 129 0 63 1 9.999708e-01 16 36 0 63 2 0 0 0 0 0 2 1 1 42 125 0 60 2 0 0 0 0 63 2 -20.000000 1 1 0 0 1 0 1 1 1.771745 1 0.380000 1.810000 0.276968 0.990000 0.830000 1.000000 1.000000 0.981676 0.990000 1 0.950000 1.000000 LINGO1 84894 broad.mit.edu 37 15 77906745 77906745 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr15:77906745C>T ENST00000355300.6 - 2 1678 c.1504G>A c.(1504-1506)Gcg>Acg p.A502T LINGO1_ENST00000561030.1_Missense_Mutation_p.A496T NM_032808.5 NP_116197.4 Q96FE5 LIGO1_HUMAN leucine rich repeat and Ig domain containing 1 31 TTGCCGCCCGCGTTGGCCGCG 0.637000 0 SO:0001583 missense ENST00000355300.6 1 1 hg19 CCDS45313.1 . . . . . . . . . . C 21.9 4.222208 0.79464 . . ENSG00000169783 ENST00000355300 T 0.67171 -0.25 5.08 5.08 0.68730 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.74230 0.3689 L 0.55743 1.74 0.80722 D 1 D 0.63046 0.992 P 0.57679 0.825 T 0.70303 -0.4909 10 0.22706 T 0.39 . 18.482 0.90815 0.0:1.0:0.0:0.0 . 502 Q96FE5 LIGO1_HUMAN T 502 ENSP00000347451:A502T ENSP00000347451:A502T A - 1 0 LINGO1 75693800 1.000000 0.71417 0.996000 0.52242 0.770000 0.43624 7.818000 0.86416 2.359000 0.80004 0.462000 0.41574 GCG TCGA-3E-AAAZ-01A-11D-A38G-08 LINGO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000419546.1 1 0 0 12 122 0 59 0 2.843508e-01 1 10 0 59 2 0 0 0 0 0 2 1 9.991887e-01 12 120 0 59 2 0 0 0 0 59 2 -18.262660 1 1 121040 1 20 1 0 1 1 1.771745 1 0.380000 1.810000 0.276968 0.400000 0.220000 0.640000 0.400000 0.423058 0.400000 0 0.300000 0.530000 HS3ST6 64711 broad.mit.edu 37 16 1962193 1962193 + Nonsense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr16:1962193G>A ENST00000293937.3 - 2 426 c.427C>T c.(427-429)Cga>Tga p.R143* HS3ST6_ENST00000454677.2_Nonsense_Mutation_p.R160*|HS3ST6_ENST00000443547.1_Nonsense_Mutation_p.R112* Q96QI5 HS3S6_HUMAN heparan sulfate (glucosamine) 3-O-sulfotransferase 6 4 TCCAGGGTTCGGGGCATCAGA 0.692000 0 SO:0001587 stop_gained ENST00000293937.3 0 1 hg19 . . . . . . . . . . G 13.70 2.316851 0.40996 2.28E-4 0.0 ENSG00000162040 ENST00000293937;ENST00000443547;ENST00000454677 . . . 4.91 4.91 0.64330 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 12.2723 0.54712 0.0:0.0:0.8304:0.1696 . . . . X 143;112;182 . ENSP00000293937:R143X R - 1 2 HS3ST6 1902194 0.990000 0.36364 0.651000 0.29564 0.066000 0.16364 2.443000 0.44881 2.287000 0.76781 0.555000 0.69702 CGA TCGA-3E-AAAZ-01A-11D-A38G-08 HS3ST6-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 1 16 57 0 27 0 0 1 0 0 27 2 0 0 0 0 0 2 1 9.999592e-01 16 55 0 27 2 0 0 0 0 27 2 -20.000000 1 1 112292 3 24 1 0 0 0 2.064610 0 0.380000 1.810000 0.377635 0.990000 0.710000 1.000000 1.000000 0.965184 0.990000 1 0.910000 1.000000 DNAH3 55567 broad.mit.edu 37 16 21049118 21049118 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr16:21049118C>T ENST00000261383.3 - 34 4914 c.4915G>A c.(4915-4917)Gcc>Acc p.A1639T DNAH3_ENST00000415178.1_Missense_Mutation_p.A1639T NM_017539.1 NP_060009.1 Q8TD57 DYH3_HUMAN dynein, axonemal, heavy chain 3 202 AAGAACTTGGCCAGATTGACA 0.498000 0 SO:0001583 missense ENST00000261383.3 0 1 hg19 CCDS10594.1 . . . . . . . . . . C 19.16 3.773845 0.69992 . . ENSG00000158486 ENST00000261383;ENST00000415178 T;T 0.39592 1.07;1.07 5.6 5.6 0.85130 . 0.127782 0.51477 D 0.000088 T 0.69566 0.3125 M 0.89214 3.015 0.80722 D 1 D 0.76494 0.999 P 0.61275 0.886 T 0.75795 -0.3192 10 0.87932 D 0 . 19.6229 0.95667 0.0:1.0:0.0:0.0 . 1639 Q8TD57 DYH3_HUMAN T 1639 ENSP00000261383:A1639T;ENSP00000394245:A1639T ENSP00000261383:A1639T A - 1 0 DNAH3 20956619 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.920000 0.56446 2.648000 0.89879 0.561000 0.74099 GCC TCGA-3E-AAAZ-01A-11D-A38G-08 DNAH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207361.1 0 0 0 4 169 1 62 0 0 0 1 62 2 0 0 0 0 0 2 1 8.899516e-01 4 168 0 61 2 0 0 0 1 62 2 -3.362364 1 1 0 0 1 0 0 0 2.064610 0 0.380000 1.810000 0.377635 0.130000 0.040000 0.290000 0.120000 0.148383 0.130000 0 0.070000 0.210000 ZNF688 146542 broad.mit.edu 37 16 30581656 30581656 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr16:30581656G>A ENST00000223459.6 - 3 1516 c.412C>T c.(412-414)Cgc>Tgc p.R138C ZNF688_ENST00000395219.1_Missense_Mutation_p.R124C|AC002310.7_ENST00000492040.1_RNA|AC002310.7_ENST00000486926.1_RNA NM_145271.3 NP_660314.1 P0C7X2 ZN688_HUMAN zinc finger protein 688 8 TCAGGGTTGCGTTCCACCAGC 0.607000 0 SO:0001583 missense ENST00000223459.6 1 1 hg19 CCDS10684.1 . . . . . . . . . . G 10.41 1.342937 0.24339 . . ENSG00000229809 ENST00000395219;ENST00000223459 T;T 0.04360 3.64;3.85 4.38 2.33 0.28932 . . . . . T 0.03477 0.0100 N 0.22421 0.69 0.09310 N 1 P;D 0.53151 0.696;0.958 B;B 0.38296 0.186;0.27 T 0.44498 -0.9324 9 0.51188 T 0.08 . 8.6385 0.33964 0.0939:0.1533:0.7528:0.0 . 138;124 P0C7X2;A8MV39 ZN688_HUMAN;. C 124;138 ENSP00000378645:R124C;ENSP00000223459:R138C ENSP00000223459:R138C R - 1 0 ZNF688 30489157 0.001000 0.12720 0.001000 0.08648 0.010000 0.07245 0.659000 0.24994 0.191000 0.20236 -1.151000 0.01829 CGC TCGA-3E-AAAZ-01A-11D-A38G-08 ZNF688-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255544.2 1 0 1 67 265 0 101 1 1 21 88 0 101 2 0 0 0 0 0 2 1 1 67 261 0 101 2 0 0 0 0 101 2 -20.000000 1 0 121412 7 39 1 0 0 0 2.064610 0 0.380000 1.810000 0.377635 0.990000 0.840000 1.000000 1.000000 0.979272 0.990000 1 0.940000 1.000000 CPNE2 221184 broad.mit.edu 37 16 57153169 57153169 + Nonsense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr16:57153169G>A ENST00000535318.2 + 7 931 c.570G>A c.(568-570)tgG>tgA p.W190* CPNE2_ENST00000290776.8_Nonsense_Mutation_p.W190*|CPNE2_ENST00000537605.1_Nonsense_Mutation_p.W88*|CPNE2_ENST00000565874.1_Nonsense_Mutation_p.W190* Q96FN4 CPNE2_HUMAN copine II 21 all_neural(199;0.224) ATGGCAAGTGGATGCTGGTCC 0.582000 0 SO:0001587 stop_gained ENST00000535318.2 0 1 hg19 CCDS10774.1 . . . . . . . . . . G 43 10.004895 0.99315 . . ENSG00000140848 ENST00000290776;ENST00000537605;ENST00000535318 . . . 5.5 5.5 0.81552 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -14.2675 19.397 0.94611 0.0:0.0:1.0:0.0 . . . . X 190;88;190 . ENSP00000290776:W190X W + 3 0 CPNE2 55710670 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.845000 0.99498 2.594000 0.87642 0.555000 0.69702 TGG TCGA-3E-AAAZ-01A-11D-A38G-08 CPNE2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432986.2 1 0 1 77 391 0 152 0 9.996848e-01 1 61 0 152 2 0 0 0 0 0 2 1 1 75 380 0 151 2 0 0 0 0 152 2 -20.000000 1 1 0 0 1 0 0 0 2.064610 0 0.380000 1.810000 0.377635 0.850000 0.690000 1.000000 1.000000 0.863851 0.850000 1 0.770000 0.950000 ZNF821 55565 broad.mit.edu 37 16 71894200 71894200 + Silent SNP C C A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr16:71894200C>A ENST00000565601.1 - 7 1367 c.960G>T c.(958-960)ctG>ctT p.L320L ZNF821_ENST00000446827.2_Silent_p.L278L|ZNF821_ENST00000564134.1_3'UTR|ZNF821_ENST00000425432.1_Silent_p.L320L|ZNF821_ENST00000313565.6_Silent_p.L278L|ATXN1L_ENST00000569119.1_Intron NM_001201553.1 NP_001188482.1 O75541 ZN821_HUMAN zinc finger protein 821 13 GATCCCGCTGCAGCCGGCGTG 0.672000 0 SO:0001819 synonymous_variant ENST00000565601.1 0 1 hg19 CCDS56006.1 TCGA-3E-AAAZ-01A-11D-A38G-08 ZNF821-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000434180.1 0 0 0 5 185 0 75 0 3.071684e-01 0 36 0 75 2 0 0 0 0 0 2 1 9.357407e-01 5 182 0 74 2 0 0 0 0 75 2 -7.228993 1 0 0 0 1 1 2 3 2.079998 0 0.380000 1.810000 0.384676 0.150000 0.050000 1.000000 0.140000 0.188390 0.150000 0 0.090000 0.240000 CHMP1A 5119 broad.mit.edu 37 16 89718035 89718035 + Missense_Mutation SNP T T C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 T C T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr16:89718035T>C ENST00000397901.3 - 3 303 c.47A>G c.(46-48)gAg>gGg p.E16G CHMP1A_ENST00000535997.2_5'UTR|CHMP1A_ENST00000550102.1_Missense_Mutation_p.E16G|CHMP1A_ENST00000253475.5_Silent_p.G9G|CHMP1A_ENST00000547614.1_5'UTR NM_002768.3 NP_002759.2 Q9HD42 CHM1A_HUMAN charged multivesicular body protein 1A 3 all_lung(18;3.07e-05)|all_hematologic(23;0.0256) GGCCAGCTTCTCCAGCTGCTT 0.632000 0 SO:0001583 missense ENST00000397901.3 0 1 hg19 CCDS45552.1 . . . . . . . . . . T 18.38 3.611348 0.66558 . . ENSG00000131165 ENST00000397901;ENST00000550102 T;T 0.74106 -0.81;-0.81 4.81 4.81 0.61882 . . . . . T 0.70202 0.3197 . . . 0.80722 D 1 P 0.38300 0.626 B 0.40782 0.34 T 0.69101 -0.5234 7 . . . -1.7391 14.6528 0.68811 0.0:0.0:0.0:1.0 . 16 Q9HD42 CHM1A_HUMAN G 16 ENSP00000380998:E16G;ENSP00000449243:E16G . E - 2 0 CHMP1A 88245536 1.000000 0.71417 1.000000 0.80357 0.901000 0.52897 7.600000 0.82769 1.905000 0.55150 0.533000 0.62120 GAG TCGA-3E-AAAZ-01A-11D-A38G-08 CHMP1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404581.1 0 0 0 5 157 0 55 0 9.970741e-01 0 399 0 55 2 0 0 0 0 0 2 1 9.343588e-01 4 154 0 54 2 0 0 0 0 55 2 -7.528092 1 0 0 0 1 0 1 1 2.068558 0 0.380000 1.810000 0.378820 0.170000 0.060000 0.350000 0.160000 0.190255 0.170000 0 0.110000 0.260000 COASY 80347 broad.mit.edu 37 17 40714982 40714982 + Silent SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr17:40714982G>A ENST00000393818.2 + 1 798 c.342G>A c.(340-342)gtG>gtA p.V114V COASY_ENST00000420359.1_Silent_p.V114V|RP11-400F19.8_ENST00000585572.1_RNA|COASY_ENST00000590958.1_Silent_p.V143V|COASY_ENST00000449624.1_De_novo_Start_InFrame|COASY_ENST00000421097.2_Silent_p.V114V NM_025233.6 NP_079509.5 Q13057 COASY_HUMAN CoA synthase 21 all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344) CAGAAGTCGTGTTGACAGATT 0.562000 0 SO:0001819 synonymous_variant ENST00000393818.2 1 0 hg19 CCDS11429.1 . . . . . . . . . . G 10.94 1.491978 0.26774 . . ENSG00000068120 ENST00000426807 . . . 5.57 -0.966 0.10320 . 0.000000 0.85682 D 0.000000 T 0.53126 0.1777 . . . 0.80722 D 1 . . . . . . T 0.51220 -0.8733 6 0.87932 D 0 -22.1199 1.666 0.02802 0.1574:0.2286:0.3692:0.2448 . . . . I 90 . ENSP00000390306:V90I V + 1 0 COASY 37968508 0.995000 0.38212 0.998000 0.56505 0.922000 0.55478 0.457000 0.21875 0.008000 0.14787 -0.305000 0.09177 GTT TCGA-3E-AAAZ-01A-11D-A38G-08 COASY-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450409.1 1 0 1 91 927 0 293 1 9.998678e-01 12 117 0 293 2 0 0 0 0 0 2 1 1 91 900 0 292 2 0 0 0 0 293 2 -19.997890 1 1 0 0 1 0 1 1 2.074202 0 0.380000 1.810000 0.378820 0.460000 0.370000 0.560000 0.470000 0.473052 0.460000 0 0.420000 0.520000 C17orf53 78995 broad.mit.edu 37 17 42225373 42225373 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr17:42225373C>T ENST00000319977.4 + 3 439 c.202C>T c.(202-204)Ccc>Tcc p.P68S C17orf53_ENST00000585683.1_Missense_Mutation_p.P68S|C17orf53_ENST00000245382.6_Missense_Mutation_p.P68S NM_001171251.1|NM_024032.3 NP_001164722.1|NP_076937.2 Q8N3J3 CQ053_HUMAN chromosome 17 open reading frame 53 22 Breast(137;0.0364)|Prostate(33;0.0376) CCCCACTGCTCCCTCAGAGGC 0.622000 0 SO:0001583 missense ENST00000319977.4 1 1 hg19 CCDS11477.1 . . . . . . . . . . C 11.32 1.604612 0.28623 . . ENSG00000125319 ENST00000319977;ENST00000245382;ENST00000253405 T;T 0.49139 0.79;0.79 5.28 2.2 0.27929 . 0.378727 0.22038 N 0.065500 T 0.38558 0.1045 L 0.55481 1.735 0.09310 N 1 B;B;B 0.29646 0.084;0.253;0.084 B;B;B 0.29663 0.022;0.105;0.022 T 0.30297 -0.9983 10 0.51188 T 0.08 -0.8579 6.2724 0.20961 0.0:0.6818:0.1524:0.1659 . 68;68;68 A8K7A9;Q8N3J3-3;Q8N3J3 .;.;CQ053_HUMAN S 68 ENSP00000313500:P68S;ENSP00000245382:P68S ENSP00000245382:P68S P + 1 0 C17orf53 39580899 0.001000 0.12720 0.001000 0.08648 0.044000 0.14063 0.181000 0.16880 0.362000 0.24319 0.561000 0.74099 CCC TCGA-3E-AAAZ-01A-11D-A38G-08 C17orf53-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000457697.1 1 0 1 85 336 0 135 1 1.866122e-01 3 1 0 135 2 0 0 0 0 0 2 1 1 81 326 0 134 2 0 0 0 0 135 2 -3.497239 1 1 0 0 1 0 1 1 2.074202 0 0.380000 1.810000 0.378820 0.990000 0.860000 1.000000 1.000000 0.983862 0.990000 1 0.950000 1.000000 RNF43 54894 broad.mit.edu 37 17 56440904 56440904 + Nonsense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr17:56440904G>A ENST00000584437.1 - 3 2388 c.433C>T c.(433-435)Cga>Tga p.R145* RNF43_ENST00000407977.2_Nonsense_Mutation_p.R145*|RNF43_ENST00000583753.1_Nonsense_Mutation_p.R104*|RNF43_ENST00000500597.2_Nonsense_Mutation_p.R104*|RNF43_ENST00000581868.1_Nonsense_Mutation_p.R18*|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Nonsense_Mutation_p.R145*|RNF43_ENST00000577625.1_Nonsense_Mutation_p.R18* Q68DV7 RNF43_HUMAN ring finger protein 43 p.R145*(1) 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) GCAGCAGCTCGATCCTCAGTG 0.597000 1 Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000584437.1 0 1 hg19 CCDS11607.1 . . . . . . . . . . G 44 10.601706 0.99435 . . ENSG00000108375 ENST00000407977;ENST00000500597 . . . 5.4 4.41 0.53225 . 0.592346 0.16161 N 0.226756 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.07813 T 0.8 -19.4207 8.5535 0.33467 0.0:0.1579:0.5559:0.2861 . . . . X 145;104 . ENSP00000385328:R145X R - 1 2 RNF43 53795903 0.980000 0.34600 0.994000 0.49952 0.991000 0.79684 2.127000 0.42035 1.234000 0.43709 0.591000 0.81541 CGA TCGA-3E-AAAZ-01A-11D-A38G-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 138 546 0 235 1 9.976352e-01 16 22 0 235 2 1 1 167 630 0 765 2 1 1 137 526 0 232 2 0 0 0 0 235 2 -3.432944 1 1 0 0 1 1 2 3 2.079788 0 0.380000 1.810000 0.381176 0.990000 0.900000 1.000000 1.000000 0.990858 0.990000 1 0.980000 1.000000 SLC16A13 201232 broad.mit.edu 37 17 6941599 6941599 + Missense_Mutation SNP T T C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr17:6941599T>C ENST00000308027.6 + 3 780 c.472T>C c.(472-474)Ttt>Ctt p.F158L NM_201566.2 NP_963860.1 Q7RTY0 MOT13_HUMAN solute carrier family 16, member 13 p.F158L(1) 10 ATTTGCCCCCTTTTTCCAGTG 0.652000 1 Substitution - Missense(1) SO:0001583 missense ENST00000308027.6 0 1 hg19 CCDS11085.1 . . . . . . . . . . T 4.647 0.120233 0.08881 . . ENSG00000174327 ENST00000308027 T 0.48522 0.81 5.54 -1.46 0.08800 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.192516 0.46442 N 0.000288 T 0.13713 0.0332 N 0.01202 -0.96 0.09310 N 0.999999 B 0.02656 0.0 B 0.04013 0.001 T 0.38001 -0.9681 10 0.02654 T 1 . 10.4076 0.44274 0.0:0.5248:0.0:0.4752 . 158 Q7RTY0 MOT13_HUMAN L 158 ENSP00000309751:F158L ENSP00000309751:F158L F + 1 0 SLC16A13 6882323 0.479000 0.25925 0.535000 0.28026 0.981000 0.71138 1.161000 0.31773 -0.053000 0.13289 -0.313000 0.08912 TTT TCGA-3E-AAAZ-01A-11D-A38G-08 SLC16A13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219923.2 0 0 0 4 280 0 90 0 5.137871e-03 0 6 0 90 2 0 0 0 0 0 2 1 8.876849e-01 4 276 0 83 2 0 0 0 0 90 2 -2.766372 1 1 0 0 1 0 1 1 2.074202 0 0.380000 1.810000 0.378820 0.080000 0.020000 0.180000 0.080000 0.091290 0.080000 0 0.040000 0.130000 SMAD2 4087 broad.mit.edu 37 18 45368211 45368211 + Nonsense_Mutation SNP G G C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr18:45368211G>C ENST00000402690.2 - 11 1785 c.1391C>G c.(1390-1392)tCa>tGa p.S464* SMAD2_ENST00000586040.1_Nonsense_Mutation_p.S434*|SMAD2_ENST00000356825.4_Nonsense_Mutation_p.S434*|SMAD2_ENST00000262160.6_Nonsense_Mutation_p.S464* NM_001003652.3 NP_001003652.1 Q15796 SMAD2_HUMAN SMAD family member 2 p.S464*(4)|p.R462fs*>4(1) 43 TGACATGCTTGAGCAACGCAC 0.423000 5 Substitution - Nonsense(4)|Deletion - Frameshift(1) SO:0001587 stop_gained ENST00000402690.2 0 1 hg19 CCDS11934.1 . . . . . . . . . . G 41 8.723736 0.98929 . . ENSG00000175387 ENST00000262160;ENST00000356825;ENST00000402690 . . . 5.65 5.65 0.86999 . 0.000000 0.85682 D 0.000000 . . . . . . 0.58432 D 0.999998 . . . . . . . . . . 0.87932 D 0 . 20.0965 0.97849 0.0:0.0:1.0:0.0 . . . . X 464;434;464 . ENSP00000262160:S464X S - 2 0 SMAD2 43622209 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.781000 0.99029 2.824000 0.97209 0.655000 0.94253 TCA TCGA-3E-AAAZ-01A-11D-A38G-08 SMAD2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450571.1 1 0 0 45 182 0 105 1 1 43 111 0 105 2 0 0 0 0 0 2 1 1 45 176 0 105 2 0 0 0 0 105 2 -20.000000 1 1 0 0 1 0 1 1 1.716701 1 0.380000 1.810000 0.234568 0.820000 0.620000 0.980000 0.830000 0.824882 0.820000 0 0.720000 0.920000 SMAD4 4089 broad.mit.edu 37 18 48591889 48591889 + Missense_Mutation SNP A A C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 A C A A Valid Somatic Phase_I WXS targeted Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr18:48591889A>C ENST00000342988.3 + 9 1590 c.1052A>C c.(1051-1053)gAt>gCt p.D351A SMAD4_ENST00000588745.1_Missense_Mutation_p.D255A|SMAD4_ENST00000398417.2_Missense_Mutation_p.D351A NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) GTTACTGTTGATGGATACGTG 0.438000 38 Whole gene deletion(36)|Unknown(2) SO:0001583 missense ENST00000342988.3 1 1 hg19 CCDS11950.1 . . . . . . . . . . A 28.7 4.942647 0.92526 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 D;D 0.98437 -4.93;-4.93 5.86 5.86 0.93980 SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3); 0.044633 0.85682 D 0.000000 D 0.99239 0.9735 H 0.94886 3.595 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.99069 1.0833 10 0.87932 D 0 . 15.2431 0.73485 1.0:0.0:0.0:0.0 . 351 Q13485 SMAD4_HUMAN A 351 ENSP00000341551:D351A;ENSP00000381452:D351A ENSP00000341551:D351A D + 2 0 SMAD4 46845887 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.159000 0.94728 2.237000 0.73441 0.460000 0.39030 GAT TCGA-3E-AAAZ-01A-11D-A38G-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 80 274 0 166 1 1 44 67 0 166 2 1 1 130 480 0 858 2 1 1 79 271 0 165 2 0 0 0 0 166 2 -20.000000 1 1 0 0 1 0 1 1 1.716701 1 0.380000 1.810000 0.234568 0.910000 0.760000 1.000000 0.950000 0.911478 0.910000 1 0.840000 0.980000 NUDT19 390916 broad.mit.edu 37 19 33183406 33183406 + Silent SNP G G C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr19:33183406G>C ENST00000397061.3 + 1 540 c.540G>C c.(538-540)cgG>cgC p.R180R CTD-2538C1.2_ENST00000592431.1_lincRNA NM_001105570.1 NP_001099040.1 A8MXV4 NUD19_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 19 8 Esophageal squamous(110;0.137) ACTTCCTGCGGCTGTGCGCCC 0.731000 0 SO:0001819 synonymous_variant ENST00000397061.3 1 1 hg19 CCDS42543.1 TCGA-3E-AAAZ-01A-11D-A38G-08 NUDT19-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000450338.3 1 0 0 14 42 0 14 1 8.313841e-01 4 8 0 14 2 0 0 0 0 0 2 1 9.996433e-01 11 37 0 12 2 0 0 0 0 14 2 -20.000000 1 1 0 0 1 0 0 0 1.992977 0 0.380000 1.810000 0.352953 0.990000 0.750000 1.000000 1.000000 0.977213 0.990000 1 0.970000 1.000000 ZNF382 84911 broad.mit.edu 37 19 37118421 37118421 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr19:37118421C>T ENST00000292928.2 + 5 1735 c.1622C>T c.(1621-1623)aCt>aTt p.T541I ZNF382_ENST00000439428.1_Missense_Mutation_p.T540I|ZNF382_ENST00000435416.1_Missense_Mutation_p.T540I|CTD-3234P18.2_ENST00000585467.1_lincRNA|ZNF382_ENST00000423582.1_Missense_Mutation_p.T492I NM_001256838.1|NM_032825.4 NP_001243767.1|NP_116214.2 Q96SR6 ZN382_HUMAN zinc finger protein 382 34 Esophageal squamous(110;0.198) COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065) CATCAGAAAACTCACAAGGTA 0.383000 0 SO:0001583 missense ENST00000292928.2 1 1 hg19 CCDS33004.1 . . . . . . . . . . C 0.024 -1.392618 0.01185 . . ENSG00000161298 ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416 T;T;T;T 0.06687 3.27;3.38;3.39;3.4 4.35 2.24 0.28232 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.155759 0.30277 N 0.009982 T 0.02380 0.0073 N 0.02802 -0.49 0.29661 N 0.843215 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.001;0.001;0.001 T 0.40997 -0.9533 10 0.07813 T 0.8 . 4.1521 0.10242 0.0:0.5955:0.1948:0.2097 . 540;540;541 Q96SR6-2;Q96SR6-3;Q96SR6 .;.;ZN382_HUMAN I 492;541;540;540 ENSP00000389722:T492I;ENSP00000292928:T541I;ENSP00000407593:T540I;ENSP00000410113:T540I ENSP00000292928:T541I T + 2 0 ZNF382 41810261 0.000000 0.05858 1.000000 0.80357 0.995000 0.86356 -0.905000 0.04075 1.192000 0.43071 0.591000 0.81541 ACT TCGA-3E-AAAZ-01A-11D-A38G-08 ZNF382-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000109562.2 1 0 1 44 286 0 113 0 1.850031e-02 0 2 0 113 2 0 0 0 0 0 2 1 1 42 281 0 113 2 0 0 0 0 113 2 -20.000000 1 1 0 0 1 0 0 0 1.992977 0 0.380000 1.810000 0.352953 0.660000 0.500000 0.860000 0.670000 0.679741 0.660000 0 0.580000 0.770000 ZNF585B 92285 broad.mit.edu 37 19 37676154 37676154 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr19:37676154C>T ENST00000532828.2 - 5 2536 c.2285G>A c.(2284-2286)aGt>aAt p.S762N ZNF585B_ENST00000531805.1_Missense_Mutation_p.S707N|ZNF585B_ENST00000312908.5_Missense_Mutation_p.S350N|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR NM_152279.3 NP_689492.3 Q52M93 Z585B_HUMAN zinc finger protein 585B 29 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) CTGATGAACACTGAACACTGA 0.463000 Melanoma(93;882 1454 18863 28917 48427) 0 SO:0001583 missense ENST00000532828.2 1 1 hg19 CCDS12500.1 . . . . . . . . . . C 5.066 0.197903 0.09652 . . ENSG00000245680 ENST00000531805;ENST00000532828;ENST00000312908 T;T;T 0.15718 2.4;2.4;2.4 2.72 -0.663 0.11410 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.836945 0.10095 N 0.716705 T 0.08492 0.0211 N 0.16233 0.39 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.37709 -0.9694 10 0.27082 T 0.32 . 4.5817 0.12262 0.0:0.4379:0.331:0.231 . 707;762 E9PQH3;Q52M93 .;Z585B_HUMAN N 707;762;350 ENSP00000436774:S707N;ENSP00000433773:S762N;ENSP00000442139:S350N ENSP00000442139:S350N S - 2 0 ZNF585B 42367994 0.000000 0.05858 0.093000 0.20910 0.199000 0.23934 -2.835000 0.00741 0.221000 0.20879 0.305000 0.20034 AGT TCGA-3E-AAAZ-01A-11D-A38G-08 ZNF585B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388272.2 1 0 1 119 498 0 195 0 7.813651e-01 1 13 0 195 2 0 0 0 0 0 2 1 1 115 489 0 192 2 0 0 0 0 195 2 -20.000000 1 1 0 0 1 0 0 0 1.992977 0 0.380000 1.810000 0.352953 0.960000 0.810000 1.000000 1.000000 0.953679 0.960000 1 0.880000 1.000000 RSPH6A 81492 broad.mit.edu 37 19 46307696 46307696 + Silent SNP C C T rs146411467 TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr19:46307696C>T ENST00000221538.3 - 3 1609 c.1467G>A c.(1465-1467)tcG>tcA p.S489S RSPH6A_ENST00000600188.1_Silent_p.S225S|RSPH6A_ENST00000597055.1_Silent_p.S489S NM_030785.3 NP_110412.1 Q9H0K4 RSH6A_HUMAN radial spoke head 6 homolog A (Chlamydomonas) 32 GCGTGGCGGCCGAGATGCGGG 0.642000 0 SO:0001819 synonymous_variant ENST00000221538.3 1 1 hg19 CCDS12675.1 TCGA-3E-AAAZ-01A-11D-A38G-08 RSPH6A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461657.1 1 0 0 12 239 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 9.990030e-01 12 232 0 78 2 0 0 0 0 78 2 -3.161500 1 1 121410 11 40 1 0 0 0 2.053708 0 0.380000 1.810000 0.375252 0.250000 0.130000 0.410000 0.250000 0.266610 0.250000 0 0.180000 0.330000 SAE1 10055 broad.mit.edu 37 19 47646755 47646755 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr19:47646755C>T ENST00000270225.7 + 2 171 c.103C>T c.(103-105)Cgg>Tgg p.R35W SAE1_ENST00000413379.3_Missense_Mutation_p.R35W|SAE1_ENST00000540850.1_5'UTR|SAE1_ENST00000392776.3_Missense_Mutation_p.R35W|SAE1_ENST00000598840.1_Missense_Mutation_p.R35W NM_005500.2 NP_005491.1 Q9UBE0 SAE1_HUMAN SUMO1 activating enzyme subunit 1 p.R35W(2) 13 all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15) TTACAGGCTGCGGGCCTCTCG 0.458000 2 Substitution - Missense(2) SO:0001583 missense ENST00000270225.7 0 1 hg19 CCDS12696.1 . . . . . . . . . . C 20.8 4.049237 0.75846 . . ENSG00000142230 ENST00000413379;ENST00000270225;ENST00000392776;ENST00000414294 T;T;T;T 0.66815 -0.23;-0.23;-0.23;-0.23 5.85 4.81 0.61882 UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.83275 0.5219 M 0.85777 2.775 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.997;0.999 D 0.86378 0.1727 10 0.72032 D 0.01 . 15.35 0.74376 0.1409:0.8591:0.0:0.0 . 35;35;35 G3XAK6;F5GXX7;Q9UBE0 .;.;SAE1_HUMAN W 35 ENSP00000416557:R35W;ENSP00000270225:R35W;ENSP00000440818:R35W;ENSP00000398818:R35W ENSP00000270225:R35W R + 1 2 SAE1 52338595 1.000000 0.71417 1.000000 0.80357 0.938000 0.57974 4.111000 0.57838 1.471000 0.48121 -0.175000 0.13238 CGG TCGA-3E-AAAZ-01A-11D-A38G-08 SAE1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466775.1 0 0 0 6 281 0 92 0 9.614088e-01 0 277 0 92 2 0 0 0 0 0 2 1 9.630720e-01 6 275 0 91 2 0 0 0 0 92 2 -2.386746 0 1 0 0 1 0 0 0 2.053708 0 0.380000 1.810000 0.375252 0.110000 0.040000 0.220000 0.110000 0.125783 0.110000 0 0.070000 0.170000 NLRP2 55655 broad.mit.edu 37 19 55494938 55494938 + Silent SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr19:55494938G>A ENST00000543010.1 + 6 2015 c.1872G>A c.(1870-1872)caG>caA p.Q624Q NLRP2_ENST00000448584.2_Silent_p.Q624Q|NLRP2_ENST00000263437.6_Silent_p.Q621Q|NLRP2_ENST00000339757.7_Silent_p.Q602Q|NLRP2_ENST00000537859.1_Silent_p.Q602Q|NLRP2_ENST00000538819.1_Silent_p.Q600Q|NLRP2_ENST00000427260.2_Silent_p.Q601Q|NLRP2_ENST00000391721.4_Silent_p.Q600Q NM_001174081.1 NP_001167552.1 Q9NX02 NALP2_HUMAN NLR family, pyrin domain containing 2 11 BRCA - Breast invasive adenocarcinoma(297;0.163) TGATGGCTCAGTTCAAAGAAA 0.502000 0 SO:0001819 synonymous_variant ENST00000543010.1 1 1 hg19 CCDS12913.1 TCGA-3E-AAAZ-01A-11D-A38G-08 NLRP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396152.1 1 0 1 39 139 0 57 1 9.999873e-01 59 7 0 57 2 0 0 0 0 0 2 1 1 39 134 0 57 2 0 0 0 0 57 2 -20.000000 1 1 0 0 1 1 2 3 2.083946 0 0.380000 1.810000 0.381176 0.990000 0.850000 1.000000 1.000000 0.987862 0.990000 1 0.990000 1.000000 CDC73 79577 broad.mit.edu 37 1 193111023 193111023 + Missense_Mutation SNP A A G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr1:193111023A>G ENST00000367435.3 + 7 740 c.556A>G c.(556-558)Aaa>Gaa p.K186E NM_024529.4 NP_078805.3 Q6P1J9 CDC73_HUMAN cell division cycle 73 87 TGCTGCAATCAAAGCCAAAAT 0.363000 0 SO:0001583 missense ENST00000367435.3 1 1 hg19 CCDS1382.1 . . . . . . . . . . A 28.4 4.913112 0.92178 . . ENSG00000134371 ENST00000367435;ENST00000445394 D 0.89617 -2.54 6.03 6.03 0.97812 . 0.000000 0.85682 D 0.000000 D 0.94009 0.8081 M 0.78916 2.43 0.80722 D 1 D 0.76494 0.999 D 0.66497 0.944 D 0.94174 0.7426 10 0.56958 D 0.05 -23.6629 16.5582 0.84512 1.0:0.0:0.0:0.0 . 186 Q6P1J9 CDC73_HUMAN E 186 ENSP00000356405:K186E ENSP00000356405:K186E K + 1 0 CDC73 191377646 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.109000 0.94291 2.308000 0.77769 0.533000 0.62120 AAA TCGA-3E-AAAZ-01A-11D-A38G-08 CDC73-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086696.2 1 0 1 35 205 0 76 1 9.404518e-01 8 22 0 76 2 0 0 0 0 0 2 1 1 35 204 0 76 2 0 0 0 0 76 2 -20.000000 1 1 0 0 1 1 2 3 2.507409 1 0.380000 1.810000 0.478992 0.910000 0.650000 1.000000 1.000000 0.898593 0.910000 1 0.770000 1.000000 NUAK2 81788 broad.mit.edu 37 1 205273036 205273036 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr1:205273036C>T ENST00000367157.3 - 7 1555 c.1429G>A c.(1429-1431)Gtg>Atg p.V477M NM_030952.1 NP_112214.1 NUAK family, SNF1-like kinase, 2 23 Breast(84;0.186) BRCA - Breast invasive adenocarcinoma(75;0.117) CTCACAAACACGTCGCCTGCG 0.587000 0 SO:0001583 missense ENST00000367157.3 1 1 hg19 CCDS1453.1 . . . . . . . . . . C 11.20 1.567476 0.28003 . . ENSG00000163545 ENST00000367157 T 0.72282 -0.64 4.86 4.86 0.63082 . 0.000000 0.40640 N 0.001045 T 0.69187 0.3083 L 0.60455 1.87 0.28049 N 0.933438 D 0.64830 0.994 P 0.52159 0.691 T 0.65911 -0.6053 10 0.37606 T 0.19 . 4.1079 0.10045 0.1634:0.5906:0.158:0.088 . 477 Q9H093 NUAK2_HUMAN M 477 ENSP00000356125:V477M ENSP00000356125:V477M V - 1 0 NUAK2 203539659 0.846000 0.29590 0.989000 0.46669 0.173000 0.22820 1.357000 0.34090 2.234000 0.73211 0.407000 0.27541 GTG TCGA-3E-AAAZ-01A-11D-A38G-08 NUAK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090390.1 1 0 1 21 181 0 61 0 3.351851e-01 1 10 0 61 2 0 0 0 0 0 2 1 9.999980e-01 21 178 0 61 2 0 0 0 0 61 2 -9.895783 1 1 121412 6 39 1 1 3 4 2.522300 1 0.380000 1.810000 0.487179 0.720000 0.440000 1.000000 0.660000 0.757985 0.720000 0 0.560000 1.000000 URB2 9816 broad.mit.edu 37 1 229763503 229763503 + Silent SNP A A G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr1:229763503A>G ENST00000258243.2 + 2 259 c.123A>G c.(121-123)gaA>gaG p.E41E TAF5L_ENST00000477957.1_5'Flank|TAF5L_ENST00000258281.2_5'Flank|TAF5L_ENST00000366675.3_5'Flank|TAF5L_ENST00000366674.1_5'Flank NM_014777.2 NP_055592.2 Q14146 URB2_HUMAN URB2 ribosome biogenesis 2 homolog (S. cerevisiae) 73 CAAATAAAGAACAAGTAAGTT 0.294000 0 SO:0001819 synonymous_variant ENST00000258243.2 0 1 hg19 CCDS31052.1 TCGA-3E-AAAZ-01A-11D-A38G-08 URB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095232.1 0 0 0 8 512 0 148 0 1.076311e-02 1 8 0 148 2 0 0 0 0 0 2 1 9.884167e-01 9 499 0 148 2 0 0 0 0 148 2 -2.931921 1 1 0 0 1 1 3 4 2.522300 1 0.380000 1.810000 0.487179 0.110000 0.040000 1.000000 0.090000 0.323202 0.110000 0 0.070000 1.000000 NLRP3 114548 broad.mit.edu 37 1 247587616 247587616 + Missense_Mutation SNP G G A rs145092553 TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr1:247587616G>A ENST00000336119.3 + 3 1617 c.871G>A c.(871-873)Gtg>Atg p.V291M NLRP3_ENST00000391827.2_Missense_Mutation_p.V291M|NLRP3_ENST00000348069.2_Missense_Mutation_p.V291M|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391828.3_Missense_Mutation_p.V291M|NLRP3_ENST00000366496.2_Missense_Mutation_p.V291M|NLRP3_ENST00000366497.2_Missense_Mutation_p.V291M NM_001127462.2|NM_001243133.1|NM_004895.4 NP_001120934.1|NP_001230062.1|NP_004886.3 Q96P20 NALP3_HUMAN NLR family, pyrin domain containing 3 142 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) CCACAAGATCGTGAGAAAACC 0.562000 0 SO:0001583 missense ENST00000336119.3 1 1 hg19 CCDS1632.1 . . . . . . . . . . G 0.829 -0.746010 0.03065 0.0 1.16E-4 ENSG00000162711 ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827 D;D;D;D;D;D 0.81659 -1.52;-1.52;-1.52;-1.52;-1.52;-1.52 4.04 -3.93 0.04143 NACHT nucleoside triphosphatase (1); 0.890365 0.09442 N 0.801583 T 0.51381 0.1671 N 0.13003 0.285 0.09310 N 1 B;B;P;B;B 0.40602 0.07;0.057;0.723;0.194;0.038 B;B;B;B;B 0.31495 0.025;0.015;0.131;0.04;0.028 T 0.51764 -0.8664 10 0.16420 T 0.52 . 2.6671 0.05056 0.1107:0.4328:0.1811:0.2754 . 291;291;291;291;291 B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20 .;.;.;.;NALP3_HUMAN M 291 ENSP00000375704:V291M;ENSP00000355453:V291M;ENSP00000337383:V291M;ENSP00000294752:V291M;ENSP00000355452:V291M;ENSP00000375703:V291M ENSP00000337383:V291M V + 1 0 NLRP3 245654239 0.004000 0.15560 0.095000 0.20976 0.012000 0.07955 0.080000 0.14802 -0.743000 0.04784 0.563000 0.77884 GTG TCGA-3E-AAAZ-01A-11D-A38G-08 NLRP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097740.1 1 0 1 168 296 0 156 0 2.995791e-01 0 3 0 156 2 0 0 0 0 0 2 1 1 163 282 0 150 2 0 0 0 0 156 2 -20.000000 1 1 121412 4 38 1 1 3 4 2.522300 1 0.380000 1.810000 0.487179 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MEGF6 1953 broad.mit.edu 37 1 3411193 3411193 + Silent SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr1:3411193C>T ENST00000356575.4 - 31 4210 c.3984G>A c.(3982-3984)ggG>ggA p.G1328G MEGF6_ENST00000294599.4_Silent_p.G1093G 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) CGCAGTGCCGCCCCGTCCAGC 0.711000 Ovarian(73;978 3658) 0 SO:0001819 synonymous_variant ENST00000356575.4 0 1 hg19 CCDS41237.1 . . . . . . . . . . C 0.026 -1.369662 0.01225 . . ENSG00000162591 ENST00000491842 D 0.82619 -1.63 3.72 0.574 0.17368 . 0.000000 0.85682 D 0.000000 D 0.85340 0.5674 . . . 0.53005 D 0.999965 . . . . . . D 0.84086 0.0387 7 0.66056 D 0.02 -26.2078 9.8377 0.40980 0.0:0.499:0.4156:0.0854 . . . . D 102 ENSP00000420386:G102D ENSP00000420386:G102D G - 2 0 MEGF6 3401053 0.000000 0.05858 0.089000 0.20774 0.012000 0.07955 -0.398000 0.07259 0.312000 0.23038 0.462000 0.41574 GGC TCGA-3E-AAAZ-01A-11D-A38G-08 MEGF6-007 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354866.1 0 0 0 3 12 0 9 0 9.750119e-01 0 37 0 9 2 0 0 0 0 0 2 1 8.136201e-01 3 12 0 9 2 0 0 0 0 9 2 -10.909080 1 1 0 0 1 0 1 1 1.706239 1 0.380000 1.810000 0.234568 0.670000 0.230000 0.980000 0.740000 0.660133 0.670000 0 0.420000 0.890000 SEL1L2 80343 broad.mit.edu 37 20 13846127 13846127 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr20:13846127C>T ENST00000284951.5 - 16 1512 c.1438G>A c.(1438-1440)Gct>Act p.A480T SEL1L2_ENST00000486903.1_Intron|SEL1L2_ENST00000378072.5_Intron Q5TEA6 SE1L2_HUMAN sel-1 suppressor of lin-12-like 2 (C. elegans) 51 AATTTCTCAGCCCAGTGGCCT 0.433000 0 SO:0001583 missense ENST00000284951.5 1 1 hg19 . . . . . . . . . . C 18.20 3.570723 0.65765 . . ENSG00000101251 ENST00000284951 T 0.50813 0.73 5.88 5.88 0.94601 . 0.000000 0.56097 D 0.000036 T 0.52403 0.1732 L 0.39245 1.2 0.46260 D 0.998956 D 0.67145 0.996 P 0.61070 0.883 T 0.36286 -0.9754 10 0.14656 T 0.56 -7.8336 12.6549 0.56782 0.165:0.835:0.0:0.0 . 480 Q5TEA6 SE1L2_HUMAN T 480 ENSP00000284951:A480T ENSP00000284951:A480T A - 1 0 SEL1L2 13794127 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 4.684000 0.61686 2.774000 0.95407 0.655000 0.94253 GCT TCGA-3E-AAAZ-01A-11D-A38G-08 SEL1L2-002 KNOWN not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000078067.3 0 0 0 18 366 0 143 0 0 0 0 143 2 0 0 0 0 0 2 1 9.999812e-01 18 361 0 143 2 0 0 0 0 143 2 -4.820165 1 1 0 0 1 0 0 0 2.055692 0 0.380000 1.810000 0.375252 0.240000 0.140000 0.370000 0.240000 0.255986 0.240000 0 0.190000 0.310000 PDYN 5173 broad.mit.edu 37 20 1961195 1961195 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr20:1961195C>T ENST00000217305.2 - 4 764 c.539G>A c.(538-540)cGc>cAc p.R180H RP4-684O24.5_ENST00000446562.1_RNA|PDYN_ENST00000540134.1_Missense_Mutation_p.R180H|PDYN_ENST00000539905.1_Missense_Mutation_p.R180H NM_001190892.1|NM_001190898.2|NM_024411.4 NP_001177821.1|NP_001177827.1|NP_077722.1 P01213 PDYN_HUMAN prodynorphin 38 GGGGTATTTGCGCAAAAAGCC 0.602000 0 SO:0001583 missense ENST00000217305.2 1 1 hg19 CCDS13023.1 . . . . . . . . . . C 26.8 4.772531 0.90108 . . ENSG00000101327 ENST00000539905;ENST00000540134;ENST00000217305 D;D;D 0.86769 -2.17;-2.17;-2.17 4.7 4.7 0.59300 . 0.000000 0.85682 D 0.000000 D 0.94162 0.8127 M 0.89095 3.005 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.95090 0.8221 10 0.87932 D 0 -18.2484 15.1657 0.72821 0.0:1.0:0.0:0.0 . 180 P01213 PDYN_HUMAN H 180 ENSP00000440185:R180H;ENSP00000442259:R180H;ENSP00000217305:R180H ENSP00000217305:R180H R - 2 0 PDYN 1909195 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 4.652000 0.61454 2.445000 0.82738 0.313000 0.20887 CGC TCGA-3E-AAAZ-01A-11D-A38G-08 PDYN-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077569.2 1 0 1 91 409 0 189 0 0 0 0 189 2 0 0 0 0 0 2 1 1 86 401 0 186 2 0 0 0 0 189 2 -3.221387 1 1 121412 5 40 1 0 0 0 2.055692 0 0.380000 1.810000 0.375252 0.940000 0.770000 1.000000 1.000000 0.936140 0.940000 1 0.850000 1.000000 BACH1 571 broad.mit.edu 37 21 30693720 30693720 + Missense_Mutation SNP T T C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr21:30693720T>C ENST00000399921.1 + 2 362 c.119T>C c.(118-120)gTg>gCg p.V40A BACH1_ENST00000286800.3_Missense_Mutation_p.V40A NM_206866.1 NP_996749.1 Q9BX63 FANCJ_HUMAN BTB and CNC homology 1, basic leucine zipper transcription factor 1 27 ACCATCTTTGTGGAGGGACAG 0.517000 0 SO:0001583 missense ENST00000399921.1 1 1 hg19 CCDS13585.1 . . . . . . . . . . T 22.3 4.270251 0.80469 . . ENSG00000156273 ENST00000286800;ENST00000399921;ENST00000451655;ENST00000447177;ENST00000435072 T;T;T;T;T 0.32753 1.44;1.44;1.44;1.44;1.44 5.4 5.4 0.78164 BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2); 0.000000 0.64402 D 0.000003 T 0.49830 0.1580 L 0.50993 1.605 0.58432 D 0.999999 D 0.89917 1.0 D 0.91635 0.999 T 0.41413 -0.9510 9 . . . -19.2783 15.7695 0.78157 0.0:0.0:0.0:1.0 . 40 O14867 BACH1_HUMAN A 40 ENSP00000286800:V40A;ENSP00000382805:V40A;ENSP00000400576:V40A;ENSP00000408605:V40A;ENSP00000392202:V40A . V + 2 0 BACH1 29615591 1.000000 0.71417 0.996000 0.52242 0.569000 0.35902 5.701000 0.68325 2.183000 0.69458 0.451000 0.29950 GTG TCGA-3E-AAAZ-01A-11D-A38G-08 BACH1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171974.1 1 0 1 104 364 0 184 1 9.997354e-01 11 34 0 184 2 0 0 0 0 0 2 1 1 103 354 0 184 2 0 0 0 0 184 2 -20.000000 1 1 0 0 1 1 2 3 2.082276 0 0.380000 1.810000 0.381176 0.990000 0.970000 1.000000 1.000000 0.998567 0.990000 1 0.990000 1.000000 PES1 23481 broad.mit.edu 37 22 30976083 30976083 + Missense_Mutation SNP G G T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr22:30976083G>T ENST00000405677.1 - 13 1652 c.709C>A c.(709-711)Cag>Aag p.Q237K PES1_ENST00000354694.7_Missense_Mutation_p.Q376K|PES1_ENST00000335214.6_Missense_Mutation_p.Q371K|PES1_ENST00000402284.3_Missense_Mutation_p.Q359K|PES1_ENST00000402281.1_Missense_Mutation_p.Q237K NM_001282328.1 NP_001269257.1 pescadillo ribosomal biogenesis factor 1 29 TCGACAATCTGATGGGTGATG 0.577000 0 SO:0001583 missense ENST00000405677.1 1 1 hg19 . . . . . . . . . . G 36 5.682142 0.96774 . . ENSG00000100029 ENST00000354694;ENST00000402281;ENST00000405677;ENST00000402284;ENST00000335214 T;T;T;T;T 0.79033 -1.23;-1.23;-1.23;-1.23;-1.23 5.28 5.28 0.74379 BRCT (4); 0.127391 0.56097 D 0.000035 D 0.89781 0.6814 M 0.89287 3.02 0.80722 D 1 D;D;P;D 0.63046 0.969;0.992;0.925;0.969 P;D;P;P 0.67382 0.72;0.951;0.616;0.72 D 0.91528 0.5240 10 0.72032 D 0.01 -34.7935 18.5306 0.90990 0.0:0.0:1.0:0.0 . 376;359;371;376 B2RDF2;B5MCF9;O00541-2;O00541 .;.;.;PESC_HUMAN K 376;237;237;359;371 ENSP00000346725:Q376K;ENSP00000384366:Q237K;ENSP00000385654:Q237K;ENSP00000384252:Q359K;ENSP00000334612:Q371K ENSP00000334612:Q371K Q - 1 0 PES1 29306083 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.655000 0.98512 2.467000 0.83353 0.655000 0.94253 CAG TCGA-3E-AAAZ-01A-11D-A38G-08 PES1-002 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000321189.2 1 0 1 113 461 0 204 1 1 125 241 0 204 2 0 0 0 0 0 2 1 1 110 442 0 200 2 0 0 0 0 204 2 -20.000000 1 1 0 0 1 1 2 3 2.102370 0 0.380000 1.810000 0.384676 0.990000 0.870000 1.000000 1.000000 0.984203 0.990000 1 0.950000 1.000000 GREB1 9687 broad.mit.edu 37 2 11780474 11780474 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr2:11780474G>A ENST00000381486.2 + 33 6044 c.5744G>A c.(5743-5745)cGc>cAc p.R1915H GREB1_ENST00000234142.5_Missense_Mutation_p.R1915H|GREB1_ENST00000396123.1_Missense_Mutation_p.R913H NM_014668.3 NP_055483.2 Q4ZG55 GREB1_HUMAN growth regulation by estrogen in breast cancer 1 30 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) ACGGTCGTCCGCCTGGAGCTC 0.622000 Ovarian(39;850 945 2785 23371 33093) 0 SO:0001583 missense ENST00000381486.2 1 1 hg19 CCDS42655.1 . . . . . . . . . . G 34 5.412272 0.96072 . . ENSG00000196208 ENST00000381486;ENST00000234142;ENST00000396123 T;T;T 0.33438 2.72;2.72;1.41 5.04 5.04 0.67666 . 0.000000 0.85682 D 0.000000 T 0.57154 0.2034 M 0.72118 2.19 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.62039 -0.6938 10 0.87932 D 0 -33.8736 18.3628 0.90380 0.0:0.0:1.0:0.0 . 1915 Q4ZG55 GREB1_HUMAN H 1915;1915;913 ENSP00000370896:R1915H;ENSP00000234142:R1915H;ENSP00000379429:R913H ENSP00000234142:R1915H R + 2 0 GREB1 11697925 1.000000 0.71417 1.000000 0.80357 0.934000 0.57294 9.227000 0.95236 2.316000 0.78162 0.563000 0.77884 CGC TCGA-3E-AAAZ-01A-11D-A38G-08 GREB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000280490.1 1 0 1 51 234 0 95 0 8.328248e-01 0 17 0 95 2 0 0 0 0 0 2 1 1 48 223 0 94 2 0 0 0 0 95 2 -20.000000 1 1 120982 2 33 1 1 2 3 2.086862 0 0.380000 1.810000 0.382347 0.940000 0.720000 1.000000 1.000000 0.924647 0.940000 1 0.820000 1.000000 DTYMK 1841 broad.mit.edu 37 2 242625239 242625239 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr2:242625239C>T ENST00000305784.2 - 2 391 c.184G>A c.(184-186)Gac>Aac p.D62N DTYMK_ENST00000493095.1_5'UTR NM_001165031.1|NM_012145.3 NP_001158503.1|NP_036277.2 P23919 KTHY_HUMAN deoxythymidylate kinase (thymidylate kinase) 7 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) TCCTCCACGTCACTTTTCTTT 0.438000 0 SO:0001583 missense ENST00000305784.2 1 1 hg19 CCDS2552.1 . . . . . . . . . . C 5.106 0.205171 0.09704 . . ENSG00000168393 ENST00000305784 T 0.41400 1.0 5.34 3.25 0.37280 . 0.614711 0.18111 N 0.151344 T 0.16085 0.0387 N 0.03881 -0.34 0.21220 N 0.999754 B;B 0.10296 0.003;0.0 B;B 0.12156 0.007;0.003 T 0.17107 -1.0380 10 0.17369 T 0.5 -13.2689 4.2064 0.10490 0.0:0.531:0.2149:0.2541 . 62;62 B7ZW70;P23919 .;KTHY_HUMAN N 62 ENSP00000304802:D62N ENSP00000304802:D62N D - 1 0 DTYMK 242273912 0.986000 0.35501 0.013000 0.15412 0.357000 0.29423 2.433000 0.44793 1.216000 0.43427 0.655000 0.94253 GAC TCGA-3E-AAAZ-01A-11D-A38G-08 DTYMK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257266.2 1 0 1 251 1008 0 420 1 1 47 95 0 420 2 0 0 0 0 0 2 1 1 246 985 0 416 2 0 0 0 0 420 2 -20.000000 1 1 0 0 1 1 2 3 2.101801 0 0.380000 1.810000 0.384676 0.990000 0.930000 1.000000 1.000000 0.995069 0.990000 1 0.990000 1.000000 IMPG2 50939 broad.mit.edu 37 3 100951770 100951770 + Missense_Mutation SNP A A T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr3:100951770A>T ENST00000193391.7 - 15 3275 c.3088T>A c.(3088-3090)Tgg>Agg p.W1030R NM_016247.3 NP_057331.2 Q9BZV3 IMPG2_HUMAN interphotoreceptor matrix proteoglycan 2 64 Hyaluronan(DB08818) TCTCCACTCCAGGGGTTGACC 0.463000 0 SO:0001583 missense ENST00000193391.7 1 1 hg19 CCDS2940.1 . . . . . . . . . . A 20.5 3.993749 0.74703 . . ENSG00000081148 ENST00000193391 T 0.25085 1.82 5.88 4.66 0.58398 Epidermal growth factor-like, type 3 (1); 0.082660 0.53938 D 0.000052 T 0.44435 0.1293 L 0.55834 1.745 0.54753 D 0.999985 D;D 0.89917 1.0;1.0 D;D 0.73380 0.98;0.98 T 0.38436 -0.9661 10 0.72032 D 0.01 -4.5245 12.8058 0.57612 0.8637:0.1363:0.0:0.0 . 1030;1030 F1T0J3;Q9BZV3 .;IMPG2_HUMAN R 1030 ENSP00000193391:W1030R ENSP00000193391:W1030R W - 1 0 IMPG2 102434460 1.000000 0.71417 0.997000 0.53966 0.992000 0.81027 5.846000 0.69444 2.257000 0.74773 0.459000 0.35465 TGG TCGA-3E-AAAZ-01A-11D-A38G-08 IMPG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353256.3 1 0 1 65 235 0 101 0 0 0 0 101 2 0 0 0 0 0 2 1 1 65 229 0 99 2 0 0 0 0 101 2 -20.000000 1 1 0 0 1 0 0 0 2.014901 0 0.380000 1.810000 0.360561 0.990000 0.870000 1.000000 1.000000 0.988714 0.990000 1 0.980000 1.000000 COL6A6 131873 broad.mit.edu 37 3 130361862 130361862 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr3:130361862G>A ENST00000358511.6 + 30 5253 c.5222G>A c.(5221-5223)cGc>cAc p.R1741H COL6A6_ENST00000453409.2_Missense_Mutation_p.R1741H NM_001102608.1 NP_001096078.1 A6NMZ7 CO6A6_HUMAN collagen, type VI, alpha 6 134 GTGCGAGACCGCAGTCGTAAG 0.393000 0 SO:0001583 missense ENST00000358511.6 1 1 hg19 CCDS46911.1 . . . . . . . . . . G 3.402 -0.122029 0.06795 2.66E-4 0.0 ENSG00000206384 ENST00000358511;ENST00000453409 D;D 0.88818 -2.42;-2.43 5.67 3.33 0.38152 . . . . . T 0.61085 0.2319 N 0.00182 -1.905 0.22253 N 0.999252 B 0.02656 0.0 B 0.01281 0.0 T 0.55755 -0.8091 9 0.12430 T 0.62 . 7.9706 0.30126 0.8354:0.0:0.1646:0.0 . 1741 A6NMZ7 CO6A6_HUMAN H 1741 ENSP00000351310:R1741H;ENSP00000399236:R1741H ENSP00000351310:R1741H R + 2 0 COL6A6 131844552 1.000000 0.71417 0.542000 0.28115 0.935000 0.57460 3.430000 0.52807 0.445000 0.26639 -0.367000 0.07326 CGC TCGA-3E-AAAZ-01A-11D-A38G-08 COL6A6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000356705.5 1 0 1 19 123 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 9.999932e-01 19 121 0 39 2 0 0 0 0 39 2 -10.725220 1 1 120810 3 32 1 0 0 0 2.014901 0 0.380000 1.810000 0.360561 0.680000 0.430000 0.980000 1.000000 0.698130 0.680000 0 0.550000 0.840000 DLEC1 9940 broad.mit.edu 37 3 38103746 38103746 + Missense_Mutation SNP G G T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr3:38103746G>T ENST00000308059.6 + 4 781 c.760G>T c.(760-762)Gat>Tat p.D254Y DLEC1_ENST00000452631.2_Missense_Mutation_p.D254Y|DLEC1_ENST00000346219.3_Missense_Mutation_p.D254Y deleted in lung and esophageal cancer 1 51 GAAGCTTGAAGATTCATGCAG 0.463000 0 SO:0001583 missense ENST00000308059.6 1 1 hg19 CCDS2672.2 . . . . . . . . . . G 9.251 1.040773 0.19669 . . ENSG00000008226 ENST00000308059;ENST00000346219;ENST00000452631 T;T;T 0.05319 3.47;3.46;3.7 3.67 1.69 0.24217 . 1.190300 0.06148 N 0.673614 T 0.08537 0.0212 L 0.46157 1.445 0.09310 N 1 B;P;B 0.35714 0.333;0.517;0.333 B;B;B 0.35413 0.187;0.202;0.187 T 0.40739 -0.9547 10 0.62326 D 0.03 -0.079 9.4496 0.38719 0.0:0.4281:0.5719:0.0 . 254;254;254 F8W6T4;Q9Y238-3;Q9Y238 .;.;DLEC1_HUMAN Y 254 ENSP00000308597:D254Y;ENSP00000315914:D254Y;ENSP00000410427:D254Y ENSP00000308597:D254Y D + 1 0 DLEC1 38078750 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 0.182000 0.16900 0.455000 0.26910 0.655000 0.94253 GAT TCGA-3E-AAAZ-01A-11D-A38G-08 DLEC1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000253745.3 1 0 0 17 222 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 9.999647e-01 17 217 0 99 2 0 0 0 0 99 2 -19.978610 1 1 0 0 1 0 0 0 2.014901 0 0.380000 1.810000 0.360561 0.360000 0.220000 0.550000 0.360000 0.378334 0.360000 0 0.280000 0.460000 CHL1 10752 broad.mit.edu 37 3 439920 439920 + Silent SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr3:439920C>T ENST00000256509.2 + 25 3747 c.3105C>T c.(3103-3105)atC>atT p.I1035I CHL1_ENST00000397491.2_Silent_p.I1019I NM_001253387.1|NM_001253388.1|NM_006614.3 NP_001240316.1|NP_001240317.1|NP_006605.2 Q96FC9 DDX11_HUMAN cell adhesion molecule L1-like p.I1035I(1) 93 all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201) GTAAAGGTATCGGGAAGATAT 0.353000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000256509.2 1 1 hg19 CCDS2556.1 TCGA-3E-AAAZ-01A-11D-A38G-08 CHL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207155.2 1 0 0 33 162 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1 32 160 0 69 2 0 0 0 0 69 2 -3.391473 1 1 121408 4 37 1 0 0 0 2.014901 0 0.380000 1.810000 0.360561 0.860000 0.610000 1.000000 1.000000 0.858773 0.860000 1 0.730000 1.000000 FILIP1L 11259 broad.mit.edu 37 3 99569205 99569205 + Nonsense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr3:99569205G>A ENST00000354552.3 - 5 1785 c.1315C>T c.(1315-1317)Caa>Taa p.Q439* CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000383694.2_Nonsense_Mutation_p.Q199*|FILIP1L_ENST00000487087.1_Nonsense_Mutation_p.Q15*|FILIP1L_ENST00000331335.5_Nonsense_Mutation_p.Q439*|FILIP1L_ENST00000471562.1_Nonsense_Mutation_p.Q199*|FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000496116.1_Intron NM_182909.2 NP_878913.2 Q4L180 FIL1L_HUMAN filamin A interacting protein 1-like 35 TAGCATTCTTGTTTGCTTTTG 0.358000 0 SO:0001587 stop_gained ENST00000354552.3 0 1 hg19 CCDS43117.1 . . . . . . . . . . G 26.4 4.736310 0.89482 . . ENSG00000168386 ENST00000354552;ENST00000487087;ENST00000471562;ENST00000331335;ENST00000383694;ENST00000441620;ENST00000495625 . . . 5.55 4.66 0.58398 . 0.000000 0.50627 D 0.000119 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.11794 T 0.64 -2.2035 16.0018 0.80297 0.0:0.1518:0.8482:0.0 . . . . X 439;15;199;439;199;185;199 . ENSP00000327880:Q439X Q - 1 0 FILIP1L 101051895 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.462000 0.66707 1.286000 0.44565 0.655000 0.94253 CAA TCGA-3E-AAAZ-01A-11D-A38G-08 FILIP1L-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000353069.1 1 0 1 107 506 0 263 0 1 0 201 0 263 2 0 0 0 0 0 2 1 1 106 496 0 262 2 0 0 0 0 263 2 -20.000000 1 1 0 0 1 0 0 0 2.014901 0 0.380000 1.810000 0.360561 0.880000 0.730000 1.000000 1.000000 0.890069 0.880000 1 0.810000 0.970000 PCDHA2 56146 broad.mit.edu 37 5 140175222 140175222 + Missense_Mutation SNP A A G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr5:140175222A>G ENST00000526136.1 + 1 673 c.673A>G c.(673-675)Acc>Gcc p.T225A PCDHA2_ENST00000520672.2_Missense_Mutation_p.T225A|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.T225A|PCDHA1_ENST00000394633.3_Intron NM_018905.2 NP_061728.1 Q9Y5H9 PCDA2_HUMAN protocadherin alpha 2 71 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCTCACGGGCACCGTTCAAAT 0.423000 0 SO:0001583 missense ENST00000526136.1 1 1 hg19 CCDS54914.1 . . . . . . . . . . a 14.46 2.541178 0.45280 . . ENSG00000204969 ENST00000520672;ENST00000378132;ENST00000526136 T;T;T 0.56275 0.47;0.47;0.47 4.02 2.83 0.33086 Cadherin (4);Cadherin-like (1); 0.000000 0.40908 U 0.000988 T 0.69735 0.3144 M 0.92077 3.27 0.31199 N 0.699996 P;B;P 0.40266 0.71;0.374;0.71 B;P;B 0.50378 0.362;0.639;0.362 T 0.75105 -0.3435 10 0.87932 D 0 . 9.9392 0.41570 0.8476:0.0:0.0:0.1524 . 225;225;225 Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2 .;PCDA2_HUMAN;. A 225 ENSP00000430584:T225A;ENSP00000367372:T225A;ENSP00000431748:T225A ENSP00000367372:T225A T + 1 0 PCDHA2 140155406 0.998000 0.40836 0.981000 0.43875 0.995000 0.86356 4.169000 0.58223 0.681000 0.31386 0.528000 0.53228 ACC TCGA-3E-AAAZ-01A-11D-A38G-08 PCDHA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372877.3 1 0 1 92 456 0 167 0 0 0 0 167 2 0 0 0 0 0 2 1 1 89 450 0 166 2 0 0 0 0 167 2 -20.000000 1 1 0 0 1 1 2 3 2.093560 0 0.380000 1.810000 0.382347 0.880000 0.720000 1.000000 1.000000 0.887473 0.880000 1 0.800000 0.980000 FAM71B 153745 broad.mit.edu 37 5 156590130 156590130 + Silent SNP G G T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr5:156590130G>T ENST00000302938.4 - 2 1241 c.1146C>A c.(1144-1146)acC>acA p.T382T NM_130899.2 NP_570969.2 Q8TC56 FA71B_HUMAN family with sequence similarity 71, member B 68 Renal(175;0.00212) Medulloblastoma(196;0.0523)|all_neural(177;0.21) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) CACACTTGCTGGTCGTAATAC 0.567000 0 SO:0001819 synonymous_variant ENST00000302938.4 1 1 hg19 CCDS4335.1 TCGA-3E-AAAZ-01A-11D-A38G-08 FAM71B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252570.2 0 0 0 10 227 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 9.966511e-01 10 221 0 77 2 0 0 0 0 78 2 -2.885356 1 1 121412 2 34 1 1 2 3 2.093560 0 0.380000 1.810000 0.382347 0.230000 0.110000 0.420000 0.220000 0.248937 0.230000 0 0.160000 0.310000 SPATA9 83890 broad.mit.edu 37 5 95011166 95011166 + Missense_Mutation SNP G G A rs140676515 byFrequency TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr5:95011166G>A ENST00000274432.8 - 3 469 c.328C>T c.(328-330)Cgt>Tgt p.R110C RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_5'UTR|SPATA9_ENST00000395899.3_Missense_Mutation_p.R110C NM_031952.3 NP_114158.2 Q9BWV2 SPAT9_HUMAN spermatogenesis associated 9 7 all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198) CTCAGCAGACGACCAGATATG 0.433000 0 SO:0001583 missense ENST00000274432.8 1 0 hg19 CCDS4076.1 3 0.0013736263736263737 3 0.006097560975609756 0 0.0 0 0.0 0 0.0 G 12.73 2.024694 0.35701 0.006582 0.0 ENSG00000145757 ENST00000274432;ENST00000395899 T 0.31510 1.49 4.76 3.88 0.44766 . 0.000000 0.51477 D 0.000082 T 0.26448 0.0646 L 0.27053 0.805 0.19300 N 0.999974 D 0.67145 0.996 P 0.57371 0.819 T 0.05818 -1.0862 10 0.87932 D 0 -8.0846 10.6281 0.45519 0.0:0.0:0.8093:0.1907 . 110 Q9BWV2 SPAT9_HUMAN C 110 ENSP00000274432:R110C ENSP00000274432:R110C R - 1 0 SPATA9 95036922 0.074000 0.21230 0.029000 0.17559 0.011000 0.07611 1.948000 0.40303 1.329000 0.45376 0.655000 0.94253 CGT TCGA-3E-AAAZ-01A-11D-A38G-08 SPATA9-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000304036.1 1 0 1 49 233 0 114 0 0 0 1 0 114 2 0 0 0 0 0 2 1 1 49 231 0 112 2 0 0 0 0 114 2 -3.273902 1 1 121412 72 51 1 1 2 3 2.093560 0 0.380000 1.810000 0.382347 0.910000 0.690000 1.000000 1.000000 0.906018 0.910000 1 0.800000 1.000000 GPRC6A 222545 broad.mit.edu 37 6 117113727 117113727 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr6:117113727C>T ENST00000310357.3 - 6 2380 c.2359G>A c.(2359-2361)Ggc>Agc p.G787S GPRC6A_ENST00000530250.1_Missense_Mutation_p.G612S|GPRC6A_ENST00000368549.3_Missense_Mutation_p.G716S NM_148963.2 NP_683766.2 Q5T6X5 GPC6A_HUMAN G protein-coupled receptor, class C, group 6, member A 65 all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234) ATGAGCATGCCAAATGTAATG 0.378000 0 SO:0001583 missense ENST00000310357.3 1 1 hg19 CCDS5112.1 . . . . . . . . . . C 8.574 0.880765 0.17467 . . ENSG00000173612 ENST00000310357;ENST00000368549;ENST00000530250 D;D;D 0.85411 -1.98;-1.98;-1.98 4.26 4.26 0.50523 GPCR, family 3, C-terminal (2); 0.000000 0.53938 D 0.000041 T 0.62146 0.2404 N 0.04669 -0.19 0.49130 D 0.999757 P;P;P 0.39903 0.65;0.504;0.694 P;B;B 0.47603 0.551;0.292;0.418 T 0.70171 -0.4945 10 0.02654 T 1 . 16.8566 0.86007 0.0:1.0:0.0:0.0 . 716;612;787 Q5T6X5-3;Q5T6X5-2;Q5T6X5 .;.;GPC6A_HUMAN S 787;716;612 ENSP00000309493:G787S;ENSP00000357537:G716S;ENSP00000433465:G612S ENSP00000309493:G787S G - 1 0 GPRC6A 117220420 1.000000 0.71417 1.000000 0.80357 0.933000 0.57130 2.930000 0.48924 2.210000 0.71456 0.591000 0.81541 GGC TCGA-3E-AAAZ-01A-11D-A38G-08 GPRC6A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041966.2 1 0 1 38 176 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 1 37 176 0 87 2 0 0 0 0 86 2 -3.185659 1 1 0 0 1 0 1 1 1.695354 1 0.380000 1.810000 0.234568 0.740000 0.540000 0.940000 0.750000 0.752837 0.740000 0 0.640000 0.860000 TULP4 56995 broad.mit.edu 37 6 158922970 158922970 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr6:158922970G>A ENST00000367097.3 + 13 3632 c.2275G>A c.(2275-2277)Gga>Aga p.G759R TULP4_ENST00000367094.2_Intron NM_020245.4 NP_064630.2 Q9NRJ4 TULP4_HUMAN tubby like protein 4 49 Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171) GGTGATTTTCGGAAGCGTGGA 0.612000 0 SO:0001583 missense ENST00000367097.3 1 1 hg19 CCDS34561.1 . . . . . . . . . . G 22.3 4.270972 0.80469 . . ENSG00000130338 ENST00000367097 T 0.61980 0.06 5.64 5.64 0.86602 . 0.395439 0.28327 N 0.015758 T 0.44932 0.1317 L 0.56769 1.78 0.80722 D 1 P 0.45011 0.848 B 0.34722 0.188 T 0.56565 -0.7958 10 0.54805 T 0.06 -15.9636 14.9195 0.70826 0.0707:0.0:0.9293:0.0 . 759 Q9NRJ4 TULP4_HUMAN R 759 ENSP00000356064:G759R ENSP00000356064:G759R G + 1 0 TULP4 158842958 1.000000 0.71417 0.998000 0.56505 0.985000 0.73830 5.865000 0.69583 2.659000 0.90383 0.650000 0.86243 GGA TCGA-3E-AAAZ-01A-11D-A38G-08 TULP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042869.1 1 0 0 41 696 0 308 0 9.008827e-02 0 9 0 308 2 0 0 0 0 0 2 1 1 40 672 0 306 2 0 0 0 0 308 2 -2.774566 1 1 121412 2 40 1 0 1 1 1.695354 1 0.380000 1.810000 0.234568 0.230000 0.160000 0.310000 0.240000 0.241214 0.230000 0 0.190000 0.280000 XPO5 57510 broad.mit.edu 37 6 43491668 43491668 + Missense_Mutation SNP T T C TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr6:43491668T>C ENST00000265351.7 - 32 3763 c.3553A>G c.(3553-3555)Atg>Gtg p.M1185V POLR1C_ENST00000304004.3_Intron NM_020750.2 NP_065801.1 Q9HAV4 XPO5_HUMAN exportin 5 34 all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243) all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524) GTCTCCAGCATTGGCTTTGTT 0.463000 0 SO:0001583 missense ENST00000265351.7 0 1 hg19 CCDS47430.1 . . . . . . . . . . T 2.456 -0.325143 0.05350 . . ENSG00000124571 ENST00000265351;ENST00000439465 T 0.27256 1.68 6.05 -7.28 0.01456 . 0.722313 0.14370 N 0.323863 T 0.02156 0.0067 N 0.04203 -0.255 0.09310 N 0.999993 B 0.02656 0.0 B 0.01281 0.0 T 0.41520 -0.9504 10 0.25106 T 0.35 -0.074 5.3159 0.15854 0.1366:0.4805:0.0853:0.2977 . 1185 Q9HAV4 XPO5_HUMAN V 1185;813 ENSP00000265351:M1185V ENSP00000265351:M1185V M - 1 0 XPO5 43599646 0.347000 0.24853 0.870000 0.34147 0.979000 0.70002 -0.064000 0.11636 -0.740000 0.04803 -0.280000 0.10049 ATG TCGA-3E-AAAZ-01A-11D-A38G-08 XPO5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040657.2 0 0 0 4 265 0 123 0 3.649573e-01 0 71 0 123 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 123 2 -4.214947 1 0 120838 1 31 1 0 1 1 1.756394 1 0.380000 1.810000 0.262256 0.070000 0.020000 0.160000 0.070000 0.080765 0.070000 0 0.040000 0.110000 GRM8 2918 broad.mit.edu 37 7 126173814 126173814 + Missense_Mutation SNP C C G TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr7:126173814C>G ENST00000339582.2 - 9 2430 c.1622G>C c.(1621-1623)tGt>tCt p.C541S GRM8_ENST00000358373.3_Missense_Mutation_p.C541S|GRM8_ENST00000444921.2_Missense_Mutation_p.C541S|GRM8_ENST00000480995.1_5'UTR O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 125 Prostate(267;0.186) GTAACCTTCACAGCGTTCACA 0.562000 HNSCC(24;0.065) 0 SO:0001583 missense ENST00000339582.2 1 1 hg19 CCDS5794.1 . . . . . . . . . . C 22.4 4.281561 0.80692 . . ENSG00000179603 ENST00000339582;ENST00000444921;ENST00000358373 D;D;D 0.99494 -6.01;-6.01;-6.01 5.8 5.8 0.92144 GPCR, family 3, conserved site (1);GPCR, family 3, nine cysteines domain (1); 0.000000 0.85682 D 0.000000 D 0.99785 0.9910 H 0.98682 4.3 0.80722 D 1 P;D 0.89917 0.867;1.0 B;D 0.87578 0.359;0.998 D 0.97086 0.9787 10 0.87932 D 0 . 19.0428 0.93008 0.0:1.0:0.0:0.0 . 541;541 O00222-2;O00222 .;GRM8_HUMAN S 541 ENSP00000344173:C541S;ENSP00000409790:C541S;ENSP00000351142:C541S ENSP00000344173:C541S C - 2 0 GRM8 125961050 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.811000 0.86092 2.758000 0.94735 0.643000 0.83706 TGT TCGA-3E-AAAZ-01A-11D-A38G-08 GRM8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059209.4 1 0 1 74 325 0 141 0 0 0 0 141 2 0 0 0 0 0 2 1 1 73 321 0 140 2 0 0 0 0 141 2 -20.000000 1 1 0 0 1 0 0 0 2.065404 0 0.380000 1.810000 0.377635 0.960000 0.770000 1.000000 1.000000 0.946398 0.960000 1 0.860000 1.000000 PTPN12 5782 broad.mit.edu 37 7 77230064 77230064 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr7:77230064G>A ENST00000248594.6 + 8 908 c.636G>A c.(634-636)atG>atA p.M212I PTPN12_ENST00000435495.2_Missense_Mutation_p.M82I|PTPN12_ENST00000415482.2_Missense_Mutation_p.M93I NM_002835.3 NP_002826.3 Q05209 PTN12_HUMAN protein tyrosine phosphatase, non-receptor type 12 39 TTCTGGACATGATAAGCTTAA 0.328000 0 SO:0001583 missense ENST00000248594.6 1 1 hg19 CCDS5592.1 . . . . . . . . . . G 33 5.202288 0.94997 . . ENSG00000127947 ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495 T;D;D 0.82893 2.85;-1.66;-1.66 5.51 5.51 0.81932 Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1); 0.000000 0.85682 D 0.000000 D 0.87478 0.6187 L 0.41573 1.285 0.80722 D 1 D 0.58620 0.983 D 0.63033 0.91 D 0.88185 0.2873 10 0.66056 D 0.02 . 19.4115 0.94675 0.0:0.0:1.0:0.0 . 212 Q05209 PTN12_HUMAN I 212;93;93;82 ENSP00000248594:M212I;ENSP00000392429:M93I;ENSP00000397991:M82I ENSP00000248594:M212I M + 3 0 PTPN12 77068000 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.824000 0.86668 2.585000 0.87301 0.557000 0.71058 ATG TCGA-3E-AAAZ-01A-11D-A38G-08 PTPN12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253183.3 1 0 1 100 354 0 129 1 1 52 75 0 129 2 0 0 0 0 0 2 1 1 99 347 0 127 2 0 0 0 0 129 2 -20.000000 1 1 0 0 1 0 0 0 2.065404 0 0.380000 1.810000 0.377635 0.990000 0.950000 1.000000 1.000000 0.997714 0.990000 1 0.990000 1.000000 BAALC 79870 broad.mit.edu 37 8 104225200 104225200 + Missense_Mutation SNP G G A TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr8:104225200G>A ENST00000297574.6 + 3 458 c.319G>A c.(319-321)Ggt>Agt p.G107S RP11-318M2.2_ENST00000499522.2_RNA|BAALC_ENST00000438105.2_Intron|BAALC_ENST00000309982.5_Missense_Mutation_p.G72S|RP11-318M2.2_ENST00000523614.2_RNA Q8WXS3 BAALC_HUMAN brain and acute leukemia, cytoplasmic 7 OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133) TACAGCCCCAGGTGGAATACC 0.577000 0 SO:0001583 missense ENST00000297574.6 1 1 hg19 . . . . . . . . . . G 12.40 1.927804 0.34002 . . ENSG00000164929 ENST00000309982;ENST00000297574 T;T 0.53206 1.02;0.63 5.47 1.85 0.25348 . 0.578794 0.17232 N 0.181915 T 0.30070 0.0753 . . . 0.80722 D 1 B;B 0.18741 0.03;0.005 B;B 0.17722 0.014;0.019 T 0.05971 -1.0853 9 0.26408 T 0.33 -6.8436 5.7463 0.18122 0.4639:0.0:0.5361:0.0 . 107;72 Q8WXS3;Q8WXS3-2 BAALC_HUMAN;. S 72;107 ENSP00000312457:G72S;ENSP00000297574:G107S ENSP00000297574:G107S G + 1 0 BAALC 104294376 0.137000 0.22531 0.196000 0.23383 0.544000 0.35116 0.274000 0.18680 0.631000 0.30412 0.650000 0.86243 GGT TCGA-3E-AAAZ-01A-11D-A38G-08 BAALC-003 KNOWN basic protein_coding protein_coding OTTHUMT00000380257.1 1 0 1 86 382 0 190 0 3.082701e-01 0 6 0 190 2 0 0 0 0 0 2 1 1 86 372 0 186 2 0 0 0 0 190 2 -2.938922 1 1 0 0 1 1 2 3 2.087904 0 0.380000 1.810000 0.382347 0.960000 0.790000 1.000000 1.000000 0.948510 0.960000 1 0.870000 1.000000 OR1N2 138882 broad.mit.edu 37 9 125315452 125315452 + Nonsense_Mutation SNP G G T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr9:125315452G>T ENST00000373688.2 + 1 62 c.4G>T c.(4-6)Gaa>Taa p.E2* NM_001004457.1 NP_001004457.1 Q8NGR9 OR1N2_HUMAN olfactory receptor, family 1, subfamily N, member 2 26 CTGACACATGGAAGGTTTTTA 0.408000 0 SO:0001587 stop_gained ENST00000373688.2 0 1 hg19 CCDS35123.1 . . . . . . . . . . G 17.59 3.426314 0.62733 . . ENSG00000171501 ENST00000373688 . . . 3.55 0.384 0.16244 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.15499 T 0.54 . 0.7679 0.01018 0.2222:0.1643:0.399:0.2145 . . . . X 2 . ENSP00000362792:E2X E + 1 0 OR1N2 124355273 0.000000 0.05858 0.000000 0.03702 0.186000 0.23388 -0.184000 0.09698 -0.024000 0.13941 0.638000 0.83543 GAA TCGA-3E-AAAZ-01A-11D-A38G-08 OR1N2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053937.2 1 0 1 81 325 1 161 0 0 0 1 161 2 1 1 146 525 0 727 2 1 1 75 322 1 160 11 0 0 0 1 161 2 -20.000000 1 1 0 0 1 0 1 1 1.897685 1 0.380000 1.810000 0.324839 0.950000 0.780000 1.000000 1.000000 0.942531 0.950000 1 0.860000 1.000000 CACNA1B 774 broad.mit.edu 37 9 141014657 141014657 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr9:141014657C>T ENST00000371372.1 + 45 6216 c.6071C>T c.(6070-6072)aCg>aTg p.T2024M CACNA1B_ENST00000277551.2_Missense_Mutation_p.T2024M|CACNA1B_ENST00000277549.5_Missense_Mutation_p.T1218M|CACNA1B_ENST00000371355.4_Missense_Mutation_p.T2025M|CACNA1B_ENST00000371363.1_Missense_Mutation_p.T2022M|CACNA1B_ENST00000371357.1_Missense_Mutation_p.T2023M NM_000718.3|NM_001243812.1 NP_000709.1|NP_001230741.1 Q00975 CAC1B_HUMAN calcium channel, voltage-dependent, N type, alpha 1B subunit 80 all_cancers(76;0.166) Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661) TCCATCTCCACGCTGGCCCAG 0.687000 0 SO:0001583 missense ENST00000371372.1 1 1 hg19 CCDS59522.1 . . . . . . . . . . C 22.8 4.339170 0.81911 . . ENSG00000148408 ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355 T;T;T;T;T;T 0.76060 -0.99;-0.99;-0.99;-0.99;-0.99;-0.99 4.78 4.78 0.61160 . 0.330500 0.29767 N 0.011255 T 0.73961 0.3654 L 0.49126 1.545 0.80722 D 1 P;P 0.48162 0.906;0.906 P;P 0.45276 0.475;0.475 T 0.77411 -0.2598 10 0.52906 T 0.07 . 17.8144 0.88627 0.0:1.0:0.0:0.0 . 2023;2022 B1AQK7;B1AQK6 .;. M 2024;2024;1218;2022;2023;2025 ENSP00000360423:T2024M;ENSP00000277551:T2024M;ENSP00000277549:T1218M;ENSP00000360414:T2022M;ENSP00000360408:T2023M;ENSP00000360406:T2025M ENSP00000277549:T1218M T + 2 0 CACNA1B 140134478 0.997000 0.39634 0.976000 0.42696 0.747000 0.42532 3.527000 0.53517 2.210000 0.71456 0.491000 0.48974 ACG TCGA-3E-AAAZ-01A-11D-A38G-08 CACNA1B-001 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000055380.1 1 0 1 24 48 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 1 24 48 0 24 2 0 0 0 0 24 2 -20.000000 1 1 0 0 1 0 0 0 1.897261 1 0.380000 1.810000 0.320622 0.990000 0.990000 1.000000 1.000000 0.998906 0.990000 1 0.990000 1.000000 C9orf3 84909 broad.mit.edu 37 9 97843044 97843044 + Missense_Mutation SNP G G T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chr9:97843044G>T ENST00000375315.2 + 14 2301 c.2301G>T c.(2299-2301)agG>agT p.R767S C9orf3_ENST00000433691.2_Missense_Mutation_p.R108S|C9orf3_ENST00000297979.5_Missense_Mutation_p.R668S|C9orf3_ENST00000425634.2_Missense_Mutation_p.R129S NM_001193329.1 NP_001180258.1 Q8N6M6 AMPO_HUMAN chromosome 9 open reading frame 3 23 GTGTGGAGAGGTTCCTTCAGG 0.502000 0 SO:0001583 missense ENST00000375315.2 1 1 hg19 CCDS55328.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 12.86|12.86 2.063994|2.063994 0.36373|0.36373 .|. .|. ENSG00000148120|ENSG00000148120 ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313;ENST00000425634;ENST00000433691;ENST00000375314|ENST00000445181 T;T;T;T;T;T|. 0.41400|. 1.0;1.0;1.0;1.0;1.0;1.0|. 5.57|5.57 -11.1|-11.1 0.00147|0.00147 Peptidase M1, leukotriene A4 hydrolase, aminopeptidase C-terminal (1);Armadillo-type fold (1);|. 0.730929|. 0.12958|. N|. 0.425271|. T|T 0.34308|0.34308 0.0893|0.0893 L|L 0.57536|0.57536 1.79|1.79 0.22156|0.22156 N|N 0.999328|0.999328 P;P;B;B;B|. 0.48834|. 0.845;0.916;0.095;0.418;0.306|. P;P;B;B;B|. 0.51657|. 0.676;0.515;0.053;0.085;0.169|. T|T 0.36939|0.36939 -0.9727|-0.9727 10|5 0.11485|. T|. 0.65|. 0.0602|0.0602 6.0437|6.0437 0.19748|0.19748 0.1409:0.4072:0.3673:0.0845|0.1409:0.4072:0.3673:0.0845 .|. 108;129;767;668;668|. B4DU39;B4DQU3;Q8N6M6;Q8N6M6-4;Q8N6M6-2|. .;.;AMPO_HUMAN;.;.|. S|F 668;767;491;549;129;108;131|132 ENSP00000297979:R668S;ENSP00000364464:R767S;ENSP00000402171:R491S;ENSP00000401854:R549S;ENSP00000411815:R129S;ENSP00000399365:R108S|. ENSP00000297979:R668S|. R|V +|+ 3|1 2|0 C9orf3|C9orf3 96882865|96882865 0.000000|0.000000 0.05858|0.05858 0.003000|0.003000 0.11579|0.11579 0.090000|0.090000 0.18270|0.18270 -1.167000|-1.167000 0.03126|0.03126 -1.392000|-1.392000 0.02082|0.02082 -0.378000|-0.378000 0.06908|0.06908 AGG|GTT TCGA-3E-AAAZ-01A-11D-A38G-08 C9orf3-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 43 246 0 112 1 1 33 244 0 112 2 0 0 0 0 0 2 1 1 42 239 0 112 2 0 0 0 0 112 2 -20.000000 1 1 0 0 1 0 1 1 1.924680 0 0.380000 1.810000 0.333118 0.720000 0.540000 0.930000 0.720000 0.734447 0.720000 0 0.620000 0.830000 HTR2C 3358 broad.mit.edu 37 X 114082716 114082716 + Missense_Mutation SNP C C T TCGA-3E-AAAZ-01A-11D-A38G-08 TCGA-3E-AAAZ-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2be6181-6c54-4ab7-bea5-d5f94e8b65e5 a03f6870-eb79-4f62-9b59-5e12dffc9a97 g.chrX:114082716C>T ENST00000276198.1 + 5 1228 c.500C>T c.(499-501)tCg>tTg p.S167L HTR2C_ENST00000371950.3_Intron|HTR2C_ENST00000371951.1_Missense_Mutation_p.S167L NM_000868.2 NP_000859.1 P28335 5HT2C_HUMAN 5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled p.S167L(1) 50 Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246) CGTTTCAATTCGCGGACTAAG 0.408000 1 Substitution - Missense(1) SO:0001583 missense ENST00000276198.1 1 1 hg19 CCDS14564.1 . . . . . . . . . . C 26.2 4.713163 0.89112 . . ENSG00000147246 ENST00000276198;ENST00000371951 T;T 0.41400 1.0;1.0 4.27 4.27 0.50696 GPCR, rhodopsin-like superfamily (1); 0.000000 0.64402 D 0.000001 T 0.69369 0.3103 M 0.89601 3.045 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.77112 -0.2708 10 0.87932 D 0 . 13.3413 0.60547 0.0:1.0:0.0:0.0 . 167 P28335 5HT2C_HUMAN L 167 ENSP00000276198:S167L;ENSP00000361019:S167L ENSP00000276198:S167L S + 2 0 HTR2C 113988972 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.686000 0.84128 1.704000 0.51252 0.544000 0.68410 TCG TCGA-3E-AAAZ-01A-11D-A38G-08 HTR2C-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057962.1 1 0 1 78 193 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 1 78 190 0 101 2 0 0 0 0 102 2 -20.000000 1 1 0 0 1 0 1 1 0.380000 1.810000 0.380000 0.740000 0.610000 0.890000 0.750000 0.756800 0.740000 0 0.680000 0.830000