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 PAPSS2 9060 broad.mit.edu 37 10 89503202 89503202 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr10:89503202G>A ENST00000361175.4 + 10 1649 c.1280G>A c.(1279-1281)cGc>cAc p.R427H PAPSS2_ENST00000456849.1_Missense_Mutation_p.R432H|PAPSS2_ENST00000427144.2_Missense_Mutation_p.R431H NM_004670.3 NP_004661.2 O95340 PAPS2_HUMAN 3'-phosphoadenosine 5'-phosphosulfate synthase 2 20 Melanoma(5;0.019)|Colorectal(252;0.123) GACACTCGCCGCAGGCTCCTA 0.582000 0 SO:0001583 missense ENST00000361175.4 0 1 hg19 CCDS7385.1 . . . . . . . . . . G 22.8 4.333777 0.81801 . . ENSG00000198682 ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981 T;T;T 0.31247 1.5;1.5;1.5 5.33 3.49 0.39957 Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1); 0.094954 0.85682 D 0.000000 T 0.52517 0.1739 M 0.76328 2.33 0.58432 D 0.999998 D;D 0.89917 0.998;1.0 D;D 0.79784 0.938;0.993 T 0.53194 -0.8473 10 0.52906 T 0.07 -19.4179 11.5618 0.50780 0.1428:0.0:0.8572:0.0 . 427;432 O95340;O95340-2 PAPS2_HUMAN;. H 427;432;431;431 ENSP00000354436:R427H;ENSP00000406157:R432H;ENSP00000397123:R431H ENSP00000354436:R427H R + 2 0 PAPSS2 89493182 1.000000 0.71417 0.027000 0.17364 0.993000 0.82548 9.257000 0.95545 0.826000 0.34661 0.561000 0.74099 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 PAPSS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049229.1 0 0 0 5 479 0 105 0 5.741555e-02 0 29 0 105 2 0 0 0 0 0 2 1 9.354227e-01 5 472 0 105 2 0 0 0 0 105 2 -2.145249 0 1 121412 1 33 1 1 2 3 2.001811 0 0.090000 2.020000 0.096909 0.270000 0.090000 1.000000 0.220000 0.367717 0.270000 0 1.600000e-01 5.100000e-01 FAM111B 374393 broad.mit.edu 37 11 58892674 58892674 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr11:58892674G>A ENST00000343597.3 + 4 1295 c.1104G>A c.(1102-1104)ccG>ccA p.P368P FAM111B_ENST00000529618.1_Silent_p.P338P|FAM111B_ENST00000411426.1_Silent_p.P338P NM_198947.3 NP_945185.1 Q6SJ93 F111B_HUMAN family with sequence similarity 111, member B 40 GACGGAGGCCGCATCTGGGTA 0.383000 0 SO:0001819 synonymous_variant ENST00000343597.3 0 1 hg19 CCDS7972.1 TCGA-Q3-A5QY-01A-12D-A32N-08 FAM111B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393974.1 0 0 0 5 584 0 114 0 1.164528e-03 0 5 0 114 2 0 0 0 0 0 2 1 9.377790e-01 5 584 0 114 2 0 0 0 0 114 2 -2.109569 0 1 121412 1 37 1 1 2 3 2.004856 0 0.090000 2.020000 0.097715 0.220000 0.070000 1.000000 0.190000 0.336839 0.220000 0 1.300000e-01 4.600000e-01 HEPHL1 341208 broad.mit.edu 37 11 93800764 93800764 + Missense_Mutation SNP A A G TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr11:93800764A>G ENST00000315765.9 + 5 919 c.911A>G c.(910-912)cAt>cGt p.H304R NM_001098672.1 NP_001092142.1 Q6MZM0 HPHL1_HUMAN hephaestin-like 1 61 Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824) ATAGACATCCATTCTATCTAT 0.463000 0 SO:0001583 missense ENST00000315765.9 0 1 hg19 CCDS44710.1 . . . . . . . . . . A 23.4 4.413281 0.83449 . . ENSG00000181333 ENST00000315765 D 0.99824 -6.96 5.36 5.36 0.76844 Cupredoxin (2); 0.000000 0.85682 D 0.000000 D 0.99866 0.9937 M 0.93978 3.48 0.58432 D 0.999999 D 0.89917 1.0 D 0.97110 1.0 D 0.96432 0.9320 10 0.87932 D 0 . 15.6458 0.77049 1.0:0.0:0.0:0.0 . 304 Q6MZM0 HPHL1_HUMAN R 304 ENSP00000313699:H304R ENSP00000313699:H304R H + 2 0 HEPHL1 93440412 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 8.991000 0.93514 2.158000 0.67659 0.459000 0.35465 CAT TCGA-Q3-A5QY-01A-12D-A32N-08 HEPHL1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396103.2 0 0 0 12 792 0 157 0 2.791171e-04 0 2 0 157 2 0 0 0 0 0 2 1 9.990811e-01 12 787 0 157 2 0 0 0 0 157 2 -8.619136 1 1 0 0 1 1 2 3 2.004856 0 0.090000 2.020000 0.097715 0.360000 0.180000 1.000000 0.330000 0.450809 0.360000 0 2.600000e-01 6.000000e-01 LRTM2 654429 broad.mit.edu 37 12 1943759 1943759 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr12:1943759G>A ENST00000543818.1 + 5 1827 c.985G>A c.(985-987)Gct>Act p.A329T LRTM2_ENST00000535041.1_Missense_Mutation_p.A329T|LRTM2_ENST00000543730.1_3'UTR|LRTM2_ENST00000299194.1_Missense_Mutation_p.A329T|CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000382722.5_Intron NM_001039029.2|NM_001163925.1|NM_001163926.1 NP_001034118.1|NP_001157397.1|NP_001157398.1 Q8N967 LRTM2_HUMAN leucine-rich repeats and transmembrane domains 2 p.A329T(1) 20 Ovarian(42;0.107) OV - Ovarian serous cystadenocarcinoma(31;0.000834) GGTGGTGGCCGCTGCCTATGG 0.662000 1 Substitution - Missense(1) SO:0001583 missense ENST00000543818.1 0 1 hg19 CCDS31726.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 17.13|17.13 3.309844|3.309844 0.60414|0.60414 .|. .|. ENSG00000166159|ENSG00000166159 ENST00000543818;ENST00000299194;ENST00000535041|ENST00000424079 T;T;T|. 0.59502|. 0.26;0.26;0.26|. 5.44|5.44 4.55|4.55 0.56014|0.56014 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.71626|0.71626 0.3362|0.3362 M|M 0.62723|0.62723 1.935|1.935 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.68765|. 0.96|. T|T 0.75010|0.75010 -0.3468|-0.3468 10|6 0.87932|0.87932 D|D 0|0 .|. 14.1474|14.1474 0.65360|0.65360 0.072:0.0:0.928:0.0|0.072:0.0:0.928:0.0 .|. 329|. Q8N967|. LRTM2_HUMAN|. T|H 329|85 ENSP00000446278:A329T;ENSP00000299194:A329T;ENSP00000444737:A329T|. ENSP00000299194:A329T|ENSP00000394967:R85H A|R +|+ 1|2 0|0 LRTM2|LRTM2 1814020|1814020 1.000000|1.000000 0.71417|0.71417 0.934000|0.934000 0.37439|0.37439 0.010000|0.010000 0.07245|0.07245 9.869000|9.869000 0.99810|0.99810 1.302000|1.302000 0.44855|0.44855 -0.136000|-0.136000 0.14681|0.14681 GCT|CGC TCGA-Q3-A5QY-01A-12D-A32N-08 LRTM2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398055.1 0 0 0 5 374 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 9.357360e-01 4 370 0 95 2 0 0 0 0 95 2 -4.419615 1 0 121182 1 35 1 0 1 1 1.995946 0 0.090000 2.020000 0.082985 0.310000 0.110000 0.620000 0.280000 0.337160 0.310000 0 1.900000e-01 4.600000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 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 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-Q3-A5QY-01A-12D-A32N-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 1 111 0 22 0 1.341435e-03 0 3 0 22 2 1 6.835965e-01 2 186 0 803 2 0 4.932735e-01 1 110 0 22 2 1 9.994317e-01 133 7882 0 22 2 -3.209571 1 1 0 0 1 0 1 1 1.995946 0 0.090000 2.020000 0.082985 0.280000 0.030000 0.890000 0.180000 0.346071 0.280000 0 1.200000e-01 5.600000e-01 HERC2 8924 broad.mit.edu 37 15 28377973 28377973 + Silent SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr15:28377973C>T ENST00000261609.7 - 80 12342 c.12234G>A c.(12232-12234)ccG>ccA p.P4078P NM_004667.5 NP_004658.3 HECT and RLD domain containing E3 ubiquitin protein ligase 2 204 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) GGCGGTCACACGGACTGCAAA 0.463000 0 SO:0001819 synonymous_variant ENST00000261609.7 0 1 hg19 CCDS10021.1 TCGA-Q3-A5QY-01A-12D-A32N-08 HERC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251358.2 0 0 0 5 570 0 121 0 2.850161e-02 0 24 0 121 2 0 0 0 0 0 2 1 9.348647e-01 5 560 0 118 2 0 0 0 0 121 2 -2.416385 0 1 121396 3 41 1 0.090000 2.020000 0 0 CA12 771 broad.mit.edu 37 15 63632565 63632565 + Silent SNP C C A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr15:63632565C>A ENST00000178638.3 - 7 1109 c.669G>T c.(667-669)ggG>ggT p.G223G CA12_ENST00000422263.2_Silent_p.G163G|CA12_ENST00000344366.3_Silent_p.G223G NM_001218.3 NP_001209.1 O43570 CAH12_HUMAN carbonic anhydrase XII 16 Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909) TGGTCAGGGACCCCCGGTAGC 0.562000 0 SO:0001819 synonymous_variant ENST00000178638.3 0 1 hg19 CCDS10185.1 TCGA-Q3-A5QY-01A-12D-A32N-08 CA12-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256370.1 0 0 0 7 344 0 78 0 0 0 1 0 78 2 0 0 0 0 0 2 1 9.800639e-01 7 340 0 78 2 0 0 0 0 78 2 -3.223503 1 1 0 0 1 1 2 3 2.000691 0 0.090000 2.020000 0.096909 0.500000 0.210000 1.000000 0.430000 0.560459 0.500000 0 3.300000e-01 8.600000e-01 GRIN2A 2903 broad.mit.edu 37 16 10274159 10274159 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr16:10274159G>A ENST00000396573.2 - 3 419 c.110C>T c.(109-111)gCg>gTg p.A37V GRIN2A_ENST00000396575.2_Missense_Mutation_p.A37V|GRIN2A_ENST00000330684.3_Missense_Mutation_p.A37V|GRIN2A_ENST00000404927.2_Missense_Mutation_p.A37V|GRIN2A_ENST00000562109.1_Missense_Mutation_p.A37V NM_000833.3 NP_000824.1 Q12879 NMDE1_HUMAN glutamate receptor, ionotropic, N-methyl D-aspartate 2A 198 Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418) CAGCATCACCGCAATATTTAG 0.692000 0 SO:0001583 missense ENST00000396573.2 0 1 hg19 CCDS10539.1 . . . . . . . . . . G 37 6.015957 0.97205 . . ENSG00000183454 ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575 D;D;D;D 0.87887 -2.31;-2.31;-2.31;-2.31 4.54 4.54 0.55810 . 0.140584 0.45361 N 0.000378 D 0.91439 0.7298 L 0.54323 1.7 0.80722 D 1 D;D;D 0.89917 1.0;0.999;1.0 D;P;D 0.85130 0.997;0.87;0.983 D 0.91038 0.4869 9 . . . . 16.2901 0.82747 0.0:0.0:1.0:0.0 . 37;37;37 Q547U9;Q17RZ6;Q12879 .;.;NMDE1_HUMAN V 37 ENSP00000379818:A37V;ENSP00000385872:A37V;ENSP00000332549:A37V;ENSP00000379820:A37V . A - 2 0 GRIN2A 10181660 1.000000 0.71417 1.000000 0.80357 0.980000 0.70556 9.557000 0.98129 2.088000 0.63022 0.561000 0.74099 GCG TCGA-Q3-A5QY-01A-12D-A32N-08 GRIN2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251930.3 0 0 0 5 412 1 95 0 0 0 1 95 2 0 0 0 0 0 2 0 1.118170e-02 5 406 1 93 16 0 0 0 1 95 2 -2.708509 1 1 0 0 1 1 2 3 2.014171 0 0.090000 2.020000 0.099723 0.320000 0.110000 1.000000 0.270000 0.434096 0.320000 0 1.900000e-01 1 MYH11 4629 broad.mit.edu 37 16 15865513 15865513 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr16:15865513G>A ENST00000300036.5 - 9 1055 c.946C>T c.(946-948)Ccc>Tcc p.P316S MYH11_ENST00000576790.2_Missense_Mutation_p.P316S|MYH11_ENST00000452625.2_Missense_Mutation_p.P323S|MYH11_ENST00000396324.3_Missense_Mutation_p.P323S NM_002474.2 NP_002465.1 P35749 MYH11_HUMAN myosin, heavy chain 11, smooth muscle 123 GCTGGGATGGGCACAAAGCCA 0.517000 T CBFB AML Dom yes 16 16p13.13-p13.12 4629 myosin, heavy polypeptide 11, smooth muscle L 0 SO:0001583 missense ENST00000300036.5 0 1 hg19 CCDS10565.1 . . . . . . . . . . G 15.51 2.854428 0.51376 . . ENSG00000133392 ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625 D;D;D;D 0.86694 -2.16;-2.16;-2.16;-2.16 5.43 5.43 0.79202 Myosin head, motor domain (2); 0.148440 0.47852 D 0.000204 T 0.75642 0.3877 N 0.04335 -0.225 0.52501 D 0.999951 B;B;B;B;B;B 0.10296 0.0;0.001;0.001;0.001;0.001;0.003 B;B;B;B;B;B 0.17098 0.007;0.017;0.017;0.017;0.017;0.017 T 0.69774 -0.5054 10 0.30854 T 0.27 . 17.7989 0.88580 0.0:0.0:1.0:0.0 . 323;316;316;323;316;323 B1PS43;D2JYH7;P35749;Q3MNF1;Q3MIV8;Q3MNF0 .;.;MYH11_HUMAN;.;.;. S 316;316;323;323;323 ENSP00000300036:P316S;ENSP00000345136:P316S;ENSP00000379616:P323S;ENSP00000407821:P323S ENSP00000300036:P316S P - 1 0 MYH11 15773014 1.000000 0.71417 1.000000 0.80357 0.830000 0.47004 3.491000 0.53252 2.538000 0.85594 0.561000 0.74099 CCC TCGA-Q3-A5QY-01A-12D-A32N-08 MYH11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252192.2 0 0 0 5 319 0 61 0 1.111103e-01 0 30 0 61 2 0 0 0 0 0 2 1 9.380095e-01 5 319 0 61 2 0 0 0 0 61 2 -2.240150 0 1 0 0 1 1 2 3 2.014171 0 0.090000 2.020000 0.099723 0.410000 0.150000 1.000000 0.340000 0.505948 0.410000 0 2.500000e-01 1 CX3CL1 6376 broad.mit.edu 37 16 57415974 57415974 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr16:57415974C>T ENST00000006053.6 + 3 335 c.224C>T c.(223-225)gCc>gTc p.A75V CX3CL1_ENST00000564948.1_Missense_Mutation_p.P35S|CX3CL1_ENST00000563383.1_Missense_Mutation_p.A81V|CX3CL1_ENST00000565912.1_Missense_Mutation_p.A37V NM_002996.3 NP_002987.1 P78423 X3CL1_HUMAN chemokine (C-X3-C motif) ligand 1 5 CTGTTCTGTGCCGACCCGAAG 0.602000 0 SO:0001583 missense ENST00000006053.6 0 1 hg19 CCDS10779.1 . . . . . . . . . . C 17.45 3.392360 0.62066 . . ENSG00000006210 ENST00000006053 T 0.05580 3.42 5.45 5.45 0.79879 Chemokine interleukin-8-like domain (3); 0.000000 0.64402 D 0.000012 T 0.27169 0.0666 M 0.81682 2.555 0.41670 D 0.989234 D 0.89917 1.0 D 0.91635 0.999 T 0.00992 -1.1488 10 0.87932 D 0 -33.9119 14.8416 0.70230 0.0:1.0:0.0:0.0 . 75 P78423 X3CL1_HUMAN V 75 ENSP00000006053:A75V ENSP00000006053:A75V A + 2 0 CX3CL1 55973475 0.995000 0.38212 0.953000 0.39169 0.012000 0.07955 3.478000 0.53158 2.560000 0.86352 0.555000 0.69702 GCC TCGA-Q3-A5QY-01A-12D-A32N-08 CX3CL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257345.3 0 0 0 5 402 0 89 0 1.036845e-01 1 35 0 89 2 0 0 0 0 0 2 1 9.350197e-01 5 395 0 88 2 0 0 0 0 89 2 -2.472070 0 1 0 0 1 1 2 3 2.014171 0 0.090000 2.020000 0.099723 0.330000 0.110000 1.000000 0.270000 0.440304 0.330000 0 2.000000e-01 1 MED1 5469 broad.mit.edu 37 17 37564496 37564496 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr17:37564496G>A ENST00000300651.6 - 17 4201 c.3978C>T c.(3976-3978)gaC>gaT p.D1326D CTB-131K11.1_ENST00000582842.1_RNA|MED1_ENST00000394287.3_Intron NM_004774.3 NP_004765.2 O95243 MBD4_HUMAN mediator complex subunit 1 59 Ovarian(249;1.78e-06)|Lung SC(565;0.0262) Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146) CCATCTGGCCGTCCAGTGGGT 0.512000 HNSCC(31;0.082) Pancreas(21;279 768 2492 4877 24026) 0 SO:0001819 synonymous_variant ENST00000300651.6 0 1 hg19 CCDS11336.1 TCGA-Q3-A5QY-01A-12D-A32N-08 MED1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256943.3 0 0 0 6 605 0 123 0 2.378175e-02 0 20 0 123 2 0 0 0 0 0 2 1 9.642096e-01 6 600 0 123 2 0 0 0 0 123 2 -2.284553 0 1 121408 1 30 1 0 1 1 1.993443 0 0.090000 2.020000 0.082569 0.220000 0.090000 0.440000 0.210000 0.247136 0.220000 0 1.500000e-01 3.300000e-01 CALCOCO2 10241 broad.mit.edu 37 17 46926637 46926637 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr17:46926637G>A ENST00000258947.3 + 5 542 c.441G>A c.(439-441)caG>caA p.Q147Q CALCOCO2_ENST00000508679.1_Silent_p.Q75Q|CALCOCO2_ENST00000448105.2_Silent_p.Q171Q|CALCOCO2_ENST00000509507.1_Silent_p.Q168Q|CALCOCO2_ENST00000416445.2_Intron NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4 NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1 Q13137 CACO2_HUMAN calcium binding and coiled-coil domain 2 15 AGATTGAGCAGCACAACAAGG 0.468000 0 SO:0001819 synonymous_variant ENST00000258947.3 0 1 hg19 CCDS11538.1 TCGA-Q3-A5QY-01A-12D-A32N-08 CALCOCO2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360866.1 0 0 0 7 565 0 121 0 4.992739e-01 0 125 0 121 2 0 0 0 0 0 2 1 9.800953e-01 7 560 0 121 2 0 0 0 0 121 2 -2.445085 0 1 0 0 1 1 2 3 2.021229 0 0.090000 2.020000 0.101323 0.320000 0.130000 1.000000 0.280000 0.442599 0.320000 0 2.100000e-01 1 DSG2 1829 broad.mit.edu 37 18 29122723 29122723 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr18:29122723G>A ENST00000261590.8 + 14 2451 c.2242G>A c.(2242-2244)Gca>Aca p.A748T RP11-75N4.2_ENST00000583706.1_RNA NM_001943.3 NP_001934.2 Q14126 DSG2_HUMAN desmoglein 2 49 OV - Ovarian serous cystadenocarcinoma(10;0.0068) CACGAAGACCGCAAGGGCCAC 0.517000 0 SO:0001583 missense ENST00000261590.8 0 1 hg19 CCDS42423.1 . . . . . . . . . . g 4.453 0.083827 0.08583 . . ENSG00000046604 ENST00000261590 T 0.58506 0.33 5.97 -2.61 0.06171 . 1.161370 0.06133 N 0.671107 T 0.20740 0.0499 N 0.02011 -0.69 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.24119 -1.0169 10 0.02654 T 1 . 2.1079 0.03695 0.1819:0.1398:0.4044:0.274 . 748 Q14126 DSG2_HUMAN T 748 ENSP00000261590:A748T ENSP00000261590:A748T A + 1 0 DSG2 27376721 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -0.708000 0.05035 -0.360000 0.08138 -0.285000 0.09966 GCA TCGA-Q3-A5QY-01A-12D-A32N-08 DSG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447506.1 0 0 0 6 569 0 115 0 2.181656e-02 0 18 0 115 2 0 0 0 0 0 2 1 9.637770e-01 6 562 0 115 2 0 0 0 0 115 2 -1.970033 0 1 120998 4 37 1 0 1 1 1.995421 0 0.090000 2.020000 0.082985 0.240000 0.100000 0.470000 0.220000 0.262399 0.240000 0 1.600000e-01 3.500000e-01 C19orf57 79173 broad.mit.edu 37 19 14000364 14000364 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr19:14000364G>A ENST00000586783.1 - 5 1304 c.1305C>T c.(1303-1305)tcC>tcT p.S435S C19orf57_ENST00000346736.2_Silent_p.S435S|C19orf57_ENST00000454313.1_Silent_p.S435S|C19orf57_ENST00000591586.1_Intron Q0VDD7 CS057_HUMAN chromosome 19 open reading frame 57 14 OV - Ovarian serous cystadenocarcinoma(19;2e-21) ATGCATGACCGGAATCTCCAG 0.622000 0 SO:0001819 synonymous_variant ENST00000586783.1 0 1 hg19 TCGA-Q3-A5QY-01A-12D-A32N-08 C19orf57-003 NOVEL basic protein_coding protein_coding OTTHUMT00000457947.1 0 0 0 5 407 0 88 0 0 0 1 0 88 2 0 0 0 0 0 2 1 9.342092e-01 5 398 0 88 2 0 0 0 0 88 2 -2.766049 1 1 121412 4 38 1 0 1 1 1.985301 0 0.090000 2.020000 0.080483 0.280000 0.100000 0.570000 0.260000 0.309905 0.280000 0 1.800000e-01 4.300000e-01 GNA15 2769 broad.mit.edu 37 19 3151725 3151725 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr19:3151725G>A ENST00000262958.3 + 4 764 c.506G>A c.(505-507)cGc>cAc p.R169H AC005264.2_ENST00000587587.1_RNA NM_002068.2 NP_002059.2 P30679 GNA15_HUMAN guanine nucleotide binding protein (G protein), alpha 15 (Gq class) 18 Hepatocellular(1079;0.137) CACCTGGAGCGCATCACCGAG 0.632000 0 SO:0001583 missense ENST00000262958.3 0 1 hg19 CCDS12104.1 . . . . . . . . . . G 29.7 5.027420 0.93518 . . ENSG00000060558 ENST00000262958 D 0.91996 -2.95 4.59 4.59 0.56863 G protein alpha subunit, helical insertion (2); 0.000000 0.85682 U 0.000000 D 0.96935 0.8999 M 0.94101 3.495 0.58432 D 0.999996 D 0.89917 1.0 D 0.87578 0.998 D 0.98010 1.0365 10 0.87932 D 0 . 14.9063 0.70721 0.0:0.0:1.0:0.0 . 169 P30679 GNA15_HUMAN H 169 ENSP00000262958:R169H ENSP00000262958:R169H R + 2 0 GNA15 3102725 1.000000 0.71417 0.987000 0.45799 0.995000 0.86356 6.643000 0.74334 2.093000 0.63338 0.546000 0.68486 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 GNA15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452320.2 0 0 0 6 598 0 125 0 5.047811e-02 0 30 0 125 2 0 0 0 0 0 2 1 9.634541e-01 5 590 0 124 2 0 0 0 0 125 2 -2.043793 0 1 121396 6 41 1 0 1 1 1.985301 0 0.090000 2.020000 0.080483 0.230000 0.090000 0.440000 0.220000 0.249236 0.230000 0 1.500000e-01 3.400000e-01 VN1R2 317701 broad.mit.edu 37 19 53762737 53762737 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr19:53762737G>A ENST00000341702.3 + 1 1193 c.1109G>A c.(1108-1110)cGt>cAt p.R370H VN1R2_ENST00000598458.1_Intron NM_173856.2 NP_776255.2 Q8NFZ6 VN1R2_HUMAN vomeronasal 1 receptor 2 31 CTCATGTGCCGTGACCCCAGC 0.428000 0 SO:0001583 missense ENST00000341702.3 0 1 hg19 CCDS12862.1 . . . . . . . . . . G 4.482 0.089310 0.08632 4.54E-4 0.0 ENSG00000196131 ENST00000341702 T 0.41065 1.01 2.94 -0.602 0.11634 . . . . . T 0.22399 0.0540 L 0.27053 0.805 0.09310 N 1 B 0.31879 0.344 B 0.29862 0.108 T 0.23154 -1.0196 9 0.12430 T 0.62 . 5.3114 0.15833 0.451:0.0:0.549:0.0 . 370 Q8NFZ6 VN1R2_HUMAN H 370 ENSP00000351244:R370H ENSP00000351244:R370H R + 2 0 VN1R2 58454549 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -0.212000 0.09319 -0.020000 0.14032 -0.234000 0.12200 CGT TCGA-Q3-A5QY-01A-12D-A32N-08 VN1R2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464285.1 0 0 0 6 666 0 124 0 0 0 0 124 2 0 0 0 0 0 2 1 9.641011e-01 6 660 0 123 2 0 0 0 0 124 2 -2.336937 0 1 121412 7 44 1 1 2 3 2.032425 0 0.090000 2.020000 0.104110 0.240000 0.090000 1.000000 0.190000 0.400344 0.240000 0 1.500000e-01 1 U2AF2 11338 broad.mit.edu 37 19 56185361 56185361 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr19:56185361G>A ENST00000308924.4 + 12 1395 c.1355G>A c.(1354-1356)cGc>cAc p.R452H EPN1_ENST00000411543.2_5'Flank|U2AF2_ENST00000450554.2_Missense_Mutation_p.R448H|U2AF2_ENST00000590551.1_Missense_Mutation_p.R284H|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|EPN1_ENST00000085079.7_5'Flank|EPN1_ENST00000270460.6_5'Flank|CTD-2537I9.13_ENST00000592252.1_RNA P26368 U2AF2_HUMAN U2 small nuclear RNA auxiliary factor 2 21 Colorectal(82;0.00244)|Ovarian(87;0.133) BRCA - Breast invasive adenocarcinoma(297;0.18) CTGACGGGCCGCAAGTTCGCC 0.577000 0 SO:0001583 missense ENST00000308924.4 0 1 hg19 CCDS12933.1 . . . . . . . . . . G 34 5.397206 0.96009 . . ENSG00000063244 ENST00000308924;ENST00000450554 T;T 0.16743 2.32;2.32 4.42 4.42 0.53409 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3); 0.000000 0.85682 U 0.000000 T 0.56963 0.2021 H 0.96996 3.92 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.74518 -0.3639 10 0.87932 D 0 -18.4012 16.161 0.81712 0.0:0.0:1.0:0.0 . 452;448 P26368;P26368-2 U2AF2_HUMAN;. H 452;448 ENSP00000307863:R452H;ENSP00000388475:R448H ENSP00000307863:R452H R + 2 0 U2AF2 60877173 1.000000 0.71417 0.999000 0.59377 0.994000 0.84299 8.751000 0.91628 2.173000 0.68751 0.478000 0.44815 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 U2AF2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000453599.1 0 0 0 6 570 0 125 0 7.917928e-01 0 278 0 125 2 0 0 0 0 0 2 1 9.633850e-01 6 561 0 124 2 0 0 0 0 125 2 -2.005133 0 1 0 0 1 1 2 3 2.016892 0 0.090000 2.020000 0.100524 0.280000 0.100000 1.000000 0.230000 0.402969 0.280000 0 1.700000e-01 1 TRIM28 10155 broad.mit.edu 37 19 59057217 59057217 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr19:59057217G>A ENST00000253024.5 + 3 829 c.540G>A c.(538-540)gcG>gcA p.A180A RN7SL525P_ENST00000579267.1_RNA|TRIM28_ENST00000341753.6_Intron NM_005762.2 NP_005753.1 Q13263 TIF1B_HUMAN tripartite motif containing 28 19 all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184) GTGTAGAGGCGCACCAGCGGG 0.577000 0 SO:0001819 synonymous_variant ENST00000253024.5 0 1 hg19 CCDS12985.1 TCGA-Q3-A5QY-01A-12D-A32N-08 TRIM28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000467074.1 0 0 0 5 342 0 85 0 7.110816e-01 0 163 0 85 2 0 0 0 0 0 2 1 9.340755e-01 5 334 0 85 2 0 0 0 0 85 2 -2.850338 1 1 0 0 1 1 2 3 2.016892 0 0.090000 2.020000 0.100524 0.390000 0.140000 1.000000 0.310000 0.491408 0.390000 0 2.300000e-01 1 TCHH 7062 broad.mit.edu 37 1 152082631 152082631 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr1:152082631C>T ENST00000368804.1 - 2 3061 c.3062G>A c.(3061-3063)cGc>cAc p.R1021H NM_007113.2 NP_009044.2 Q07283 TRHY_HUMAN trichohyalin 105 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GTCTTTTTTGCGGTActgcct 0.557000 0 SO:0001583 missense ENST00000368804.1 0 1 hg19 CCDS41396.1 . . . . . . . . . . C 7.212 0.595657 0.13875 . . ENSG00000159450 ENST00000368804 T 0.14144 2.53 2.67 -1.04 0.10068 . . . . . T 0.01489 0.0048 N 0.19112 0.55 0.09310 N 1 P 0.39624 0.681 B 0.24541 0.054 T 0.43032 -0.9416 9 0.41790 T 0.15 . 2.5479 0.04742 0.3961:0.3433:0.0:0.2606 . 1021 Q07283 TRHY_HUMAN H 1021 ENSP00000357794:R1021H ENSP00000357794:R1021H R - 2 0 TCHH 150349255 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 0.086000 0.14935 -0.613000 0.05694 0.462000 0.41574 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 TCHH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000036671.2 0 0 0 6 721 1 156 0 0 0 1 1 156 2 0 0 0 0 0 2 0 2.277013e-02 6 708 1 155 16 0 0 0 1 156 2 -1.917199 0 1 120964 3 36 1 1 2 3 2.004596 0 0.090000 2.020000 0.097715 0.210000 0.080000 1.000000 0.180000 0.327014 0.210000 0 1.300000e-01 4.100000e-01 KCNH1 3756 broad.mit.edu 37 1 211263994 211263994 + Nonsense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr1:211263994G>A ENST00000271751.4 - 4 376 c.349C>T c.(349-351)Cga>Tga p.R117* KCNH1_ENST00000367007.4_Nonsense_Mutation_p.R117* O95259 KCNH1_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 1 68 TGTTCGTTTCGAATTGGAGCA 0.378000 0 SO:0001587 stop_gained ENST00000271751.4 0 1 hg19 CCDS1496.1 . . . . . . . . . . G 38 7.239776 0.98157 . . ENSG00000143473 ENST00000271751;ENST00000367007 . . . 5.22 4.28 0.50868 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.05351 T 0.99 . 11.8706 0.52519 0.0:0.0:0.6718:0.3282 . . . . X 117 . ENSP00000271751:R117X R - 1 2 KCNH1 209330617 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 2.394000 0.44450 1.141000 0.42275 0.655000 0.94253 CGA TCGA-Q3-A5QY-01A-12D-A32N-08 KCNH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000088332.1 0 0 0 8 305 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 9.884484e-01 8 297 0 48 2 0 0 0 0 49 2 -3.319839 1 1 0 0 1 1 2 3 2.004596 0 0.090000 2.020000 0.097715 0.630000 0.290000 1.000000 1.000000 0.671910 0.630000 0 4.300000e-01 1 EGLN1 54583 broad.mit.edu 37 1 231557097 231557097 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr1:231557097G>A ENST00000366641.3 - 1 3693 c.538C>T c.(538-540)Cgg>Tgg p.R180W EGLN1_ENST00000476717.1_5'Flank NM_022051.2 NP_071334.1 egl-9 family hypoxia-inducible factor 1 16 Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244) CCGTTGGGCCGCAGGCCGCCG 0.687000 0 SO:0001583 missense ENST00000366641.3 0 1 hg19 CCDS1595.1 . . . . . . . . . . G 13.82 2.352116 0.41700 . . ENSG00000135766 ENST00000366641 D 0.87256 -2.23 5.23 0.483 0.16820 . 0.411550 0.22376 N 0.060876 T 0.75968 0.3922 L 0.43923 1.385 0.25462 N 0.98791 B 0.32800 0.385 B 0.16289 0.015 T 0.67237 -0.5721 10 0.87932 D 0 -11.8165 5.589 0.17291 0.0734:0.1143:0.5506:0.2617 . 180 Q9GZT9 EGLN1_HUMAN W 180 ENSP00000355601:R180W ENSP00000355601:R180W R - 1 2 EGLN1 229623720 1.000000 0.71417 0.056000 0.19401 0.369000 0.29798 0.806000 0.27126 0.175000 0.19841 0.557000 0.71058 CGG TCGA-Q3-A5QY-01A-12D-A32N-08 EGLN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092879.1 0 0 0 4 127 0 32 0 1.526191e-01 0 18 0 32 2 0 0 0 0 0 2 1 8.915402e-01 4 127 0 31 2 0 0 0 0 32 2 -6.547447 1 1 119718 5 24 1 1 2 3 2.004596 0 0.090000 2.020000 0.097715 0.800000 0.260000 1.000000 1.000000 0.762988 0.800000 0 4.700000e-01 1 ADPRHL2 54936 broad.mit.edu 37 1 36557376 36557376 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr1:36557376C>T ENST00000373178.4 + 3 496 c.466C>T c.(466-468)Cgg>Tgg p.R156W NM_017825.2 NP_060295.1 Q9NX46 ARHL2_HUMAN ADP-ribosylhydrolase like 2 8 Myeloproliferative disorder(586;0.0393) AGGTGCCATGCGGGTGGCTGG 0.582000 0 SO:0001583 missense ENST00000373178.4 0 1 hg19 CCDS402.1 . . . . . . . . . . C 19.12 3.766089 0.69878 . . ENSG00000116863 ENST00000373178;ENST00000540867;ENST00000543954 T 0.59906 0.23 5.35 2.31 0.28768 . 0.000000 0.85682 D 0.000000 D 0.82444 0.5038 H 0.96269 3.795 0.58432 D 0.999991 D 0.89917 1.0 D 0.97110 1.0 D 0.88017 0.2766 10 0.87932 D 0 -16.3839 14.9511 0.71074 0.6175:0.3825:0.0:0.0 . 156 Q9NX46 ARHL2_HUMAN W 156;76;2 ENSP00000362273:R156W ENSP00000362273:R156W R + 1 2 ADPRHL2 36329963 1.000000 0.71417 1.000000 0.80357 0.882000 0.50991 4.643000 0.61390 0.608000 0.30000 -0.261000 0.10672 CGG TCGA-Q3-A5QY-01A-12D-A32N-08 ADPRHL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000020199.1 0 0 0 5 456 0 99 0 3.327492e-01 0 93 0 99 2 0 0 0 0 0 2 1 9.353167e-01 5 449 0 99 2 0 0 0 0 99 2 -2.628917 1 1 0 0 1 1 2 3 2.020181 0 0.090000 2.020000 0.101323 0.300000 0.100000 1.000000 0.250000 0.424246 0.300000 0 1.800000e-01 1 PTGFR 5737 broad.mit.edu 37 1 79002208 79002208 + Missense_Mutation SNP C C A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr1:79002208C>A ENST00000370757.3 + 3 1153 c.916C>A c.(916-918)Ctt>Att p.L306I PTGFR_ENST00000370758.1_Missense_Mutation_p.L306I|PTGFR_ENST00000370756.3_3'UTR NM_000959.3 NP_000950.1 P43088 PF2R_HUMAN prostaglandin F receptor (FP) 33 Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287) GGTATATATTCTTCTACGAAA 0.388000 0 SO:0001583 missense ENST00000370757.3 0 1 hg19 CCDS686.1 . . . . . . . . . . C 26.5 4.743931 0.89663 . . ENSG00000122420 ENST00000370758;ENST00000370757 T;T 0.44881 0.91;0.91 5.66 5.66 0.87406 . 0.000000 0.85682 D 0.000000 T 0.59473 0.2196 M 0.65498 2.005 0.52501 D 0.999954 D 0.76494 0.999 D 0.78314 0.991 T 0.57551 -0.7792 10 0.54805 T 0.06 -21.887 20.1454 0.98074 0.0:1.0:0.0:0.0 . 306 P43088 PF2R_HUMAN I 306 ENSP00000359794:L306I;ENSP00000359793:L306I ENSP00000359793:L306I L + 1 0 PTGFR 78774796 1.000000 0.71417 1.000000 0.80357 0.918000 0.54935 5.903000 0.69877 2.840000 0.97914 0.655000 0.94253 CTT TCGA-Q3-A5QY-01A-12D-A32N-08 PTGFR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026582.1 0 0 0 7 546 0 82 0 2.333269e-04 0 2 0 82 2 0 0 0 0 0 2 1 9.803414e-01 7 543 0 82 2 0 0 0 0 82 2 -2.968589 1 1 0 0 1 1 2 3 2.020181 0 0.090000 2.020000 0.101323 0.330000 0.130000 1.000000 0.280000 0.450983 0.330000 0 2.100000e-01 1 EEF1A2 1917 broad.mit.edu 37 20 62122019 62122019 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr20:62122019G>A ENST00000298049.7 - 5 912 c.842C>T c.(841-843)gCg>gTg p.A281V EEF1A2_ENST00000217182.3_Missense_Mutation_p.A281V Q05639 EF1A2_HUMAN eukaryotic translation elongation factor 1 alpha 2 20 all_cancers(38;9.45e-12) BRCA - Breast invasive adenocarcinoma(10;1.22e-05) GTTCACTGGCGCAAAGGTCAC 0.637000 0 SO:0001583 missense ENST00000298049.7 0 1 hg19 CCDS13522.1 . . . . . . . . . . G 17.45 3.392399 0.62066 . . ENSG00000101210 ENST00000298049;ENST00000217182 T;T 0.62364 0.03;0.03 3.82 3.82 0.43975 Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1); 0.060894 0.64402 D 0.000005 T 0.80919 0.4716 M 0.86420 2.815 0.80722 D 1 D;D 0.89917 1.0;0.989 D;P 0.71414 0.973;0.824 D 0.85861 0.1410 10 0.87932 D 0 -14.6002 16.0768 0.80974 0.0:0.0:1.0:0.0 . 257;281 Q59GP5;Q05639 .;EF1A2_HUMAN V 281 ENSP00000298049:A281V;ENSP00000217182:A281V ENSP00000217182:A281V A - 2 0 EEF1A2 61592463 1.000000 0.71417 0.393000 0.26258 0.050000 0.14768 9.616000 0.98359 1.847000 0.53656 0.556000 0.70494 GCG TCGA-Q3-A5QY-01A-12D-A32N-08 EEF1A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080495.1 0 0 0 6 420 0 113 0 9.961369e-03 0 9 0 113 2 0 0 0 0 0 2 1 9.644561e-01 6 417 0 113 2 0 0 0 0 113 2 -2.701258 1 1 0 0 1 1 2 3 2.009314 0 0.090000 2.020000 0.098921 0.370000 0.140000 1.000000 0.310000 0.463850 0.370000 0 2.300000e-01 1 BRWD1 54014 broad.mit.edu 37 21 40630429 40630429 + Silent SNP T T C TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr21:40630429T>C ENST00000333229.2 - 18 2382 c.2055A>G c.(2053-2055)gaA>gaG p.E685E BRWD1_ENST00000342449.3_Silent_p.E685E|BRWD1_ENST00000380800.3_Silent_p.E685E NM_018963.4 NP_061836.2 Q9NSI6 BRWD1_HUMAN bromodomain and WD repeat domain containing 1 58 Prostate(19;8.44e-08)|all_epithelial(19;0.223) GGGGTGTTTCTTCACCATTTG 0.388000 Melanoma(170;988 1986 4794 16843 39731) 0 SO:0001819 synonymous_variant ENST00000333229.2 0 1 hg19 CCDS13662.1 . . . . . . . . . . T 4.863 0.160340 0.09287 . . ENSG00000185658 ENST00000455867 . . . 5.46 1.8 0.24995 . . . . . T 0.57140 0.2033 . . . 0.80722 D 1 . . . . . . T 0.48031 -0.9070 4 . . . -13.145 8.7115 0.34387 0.0:0.2966:0.0:0.7034 . . . . G 397 . . R - 1 2 BRWD1 39552299 1.000000 0.71417 0.992000 0.48379 0.658000 0.38924 1.633000 0.37113 0.075000 0.16796 0.533000 0.62120 AGA TCGA-Q3-A5QY-01A-12D-A32N-08 BRWD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141398.3 0 0 0 13 783 0 170 0 9.749028e-04 0 3 0 170 2 0 0 0 0 0 2 1 9.994995e-01 13 775 0 167 2 0 0 0 0 170 2 -3.080258 1 1 0 0 1 0 1 1 1.985676 0 0.090000 2.020000 0.080901 0.360000 0.200000 0.580000 0.360000 0.380501 0.360000 0 2.700000e-01 4.800000e-01 TRIOBP 11078 broad.mit.edu 37 22 38120997 38120997 + Nonsense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr22:38120997C>T ENST00000406386.3 + 7 2689 c.2434C>T c.(2434-2436)Cag>Tag p.Q812* NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 12 Melanoma(58;0.0574) AGCCACCCAACAGGACAACCC 0.517000 0 SO:0001587 stop_gained ENST00000406386.3 0 1 hg19 CCDS43015.1 . . . . . . . . . . C 39 7.393041 0.98255 . . ENSG00000100106 ENST00000406386;ENST00000417174 . . . 4.21 0.597 0.17504 . . . . . . . . . . . 0.09310 N 1 . . . . . . . . . . 0.07175 T 0.84 . 9.6691 0.40002 0.5296:0.4704:0.0:0.0 . . . . X 812 . ENSP00000384312:Q812X Q + 1 0 TRIOBP 36450943 0.000000 0.05858 0.000000 0.03702 0.516000 0.34256 -3.739000 0.00379 0.030000 0.15379 0.460000 0.39030 CAG TCGA-Q3-A5QY-01A-12D-A32N-08 TRIOBP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000319439.2 0 0 0 8 410 0 105 0 0 0 1 0 105 2 0 0 0 0 0 2 1 9.893118e-01 8 408 0 105 2 0 0 0 0 105 2 -7.511531 1 1 0 0 1 1 2 3 2.016604 0 0.090000 2.020000 0.100524 0.490000 0.210000 1.000000 0.430000 0.568694 0.490000 0 3.300000e-01 1 XRCC6 2547 broad.mit.edu 37 22 42018069 42018069 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr22:42018069G>A ENST00000359308.4 + 1 716 c.61G>A c.(61-63)Gaa>Aaa p.E21K XRCC6_ENST00000360079.3_Missense_Mutation_p.E21K|XRCC6_ENST00000428575.2_5'UTR|XRCC6_ENST00000405878.1_Missense_Mutation_p.E21K|XRCC6_ENST00000405506.1_Silent_p.K8K|XRCC6_ENST00000402580.3_Missense_Mutation_p.E21K|DESI1_ENST00000263256.6_5'Flank P12956 XRCC6_HUMAN X-ray repair complementing defective repair in Chinese hamster cells 6 31 GGAAGAACAAGAAGAGAACCT 0.483000 Non-homologous end-joining 0 SO:0001583 missense ENST00000359308.4 0 1 hg19 CCDS14021.1 . . . . . . . . . . G 22.9 4.350682 0.82132 . . ENSG00000196419 ENST00000360079;ENST00000402580;ENST00000359308;ENST00000405878;ENST00000402409 . . . 5.36 4.33 0.51752 . 0.457363 0.21898 N 0.067499 T 0.58148 0.2102 M 0.61703 1.905 0.80722 D 1 B;B;B 0.16166 0.016;0.01;0.01 B;B;B 0.14578 0.011;0.007;0.007 T 0.53885 -0.8375 9 0.24483 T 0.36 -1.1576 13.523 0.61578 0.0:0.1562:0.8438:0.0 . 21;21;21 B1AHC7;B1AHC8;P12956 .;.;XRCC6_HUMAN K 21 . ENSP00000352257:E21K E + 1 0 XRCC6 40348015 0.996000 0.38824 0.051000 0.19133 0.208000 0.24298 2.401000 0.44513 1.229000 0.43630 0.655000 0.94253 GAA TCGA-Q3-A5QY-01A-12D-A32N-08 XRCC6-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321688.1 0 0 0 6 284 0 60 0 9.229783e-01 0 219 0 60 2 0 0 0 0 0 2 1 9.638869e-01 6 280 0 60 2 0 0 0 0 60 2 -6.786469 1 1 0 0 1 1 2 3 2.016604 0 0.090000 2.020000 0.100524 0.550000 0.210000 1.000000 0.450000 0.608734 0.550000 0 3.400000e-01 1 TTLL8 164714 broad.mit.edu 37 22 50487686 50487686 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr22:50487686C>T ENST00000266182.6 - 3 255 c.256G>A c.(256-258)Gac>Aac p.D86N TTLL8_ENST00000440475.1_Missense_Mutation_p.D86N|TTLL8_ENST00000477219.1_5'UTR A6PVC2 TTLL8_HUMAN tubulin tyrosine ligase-like family, member 8 12 all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162) ACCATCACGTCGTGGATGTTG 0.527000 0 SO:0001583 missense ENST00000266182.6 0 1 hg19 . . . . . . . . . . C 3.584 -0.084930 0.07097 . . ENSG00000138892 ENST00000266182;ENST00000440475;ENST00000433387 T;T;T 0.16743 2.32;2.32;2.32 4.67 2.56 0.30785 . 0.851391 0.09565 U 0.785033 T 0.12050 0.0293 N 0.19112 0.55 0.20638 N 0.999876 B 0.13145 0.007 B 0.06405 0.002 T 0.33727 -0.9857 10 0.30078 T 0.28 . 11.2427 0.48979 0.0:0.8981:0.0:0.1019 . 86 B5MDV0 . N 86;86;122 ENSP00000266182:D86N;ENSP00000387509:D86N;ENSP00000392252:D122N ENSP00000266182:D86N D - 1 0 TTLL8 48829813 0.009000 0.17119 0.054000 0.19295 0.000000 0.00434 1.434000 0.34958 0.390000 0.25115 -1.149000 0.01842 GAC TCGA-Q3-A5QY-01A-12D-A32N-08 TTLL8-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 0 12 641 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 9.990270e-01 12 630 0 136 2 0 0 0 0 138 2 -2.508987 1 1 121062 1 33 1 0 0 0 1.973348 0 0.090000 2.020000 0.071618 0.400000 0.220000 0.660000 0.390000 0.423747 0.400000 0 3.000000e-01 5.300000e-01 FIGN 55137 broad.mit.edu 37 2 164467288 164467288 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:164467288G>A ENST00000333129.3 - 3 1368 c.1054C>T c.(1054-1056)Ccc>Tcc p.P352S FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron NM_018086.2 NP_060556.2 Q5HY92 FIGN_HUMAN fidgetin 47 CTGTTGTCGGGCATTCTGTAC 0.448000 0 SO:0001583 missense ENST00000333129.3 0 1 hg19 CCDS2221.2 . . . . . . . . . . G 3.349 -0.132926 0.06711 . . ENSG00000182263 ENST00000333129 D 0.91843 -2.92 5.94 4.15 0.48705 . 0.456711 0.22595 N 0.058032 D 0.85375 0.5682 L 0.29908 0.895 0.54753 D 0.999989 B 0.17465 0.022 B 0.19666 0.026 T 0.76575 -0.2909 10 0.10636 T 0.68 -4.4398 12.098 0.53765 0.065:0.1212:0.8138:0.0 . 352 Q5HY92 FIGN_HUMAN S 352 ENSP00000333836:P352S ENSP00000333836:P352S P - 1 0 FIGN 164175534 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.220000 0.51207 0.852000 0.35287 0.563000 0.77884 CCC TCGA-Q3-A5QY-01A-12D-A32N-08 FIGN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000157220.2 0 0 0 6 528 0 99 0 0 0 1 0 99 2 0 0 0 0 0 2 1 9.641183e-01 6 524 0 97 2 0 0 0 0 99 2 -1.801253 0 1 0 0 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.290000 0.110000 1.000000 0.240000 0.386585 0.290000 0 1.800000e-01 5.400000e-01 UBR3 130507 broad.mit.edu 37 2 170814986 170814986 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:170814986C>T ENST00000272793.5 + 24 3634 c.3584C>T c.(3583-3585)gCg>gTg p.A1195V UBR3_ENST00000418381.1_Missense_Mutation_p.A1195V Q6ZT12 UBR3_HUMAN ubiquitin protein ligase E3 component n-recognin 3 (putative) 33 AAATTGCTTGCGGAGTTTGCT 0.348000 0 SO:0001583 missense ENST00000272793.5 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 36|36 5.812118|5.812118 0.96975|0.96975 .|. .|. ENSG00000144357|ENSG00000144357 ENST00000272793;ENST00000442603;ENST00000418381|ENST00000392632 T;T|. 0.57595|. 0.39;0.39|. 6.15|6.15 6.15|6.15 0.99193|0.99193 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.81842|0.81842 0.4908|0.4908 M|M 0.77103|0.77103 2.36|2.36 0.80722|0.80722 D|D 1|1 D;D|. 0.89917|. 1.0;1.0|. D;D|. 0.75484|. 0.986;0.986|. T|T 0.79642|0.79642 -0.1718|-0.1718 10|5 0.59425|. D|. 0.04|. .|. 20.8387|20.8387 0.99724|0.99724 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 1195;1195|. Q6ZT12;E7EVK3|. UBR3_HUMAN;.|. V|W 1195|253 ENSP00000272793:A1195V;ENSP00000396068:A1195V|. ENSP00000272793:A1195V|. A|R +|+ 2|1 0|2 UBR3|UBR3 170523232|170523232 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.949000|0.949000 0.60115|0.60115 7.786000|7.786000 0.85741|0.85741 2.932000|2.932000 0.99384|0.99384 0.643000|0.643000 0.83706|0.83706 GCG|CGG TCGA-Q3-A5QY-01A-12D-A32N-08 UBR3-001 KNOWN non_canonical_conserved|basic|appris_principal protein_coding protein_coding OTTHUMT00000255290.2 0 0 0 19 507 0 91 0 7.543373e-02 1 11 0 91 2 0 0 0 0 0 2 1 9.999895e-01 17 501 0 89 2 0 0 0 0 91 2 -3.239632 1 1 0 0 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.850000 0.510000 1.000000 1.000000 0.838982 0.850000 1 6.600000e-01 1 TTN 7273 broad.mit.edu 37 2 179476531 179476531 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:179476531G>A ENST00000591111.1 - 218 45806 c.45582C>T c.(45580-45582)ggC>ggT p.G15194G TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Silent_p.G14267G|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.G7770G|TTN_ENST00000589042.1_Silent_p.G16835G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Silent_p.G7962G|TTN_ENST00000359218.5_Silent_p.G7895G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CACTTGGGTGGCCAACTCCAG 0.443000 0 SO:0001819 synonymous_variant ENST00000591111.1 0 1 hg19 TCGA-Q3-A5QY-01A-12D-A32N-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 6 647 0 127 0 1.299328e-04 0 2 0 127 2 0 0 0 0 0 2 1 9.640804e-01 6 642 0 125 2 0 0 0 0 127 2 -2.015166 0 1 0 0 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.230000 0.090000 1.000000 0.200000 0.342268 0.230000 0 1.500000e-01 4.400000e-01 RNF25 64320 broad.mit.edu 37 2 219529962 219529962 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:219529962G>A ENST00000295704.2 - 8 1022 c.582C>T c.(580-582)gtC>gtT p.V194V NM_022453.2 NP_071898.2 Q96BH1 RNF25_HUMAN ring finger protein 25 24 Renal(207;0.0474) ACTGCACACCGACTGCCTTCT 0.532000 0 SO:0001819 synonymous_variant ENST00000295704.2 0 1 hg19 CCDS2420.1 TCGA-Q3-A5QY-01A-12D-A32N-08 RNF25-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256721.1 0 0 1 7 296 0 65 1 4.756698e-01 12 51 0 65 2 0 0 0 0 0 2 1 9.802361e-01 7 293 0 65 2 0 0 0 0 65 2 -3.052348 1 1 121412 2 32 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.580000 0.250000 1.000000 1.000000 0.626736 0.580000 0 3.800000e-01 1 IRS1 3667 broad.mit.edu 37 2 227662683 227662683 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:227662683G>A ENST00000305123.5 - 1 1792 c.772C>T c.(772-774)Cgg>Tgg p.R258W IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA NM_005544.2 NP_005535.1 P35568 IRS1_HUMAN insulin receptor substrate 1 69 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) CTCATGGCCCGCATGGCCTCC 0.637000 OREG0015248 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000305123.5 0 1 hg19 CCDS2463.1 . . . . . . . . . . G 17.13 3.310295 0.60414 . . ENSG00000169047 ENST00000305123 T 0.47177 0.85 5.79 2.9 0.33743 Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4); 0.117936 0.39146 N 0.001442 T 0.55800 0.1943 L 0.34521 1.04 0.47214 D 0.999354 D 0.89917 1.0 D 0.66716 0.946 T 0.57785 -0.7751 10 0.87932 D 0 -30.8633 14.6021 0.68447 0.0:0.0:0.4974:0.5026 . 258 P35568 IRS1_HUMAN W 258 ENSP00000304895:R258W ENSP00000304895:R258W R - 1 2 IRS1 227370927 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 2.388000 0.44398 0.306000 0.22856 0.561000 0.74099 CGG TCGA-Q3-A5QY-01A-12D-A32N-08 IRS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256886.3 0 0 0 5 444 0 119 0 2.948144e-03 0 6 0 119 2 0 0 0 0 0 2 1 9.344885e-01 5 435 0 117 2 0 0 0 0 119 2 -2.217217 0 1 0 0 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.290000 0.100000 1.000000 0.240000 0.390369 0.290000 0 1.800000e-01 5.700000e-01 COL6A3 1293 broad.mit.edu 37 2 238305387 238305387 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:238305387G>A ENST00000295550.4 - 2 526 c.74C>T c.(73-75)gCc>gTc p.A25V COL6A3_ENST00000472056.1_Missense_Mutation_p.A25V|COL6A3_ENST00000409809.1_Missense_Mutation_p.A25V|COL6A3_ENST00000392004.3_Missense_Mutation_p.A25V|COL6A3_ENST00000353578.4_Missense_Mutation_p.A25V|COL6A3_ENST00000346358.4_Missense_Mutation_p.A25V|COL6A3_ENST00000392003.2_Missense_Mutation_p.A25V|COL6A3_ENST00000347401.3_Missense_Mutation_p.A25V NM_004369.3 NP_004360.2 P12111 CO6A3_HUMAN collagen, type VI, alpha 3 217 Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203) CTGCTGCTGGGCATGAGTTGT 0.423000 0 SO:0001583 missense ENST00000295550.4 0 1 hg19 CCDS33412.1 . . . . . . . . . . G 10.40 1.339245 0.24339 . . ENSG00000163359 ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762 T;T;T;D;T;T;T;T;T 0.88509 -1.09;-1.09;-1.08;-2.39;-1.08;-1.09;-1.08;-0.04;-1.09 5.46 3.62 0.41486 . 0.124395 0.35805 N 0.002975 D 0.92446 0.7602 M 0.61703 1.905 0.25430 N 0.988196 D;B;B;D;D;P 0.71674 0.977;0.006;0.013;0.971;0.998;0.943 P;B;B;P;D;P 0.66602 0.597;0.004;0.017;0.659;0.945;0.5 D 0.86732 0.1949 10 0.56958 D 0.05 . 14.2564 0.66055 0.0:0.3088:0.6912:0.0 . 25;25;25;25;25;25 E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111 .;.;.;.;.;CO6A3_HUMAN V 25 ENSP00000295550:A25V;ENSP00000315609:A25V;ENSP00000315873:A25V;ENSP00000418285:A25V;ENSP00000386844:A25V;ENSP00000295546:A25V;ENSP00000375861:A25V;ENSP00000375860:A25V;ENSP00000389539:A25V ENSP00000295550:A25V A - 2 0 COL6A3 237970126 0.997000 0.39634 0.295000 0.24960 0.037000 0.13140 2.286000 0.43496 0.638000 0.30545 0.650000 0.86243 GCC TCGA-Q3-A5QY-01A-12D-A32N-08 COL6A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315790.2 0 0 0 5 453 0 81 0 9.365902e-02 0 38 0 81 2 0 0 0 0 0 2 1 9.364127e-01 6 448 0 81 2 0 0 0 0 81 2 -2.274683 0 1 0 0 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.280000 0.100000 1.000000 0.240000 0.385554 0.280000 0 1.700000e-01 5.600000e-01 NRXN1 9378 broad.mit.edu 37 2 51254959 51254959 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:51254959G>A ENST00000406316.2 - 2 1929 c.453C>T c.(451-453)agC>agT p.S151S NRXN1_ENST00000405581.1_Silent_p.S151S|NRXN1_ENST00000406859.3_Silent_p.S151S|NRXN1_ENST00000404971.1_Silent_p.S151S|NRXN1_ENST00000401669.2_Silent_p.S151S|NRXN1_ENST00000402717.3_Silent_p.S151S|NRXN1_ENST00000405472.3_Silent_p.S151S NM_004801.4 NP_004792.1 Q9ULB1 NRX1A_HUMAN neurexin 1 58 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192) Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116) CGAAAAGGCCGCTGAACACCG 0.672000 0 SO:0001819 synonymous_variant ENST00000406316.2 0 1 hg19 CCDS54360.1 TCGA-Q3-A5QY-01A-12D-A32N-08 NRXN1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000325291.2 0 0 0 4 136 0 50 0 0 0 1 0 50 2 0 0 0 0 0 2 1 8.914801e-01 4 136 0 50 2 0 0 0 0 50 2 -6.547907 1 1 120970 1 24 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.750000 0.240000 1.000000 1.000000 0.734778 0.750000 0 4.400000e-01 1 RNF181 51255 broad.mit.edu 37 2 85824016 85824016 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr2:85824016C>T ENST00000306368.4 + 3 319 c.289C>T c.(289-291)Ctt>Ttt p.L97F RNF181_ENST00000441634.1_Missense_Mutation_p.L97F NM_016494.3 NP_057578.1 Q9P0P0 RN181_HUMAN ring finger protein 181 2 TTGCCATCACCTTTTCCATTC 0.522000 0 SO:0001583 missense ENST00000306368.4 0 1 hg19 CCDS1981.1 . . . . . . . . . . C 14.21 2.466170 0.43839 . . ENSG00000168894 ENST00000441634;ENST00000306368 T;T 0.44482 0.92;0.92 5.75 4.88 0.63580 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1); 0.059226 0.64402 N 0.000002 T 0.23965 0.0580 N 0.11106 0.095 0.54753 D 0.999988 B 0.16603 0.018 B 0.21917 0.037 T 0.06716 -1.0811 10 0.14252 T 0.57 . 12.4863 0.55874 0.0:0.9193:0.0:0.0807 . 97 Q9P0P0 RN181_HUMAN F 97 ENSP00000412025:L97F;ENSP00000306906:L97F ENSP00000306906:L97F L + 1 0 RNF181 85677527 0.986000 0.35501 1.000000 0.80357 0.993000 0.82548 1.548000 0.36201 1.432000 0.47375 0.655000 0.94253 CTT TCGA-Q3-A5QY-01A-12D-A32N-08 RNF181-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252500.1 0 0 0 11 684 0 155 1 9.962398e-01 48 548 0 155 2 0 0 0 0 0 2 1 9.981323e-01 11 669 0 154 2 0 0 0 0 155 2 -2.313619 0 1 0 0 1 1 2 3 2.001904 0 0.090000 2.020000 0.097312 0.380000 0.190000 1.000000 0.350000 0.466700 0.380000 0 2.700000e-01 6.200000e-01 ZIC1 7545 broad.mit.edu 37 3 147128819 147128819 + Missense_Mutation SNP C C A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:147128819C>A ENST00000282928.4 + 1 1649 c.920C>A c.(919-921)cCt>cAt p.P307H NM_003412.3 NP_003403.2 Q15915 ZIC1_HUMAN Zic family member 1 63 TGCCCCTTCCCTGGCTGTGGC 0.572000 0 SO:0001583 missense ENST00000282928.4 0 1 hg19 CCDS3136.1 . . . . . . . . . . C 19.82 3.898249 0.72639 . . ENSG00000152977 ENST00000282928 D 0.91237 -2.81 3.89 3.89 0.44902 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 D 0.93331 0.7874 L 0.49350 1.555 0.80722 D 1 D 0.58970 0.984 D 0.71414 0.973 D 0.93988 0.7264 10 0.59425 D 0.04 . 16.2006 0.82071 0.0:1.0:0.0:0.0 . 307 Q15915 ZIC1_HUMAN H 307 ENSP00000282928:P307H ENSP00000282928:P307H P + 2 0 ZIC1 148611509 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.736000 0.68597 1.862000 0.54008 0.561000 0.74099 CCT TCGA-Q3-A5QY-01A-12D-A32N-08 ZIC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355497.1 0 0 0 5 409 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 9.362957e-01 5 405 0 80 2 0 0 0 0 81 2 -2.871001 1 1 0 0 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.320000 0.110000 1.000000 0.260000 0.415526 0.320000 0 1.900000e-01 6.400000e-01 WWTR1 25937 broad.mit.edu 37 3 149260145 149260145 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:149260145G>A ENST00000465804.1 - 5 1004 c.748C>T c.(748-750)Cgc>Tgc p.R250C WWTR1_ENST00000360632.3_Missense_Mutation_p.R250C|WWTR1_ENST00000467467.1_Missense_Mutation_p.R250C NM_001168278.1 NP_001161750.1 Q9GZV5 WWTR1_HUMAN WW domain containing transcription regulator 1 23 LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048) TCCTCTTGGCGCATTCGAATC 0.552000 T CAMTA1 epitheliod hemangioendothelioma Dom yes 3 3q23-q24 607392 WW domain containing transcription regulator 1 M 0 SO:0001583 missense ENST00000465804.1 0 1 hg19 CCDS3144.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 22.0 4.225035 0.79576 . . ENSG00000018408 ENST00000465804;ENST00000360632;ENST00000467467;ENST00000472417 T;T;T 0.55052 0.54;0.54;0.54 5.26 5.26 0.73747 . 0.229595 0.38381 N 0.001711 T 0.74496 0.3724 M 0.78637 2.42 0.80722 D 1 D 0.89917 1.0 D 0.77557 0.99 T 0.77302 -0.2638 10 0.87932 D 0 -28.3108 19.0748 0.93156 0.0:0.0:1.0:0.0 . 250 Q9GZV5 WWTR1_HUMAN C 250;250;250;108 ENSP00000419465:R250C;ENSP00000353847:R250C;ENSP00000419234:R250C ENSP00000353847:R250C R - 1 0 WWTR1 150742835 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.272000 0.58908 2.733000 0.93635 0.655000 0.94253 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 WWTR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356498.1 0 0 0 5 315 0 69 0 1.567025e-01 0 37 0 69 2 0 0 0 0 0 2 1 9.364633e-01 5 312 0 69 2 0 0 0 0 69 2 -3.138315 1 1 121412 1 36 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.410000 0.150000 1.000000 0.350000 0.491846 0.410000 0 2.500000e-01 8.200000e-01 PARL 55486 broad.mit.edu 37 3 183547482 183547482 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:183547482G>A ENST00000317096.4 - 10 1104 c.1044C>T c.(1042-1044)taC>taT p.Y348Y PARL_ENST00000311101.5_Silent_p.Y298Y|PARL_ENST00000435888.1_Silent_p.Y264Y NM_018622.5 NP_061092.3 Q9H300 PARL_HUMAN presenilin associated, rhomboid-like p.Y348Y(1) 17 all_cancers(143;6.55e-10)|Ovarian(172;0.0303) all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22) GTTCATGACCGTAAGTAACAT 0.423000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000317096.4 0 1 hg19 CCDS3248.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 11.66|11.66 1.706359|1.706359 0.30232|0.30232 .|. .|. ENSG00000175193|ENSG00000175193 ENST00000450375;ENST00000417784|ENST00000418450 T|. 0.51325|. 0.71|. 5.71|5.71 -6.81|-6.81 0.01704|0.01704 .|. .|. .|. .|. .|. T|T 0.65883|0.65883 0.2734|0.2734 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. T|T 0.68981|0.68981 -0.5266|-0.5266 5|4 .|. .|. .|. -19.5416|-19.5416 18.3207|18.3207 0.90237|0.90237 0.3327:0.0:0.6673:0.0|0.3327:0.0:0.6673:0.0 .|. .|. .|. .|. W|M 62;140|81 ENSP00000402689:R62W|. .|. R|T -|- 1|2 2|0 PARL|PARL 185030176|185030176 0.001000|0.001000 0.12720|0.12720 0.801000|0.801000 0.32222|0.32222 0.966000|0.966000 0.64601|0.64601 -1.489000|-1.489000 0.02306|0.02306 -1.663000|-1.663000 0.01481|0.01481 -0.414000|-0.414000 0.06135|0.06135 CGG|ACG TCGA-Q3-A5QY-01A-12D-A32N-08 PARL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346465.1 0 0 0 6 749 0 159 0 6.658049e-01 0 270 0 159 2 0 0 0 0 0 2 1 9.637357e-01 5 741 0 159 2 0 0 0 0 159 2 -1.822656 0 1 121410 1 32 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.200000 0.070000 1.000000 0.180000 0.320381 0.200000 0 1.300000e-01 4.000000e-01 ATP13A5 344905 broad.mit.edu 37 3 193039478 193039478 + Missense_Mutation SNP G G T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:193039478G>T ENST00000342358.4 - 16 2024 c.1907C>A c.(1906-1908)tCt>tAt p.S636Y NM_198505.2 NP_940907.2 Q4VNC0 AT135_HUMAN ATPase type 13A5 p.S636F(1) 76 all_cancers(143;1.08e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06) ACCTGTTTCAGATCTGCAGAA 0.463000 1 Substitution - Missense(1) SO:0001583 missense ENST00000342358.4 0 1 hg19 CCDS33914.1 . . . . . . . . . . G 8.022 0.759846 0.15846 . . ENSG00000187527 ENST00000342358 T 0.71579 -0.58 5.5 4.62 0.57501 ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1); 0.676384 0.14815 N 0.296831 T 0.65852 0.2731 L 0.41124 1.26 0.20196 N 0.999929 P 0.37176 0.586 B 0.42495 0.389 T 0.60306 -0.7289 10 0.62326 D 0.03 -1.1021 9.2597 0.37605 0.0772:0.0:0.7782:0.1446 . 636 Q4VNC0 AT135_HUMAN Y 636 ENSP00000341942:S636Y ENSP00000341942:S636Y S - 2 0 ATP13A5 194522172 0.001000 0.12720 0.470000 0.27216 0.062000 0.15995 1.160000 0.31761 1.476000 0.48215 -0.140000 0.14226 TCT TCGA-Q3-A5QY-01A-12D-A32N-08 ATP13A5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000343012.1 0 0 0 5 365 0 60 0 0 0 0 60 2 0 0 0 0 0 2 0 9.352304e-01 1 363 0 58 2 0 0 0 0 60 2 -4.691728 1 0 0 0 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.350000 0.120000 1.000000 0.290000 0.446630 0.350000 0 2.200000e-01 7.200000e-01 CDCP1 64866 broad.mit.edu 37 3 45159953 45159953 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:45159953G>A ENST00000296129.1 - 2 377 c.243C>T c.(241-243)agC>agT p.S81S CDCP1_ENST00000425231.2_Silent_p.S81S|CDCP1_ENST00000490471.1_5'UTR NM_022842.3 NP_073753.3 Q9H5V8 CDCP1_HUMAN CUB domain containing protein 1 29 GACTCTGGCAGCTAAAGGTAA 0.393000 0 SO:0001819 synonymous_variant ENST00000296129.1 0 1 hg19 CCDS2727.1 TCGA-Q3-A5QY-01A-12D-A32N-08 CDCP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256748.3 0 0 0 5 433 0 87 0 6.415153e-04 0 3 0 87 2 0 0 0 0 0 2 1 9.351994e-01 5 426 0 87 2 0 0 0 0 87 2 -3.068501 1 1 0 0 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.300000 0.100000 1.000000 0.250000 0.401115 0.300000 0 1.800000e-01 6.100000e-01 SMARCC1 6599 broad.mit.edu 37 3 47651727 47651727 + Missense_Mutation SNP T T C TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:47651727T>C ENST00000254480.5 - 26 2991 c.2872A>G c.(2872-2874)Atg>Gtg p.M958V SMARCC1_ENST00000425518.1_5'UTR NM_003074.3 NP_003065.3 Q92922 SMRC1_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 33 TGCTGTTCCATTTGCTGTCGT 0.542000 0 SO:0001583 missense ENST00000254480.5 0 1 hg19 CCDS2758.1 . . . . . . . . . . T 2.078 -0.411502 0.04799 . . ENSG00000173473 ENST00000254480 T 0.62498 0.02 5.85 4.68 0.58851 . 0.177402 0.64402 D 0.000018 T 0.31451 0.0797 N 0.02011 -0.69 0.38545 D 0.949318 B 0.06786 0.001 B 0.06405 0.002 T 0.17806 -1.0357 10 0.08837 T 0.75 -19.8043 11.3715 0.49702 0.0:0.0:0.2894:0.7106 . 958 Q92922 SMRC1_HUMAN V 958 ENSP00000254480:M958V ENSP00000254480:M958V M - 1 0 SMARCC1 47626731 1.000000 0.71417 1.000000 0.80357 0.104000 0.19210 3.897000 0.56273 1.014000 0.39417 -0.316000 0.08728 ATG TCGA-Q3-A5QY-01A-12D-A32N-08 SMARCC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257491.1 0 0 0 14 1006 0 205 0 1.238906e-01 0 41 0 205 2 0 0 0 0 0 2 1 9.997248e-01 14 992 0 204 2 0 0 0 0 205 2 -2.921096 1 1 0 0 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.330000 0.180000 1.000000 0.310000 0.424002 0.330000 0 2.400000e-01 5.300000e-01 GNAT1 2779 broad.mit.edu 37 3 50231284 50231284 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr3:50231284C>T ENST00000433068.1 + 5 604 c.548C>T c.(547-549)aCg>aTg p.T183M GNAT1_ENST00000481246.1_3'UTR|GNAT1_ENST00000232461.3_Missense_Mutation_p.T183M NM_000172.3 NP_000163.2 P11488 GNAT1_HUMAN guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 17 ATCATCGAGACGCAGTTCTCC 0.652000 0 SO:0001583 missense ENST00000433068.1 0 1 hg19 CCDS2812.1 . . . . . . . . . . C 23.4 4.407214 0.83230 0.0 1.16E-4 ENSG00000114349 ENST00000232461;ENST00000433068 D;D 0.89196 -2.48;-2.48 5.7 5.7 0.88788 . 0.045321 0.85682 D 0.000000 D 0.94945 0.8365 M 0.83118 2.625 0.47374 D 0.999403 D 0.89917 1.0 D 0.77004 0.989 D 0.95088 0.8219 10 0.72032 D 0.01 . 18.6092 0.91277 0.0:1.0:0.0:0.0 . 183 P11488 GNAT1_HUMAN M 183 ENSP00000232461:T183M;ENSP00000387555:T183M ENSP00000232461:T183M T + 2 0 GNAT1 50206288 1.000000 0.71417 0.981000 0.43875 0.984000 0.73092 4.464000 0.60134 2.711000 0.92665 0.561000 0.74099 ACG TCGA-Q3-A5QY-01A-12D-A32N-08 GNAT1-002 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000345957.1 0 0 0 7 367 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 9.794984e-01 7 360 0 95 2 0 0 0 0 95 2 -3.376190 1 1 121396 2 32 1 1 2 3 2.004667 0 0.090000 2.020000 0.097715 0.470000 0.200000 1.000000 0.410000 0.542609 0.470000 0 3.100000e-01 8.700000e-01 GRIK2 2898 broad.mit.edu 37 6 102134137 102134137 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr6:102134137C>T ENST00000421544.1 + 6 1350 c.860C>T c.(859-861)aCc>aTc p.T287I GRIK2_ENST00000369138.1_Missense_Mutation_p.T287I|GRIK2_ENST00000413795.1_Missense_Mutation_p.T287I|GRIK2_ENST00000318991.6_Missense_Mutation_p.T287I|GRIK2_ENST00000369137.3_Missense_Mutation_p.T287I|GRIK2_ENST00000369134.4_Missense_Mutation_p.T238I|GRIK2_ENST00000358361.3_Missense_Mutation_p.T287I NM_021956.4 NP_068775.1 Q13002 GRIK2_HUMAN glutamate receptor, ionotropic, kainate 2 83 all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599) ACAGAAAATACCCAAGTCTCC 0.423000 0 SO:0001583 missense ENST00000421544.1 0 1 hg19 CCDS5048.1 . . . . . . . . . . C 12.95 2.092200 0.36952 . . ENSG00000164418 ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076 D;D;D;D;D;D;D 0.83591 -1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74 5.84 4.03 0.46877 Extracellular ligand-binding receptor (1); 0.157085 0.53938 D 0.000043 T 0.47857 0.1468 N 0.04508 -0.205 0.26912 N 0.966869 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.06405 0.001;0.002;0.001 T 0.49082 -0.8976 10 0.66056 D 0.02 . 10.6595 0.45694 0.0:0.6482:0.2676:0.0843 . 287;287;287 Q13002-5;Q13002;Q13002-2 .;GRIK2_HUMAN;. I 287;287;287;287;287;287;287;238;249 ENSP00000397026:T287I;ENSP00000405596:T287I;ENSP00000358134:T287I;ENSP00000351128:T287I;ENSP00000358133:T287I;ENSP00000313276:T287I;ENSP00000358130:T238I ENSP00000313276:T287I T + 2 0 GRIK2 102240830 0.997000 0.39634 0.911000 0.35937 0.907000 0.53573 2.346000 0.44027 1.471000 0.48121 0.655000 0.94253 ACC TCGA-Q3-A5QY-01A-12D-A32N-08 GRIK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043718.1 0 0 0 6 325 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 9.650124e-01 6 324 0 61 2 0 0 0 0 61 2 -4.206827 1 1 0 0 1 1 2 3 2.007314 0 0.090000 2.020000 0.098519 0.470000 0.180000 1.000000 0.400000 0.543423 0.470000 0 3.000000e-01 1 RXRB 6257 broad.mit.edu 37 6 33166123 33166123 + Missense_Mutation SNP C C T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr6:33166123C>T ENST00000374680.3 - 3 813 c.602G>A c.(601-603)gGc>gAc p.G201D RXRB_ENST00000374685.4_Missense_Mutation_p.G201D|SLC39A7_ENST00000374675.3_5'Flank|RXRB_ENST00000413614.2_Missense_Mutation_p.G105D|SLC39A7_ENST00000374677.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000544186.1_Missense_Mutation_p.G11D NM_001270401.1|NM_021976.4 NP_001257330.1|NP_068811.1 P28702 RXRB_HUMAN retinoid X receptor, beta 15 Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755) TAGCCGTTTGCCAGCCCCAGG 0.622000 0 SO:0001583 missense ENST00000374680.3 0 1 hg19 CCDS4768.1 . . . . . . . . . . C 15.54 2.864280 0.51482 . . ENSG00000204231 ENST00000374685;ENST00000374680;ENST00000544186;ENST00000413614 D;D;D;D 0.93189 -3.16;-3.16;-3.18;-3.0 5.11 5.11 0.69529 . 0.376195 0.30649 N 0.009176 D 0.91553 0.7332 N 0.19112 0.55 0.43187 D 0.995017 D;D;D;B;B;P;P;P 0.69078 0.997;0.988;0.995;0.04;0.305;0.737;0.92;0.737 D;P;P;B;B;B;B;B 0.63597 0.916;0.837;0.72;0.045;0.109;0.22;0.345;0.22 D 0.92106 0.5692 10 0.45353 T 0.12 . 16.0896 0.81084 0.0:1.0:0.0:0.0 . 105;201;84;11;201;201;241;201 B7Z3E4;B7Z6J2;B7Z6X3;E9PK95;Q5STQ1;Q5STP9;Q59G65;P28702 .;.;.;.;.;.;.;RXRB_HUMAN D 201;201;11;105 ENSP00000363817:G201D;ENSP00000363812:G201D;ENSP00000439222:G11D;ENSP00000415561:G105D ENSP00000363812:G201D G - 2 0 RXRB 33274101 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 2.205000 0.42770 2.644000 0.89710 0.549000 0.68633 GGC TCGA-Q3-A5QY-01A-12D-A32N-08 RXRB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000076642.2 0 0 0 6 958 1 228 0 1.786801e-02 0 69 1 228 3 0 0 0 0 0 2 0 3.583610e-02 6 946 1 227 15 0 0 0 1 228 2 -1.713247 0 1 0 0 1 0 1 1 1.994193 0 0.090000 2.020000 0.082569 0.140000 0.050000 0.280000 0.140000 0.157888 0.140000 0 9.000000e-02 2.100000e-01 RNF133 168433 broad.mit.edu 37 7 122338787 122338787 + Missense_Mutation SNP A A T TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr7:122338787A>T ENST00000340112.2 - 1 423 c.186T>A c.(184-186)ttT>ttA p.F62L CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron NM_139175.1 NP_631914.1 Q8WVZ7 RN133_HUMAN ring finger protein 133 21 AGCTTCTTCCAAAGACTCCAG 0.423000 Colon(198;1778 2057 7449 19869 45985) 0 SO:0001583 missense ENST00000340112.2 0 1 hg19 CCDS5784.1 . . . . . . . . . . A 21.0 4.079128 0.76528 . . ENSG00000188050 ENST00000340112 T 0.24538 1.85 6.06 3.71 0.42584 . 0.154247 0.43747 D 0.000537 T 0.42471 0.1204 M 0.65498 2.005 0.80722 D 1 D 0.55605 0.972 P 0.60012 0.867 T 0.25710 -1.0124 10 0.87932 D 0 . 9.7273 0.40339 0.8574:0.0:0.1426:0.0 . 62 Q8WVZ7 RN133_HUMAN L 62 ENSP00000344489:F62L ENSP00000344489:F62L F - 3 2 RNF133 122126023 1.000000 0.71417 0.997000 0.53966 0.845000 0.48019 0.994000 0.29693 0.542000 0.28846 0.533000 0.62120 TTT TCGA-Q3-A5QY-01A-12D-A32N-08 RNF133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347413.1 0 0 0 9 580 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 9.940486e-01 9 575 0 121 2 0 0 0 0 121 2 -7.374735 1 1 0 0 1 1 2 3 2.008899 0 0.090000 2.020000 0.098519 0.380000 0.170000 1.000000 0.340000 0.472356 0.380000 0 2.600000e-01 7.700000e-01 SRI 6717 broad.mit.edu 37 7 87840221 87840221 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr7:87840221G>A ENST00000265729.2 - 4 277 c.225C>T c.(223-225)tgC>tgT p.C75C SRI_ENST00000419179.1_Silent_p.C75C|SRI_ENST00000490437.1_Silent_p.C32C|SRI_ENST00000431660.1_Silent_p.C60C|SRI_ENST00000394641.3_Silent_p.C60C NM_003130.3 NP_003121.1 P30626 SORCN_HUMAN sorcin 5 Esophageal squamous(14;0.00202) CCATAAGCCGGCAAGTCTCCA 0.284000 0 SO:0001819 synonymous_variant ENST00000265729.2 0 1 hg19 CCDS5612.1 TCGA-Q3-A5QY-01A-12D-A32N-08 SRI-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253680.1 0 0 0 5 277 0 32 0 9.863947e-01 0 463 0 32 2 0 0 0 0 0 2 1 9.338797e-01 5 270 0 32 2 0 0 0 0 32 2 -2.773713 1 1 0 0 1 1 2 3 2.014809 0 0.090000 2.020000 0.100124 0.480000 0.170000 1.000000 0.400000 0.555811 0.480000 0 2.900000e-01 1 ZC3H3 23144 broad.mit.edu 37 8 144547942 144547942 + Missense_Mutation SNP C C T rs113716075 byFrequency TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr8:144547942C>T ENST00000262577.5 - 9 2283 c.2252G>A c.(2251-2253)cGc>cAc p.R751H NM_015117.2 NP_055932.2 Q8IXZ2 ZC3H3_HUMAN zinc finger CCCH-type containing 3 23 all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155) Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107) CTCGGCCTTGCGGGACACGTA 0.632000 0 SO:0001583 missense ENST00000262577.5 0 1 hg19 CCDS6402.1 . . . . . . . . . . C 15.71 2.915110 0.52546 4.54E-4 1.16E-4 ENSG00000014164 ENST00000262577 T 0.71341 -0.56 4.9 2.7 0.31948 Zinc finger, CCCH-type (2); 0.132811 0.49305 D 0.000156 T 0.53174 0.1780 L 0.31526 0.94 0.38805 D 0.955289 P 0.39520 0.676 B 0.32022 0.139 T 0.60637 -0.7224 10 0.72032 D 0.01 -20.5515 10.588 0.45294 0.1341:0.7844:0.0:0.0815 . 751 Q8IXZ2 ZC3H3_HUMAN H 751 ENSP00000262577:R751H ENSP00000262577:R751H R - 2 0 ZC3H3 144619085 1.000000 0.71417 0.993000 0.49108 0.843000 0.47879 3.695000 0.54749 1.057000 0.40506 0.561000 0.74099 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 ZC3H3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382011.2 0 0 0 5 334 0 81 0 4.291309e-01 0 86 0 81 2 0 0 0 0 0 2 1 9.370146e-01 5 332 0 81 2 0 0 0 0 81 2 -2.994690 1 1 121408 11 42 1 1 2 3 2.000125 0 0.090000 2.020000 0.096909 0.380000 0.140000 1.000000 0.330000 0.464827 0.380000 0 2.300000e-01 7.200000e-01 RAB11FIP1 80223 broad.mit.edu 37 8 37732058 37732058 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr8:37732058G>A ENST00000330843.4 - 3 1609 c.1597C>T c.(1597-1599)Ccc>Tcc p.P533S RAB11FIP1_ENST00000523182.1_5'Flank|RAB11FIP1_ENST00000522727.1_Missense_Mutation_p.P385S|RAB11FIP1_ENST00000524118.1_Missense_Mutation_p.P385S|RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.P533S NM_001002814.2 NP_001002814.2 Q6WKZ4 RFIP1_HUMAN RAB11 family interacting protein 1 (class I) 49 Lung NSC(58;0.118)|all_lung(54;0.195) LUSC - Lung squamous cell carcinoma(8;3.62e-11) CTGGTCTGGGGAGCCCTCGGA 0.542000 0 SO:0001583 missense ENST00000330843.4 0 1 hg19 CCDS34882.1 . . . . . . . . . . G 15.79 2.937277 0.52972 . . ENSG00000156675 ENST00000287263;ENST00000330843;ENST00000522727;ENST00000524118 T;T;T;T 0.31247 2.24;2.1;1.51;1.5 5.03 4.14 0.48551 . 0.408600 0.23672 N 0.045718 T 0.16300 0.0392 L 0.32530 0.975 0.19300 N 0.999972 B;B;P;P 0.38148 0.068;0.194;0.617;0.62 B;B;B;B 0.33960 0.009;0.066;0.173;0.138 T 0.10428 -1.0630 10 0.12766 T 0.61 -6.1245 4.077 0.09909 0.0874:0.1748:0.5807:0.1571 . 385;385;533;533 E7EX40;Q6WKZ4-2;Q6WKZ4-3;Q6WKZ4 .;.;.;RFIP1_HUMAN S 533;533;385;385 ENSP00000287263:P533S;ENSP00000331342:P533S;ENSP00000430009:P385S;ENSP00000430680:P385S ENSP00000287263:P533S P - 1 0 RAB11FIP1 37851216 0.984000 0.35163 0.794000 0.32065 0.871000 0.50021 2.561000 0.45905 1.071000 0.40834 0.655000 0.94253 CCC TCGA-Q3-A5QY-01A-12D-A32N-08 RAB11FIP1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000376816.1 0 0 0 7 445 0 110 1 1.250887e-01 2 31 0 110 2 0 0 0 0 0 2 1 9.798331e-01 7 439 0 109 2 0 0 0 0 110 2 -3.238021 1 1 0 0 1 1 2 3 2.000125 0 0.090000 2.020000 0.096909 0.390000 0.160000 1.000000 0.330000 0.467739 0.390000 0 2.500000e-01 6.700000e-01 ZBTB26 57684 broad.mit.edu 37 9 125681305 125681305 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr9:125681305G>A ENST00000373656.3 - 2 982 c.909C>T c.(907-909)tgC>tgT p.C303C ZBTB26_ENST00000373654.1_Silent_p.C303C NM_020924.2 NP_065975.1 Q9HCK0 ZBT26_HUMAN zinc finger and BTB domain containing 26 11 AAGTCTTGCCGCAGAGTAGAC 0.458000 0 SO:0001819 synonymous_variant ENST00000373656.3 0 1 hg19 CCDS6847.1 TCGA-Q3-A5QY-01A-12D-A32N-08 ZBTB26-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053960.1 0 0 0 6 481 1 97 0 2.252751e-03 0 5 1 97 2 0 0 0 0 0 2 0 1.512280e-02 6 476 1 97 17 0 0 0 1 97 2 -2.269370 0 1 121412 1 27 1 1 2 3 2.014814 0 0.090000 2.020000 0.100124 0.320000 0.120000 1.000000 0.270000 0.438496 0.320000 0 2.000000e-01 1 FUBP3 8939 broad.mit.edu 37 9 133499056 133499056 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr9:133499056G>A ENST00000319725.9 + 11 1008 c.933G>A c.(931-933)caG>caA p.Q311Q NM_003934.1 NP_003925.1 Q96I24 FUBP3_HUMAN far upstream element (FUSE) binding protein 3 21 ATCGGTGTCAGCATGCAGCGC 0.547000 0 SO:0001819 synonymous_variant ENST00000319725.9 0 1 hg19 CCDS43893.1 TCGA-Q3-A5QY-01A-12D-A32N-08 FUBP3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054666.1 0 0 0 5 458 0 111 0 1.903740e-01 0 61 0 111 2 0 0 0 0 0 2 1 9.349555e-01 5 450 0 111 2 0 0 0 0 111 2 -2.870389 1 1 0 0 1 1 2 3 2.014814 0 0.090000 2.020000 0.100124 0.290000 0.100000 1.000000 0.240000 0.412716 0.290000 0 1.700000e-01 1 KIAA1045 23349 broad.mit.edu 37 9 34972446 34972446 + Missense_Mutation SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr9:34972446G>A ENST00000242315.3 + 3 564 c.482G>A c.(481-483)cGc>cAc p.R161H KIAA1045_ENST00000544237.1_Missense_Mutation_p.R161H|KIAA1045_ENST00000476115.2_3'UTR NM_015297.1 NP_056112.1 Q9UPV7 K1045_HUMAN KIAA1045 19 LUSC - Lung squamous cell carcinoma(32;0.00575) TGCCTGCGCCGCATGGGCTAC 0.577000 0 SO:0001583 missense ENST00000242315.3 0 1 hg19 CCDS43796.1 . . . . . . . . . . g 26.1 4.706470 0.89018 . . ENSG00000122733 ENST00000544237;ENST00000242315 . . . 5.73 4.84 0.62591 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, FYVE/PHD-type (1); 0.131353 0.53938 D 0.000049 T 0.51822 0.1697 M 0.62723 1.935 0.43304 D 0.995305 P 0.37141 0.584 B 0.29598 0.104 T 0.56195 -0.8019 9 0.51188 T 0.08 -11.7038 13.7849 0.63104 0.0733:0.0:0.9267:0.0 . 161 Q9UPV7 K1045_HUMAN H 161 . ENSP00000242315:R161H R + 2 0 KIAA1045 34962446 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 5.616000 0.67709 1.429000 0.47314 0.655000 0.94253 CGC TCGA-Q3-A5QY-01A-12D-A32N-08 KIAA1045-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052256.2 0 0 0 6 574 1 139 0 0 0 1 139 2 0 0 0 0 0 2 0 2.490685e-02 6 574 1 136 16 0 0 0 1 139 2 -1.989670 0 1 121006 5 42 1 0 1 1 1.991205 0 0.090000 2.020000 0.082152 0.240000 0.090000 0.460000 0.220000 0.259895 0.240000 0 1.500000e-01 3.500000e-01 C9orf131 138724 broad.mit.edu 37 9 35044336 35044336 + Silent SNP G G A rs115027328 by1000genomes TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr9:35044336G>A ENST00000312292.5 + 2 1757 c.1710G>A c.(1708-1710)ccG>ccA p.P570P C9orf131_ENST00000354479.5_Silent_p.P497P|FLJ00273_ENST00000595331.1_5'Flank|C9orf131_ENST00000421362.2_Silent_p.P522P NM_001040410.1|NM_203299.2 NP_001035500.1|NP_976044.2 Q5VYM1 CI131_HUMAN chromosome 9 open reading frame 131 39 all_epithelial(49;0.22) LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309) CTCTTGCACCGGAGCTGCTCA 0.527000 0 SO:0001819 synonymous_variant ENST00000312292.5 0 1 hg19 CCDS6572.2 TCGA-Q3-A5QY-01A-12D-A32N-08 C9orf131-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000052283.5 0 0 0 7 835 0 176 0 0 0 0 176 2 0 0 0 0 0 2 1 9.796999e-01 6 826 0 176 2 0 0 0 0 176 2 -1.883202 0 1 121410 9 46 1 0 1 1 1.991205 0 0.090000 2.020000 0.082152 0.190000 0.080000 0.360000 0.180000 0.206068 0.190000 0 1.200000e-01 2.700000e-01 RLN2 6019 broad.mit.edu 37 9 5304440 5304440 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chr9:5304440G>A ENST00000381627.3 - 1 529 c.141C>T c.(139-141)tgC>tgT p.C47C RLN2_ENST00000308420.3_Silent_p.C47C NM_134441.2 NP_604390.1 P04090 REL2_HUMAN relaxin 2 11 all_hematologic(13;0.137) Acute lymphoblastic leukemia(23;0.158) TGCTCATGCCGCAAATGGCAA 0.552000 0 SO:0001819 synonymous_variant ENST00000381627.3 0 1 hg19 CCDS6460.1 TCGA-Q3-A5QY-01A-12D-A32N-08 RLN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051619.1 0 0 0 5 280 0 63 0 0 0 0 63 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 63 2 -3.030533 1 1 121400 1 34 1 0 1 1 1.991205 0 0.090000 2.020000 0.082152 0.410000 0.150000 0.810000 0.360000 0.441984 0.410000 0 2.600000e-01 6.100000e-01 IRS4 8471 broad.mit.edu 37 X 107978822 107978822 + Silent SNP G G A TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chrX:107978822G>A ENST00000372129.2 - 1 829 c.753C>T c.(751-753)agC>agT p.S251S RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank NM_003604.2 NP_003595.1 O14654 IRS4_HUMAN insulin receptor substrate 4 78 GGAACACGCCGCTCAGCTCTT 0.627000 0 SO:0001819 synonymous_variant ENST00000372129.2 0 1 hg19 CCDS14544.1 TCGA-Q3-A5QY-01A-12D-A32N-08 IRS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057879.1 0 0 0 4 205 0 33 0 0 0 0 33 2 0 0 0 0 0 2 1 8.889266e-01 4 203 0 33 2 0 0 0 0 33 2 -3.288630 1 1 0 0 1 0 1 1 0.090000 2.020000 0.090000 0.220000 0.070000 0.480000 0.200000 0.250611 0.220000 0 1.300000e-01 3.500000e-01 DMD 1756 broad.mit.edu 37 X 31222081 31222081 + Silent SNP T T C rs12690372 byFrequency TCGA-Q3-A5QY-01A-12D-A32N-08 TCGA-Q3-A5QY-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac05724b-42c0-4cb3-806b-aadc13554d38 db4aed26-55eb-44b7-91d4-d8c50b9ccce3 g.chrX:31222081T>C ENST00000357033.4 - 67 10010 c.9804A>G c.(9802-9804)caA>caG p.Q3268Q DMD_ENST00000378723.3_Silent_p.Q200Q|DMD_ENST00000343523.2_Silent_p.Q808Q|DMD_ENST00000474231.1_Silent_p.Q808Q|DMD_ENST00000378702.4_Silent_p.Q200Q|DMD_ENST00000378707.3_Silent_p.Q808Q|DMD_ENST00000359836.1_Silent_p.Q808Q|DMD_ENST00000378680.2_Silent_p.Q200Q|DMD_ENST00000541735.1_Silent_p.Q808Q|DMD_ENST00000361471.4_Silent_p.Q200Q|DMD_ENST00000378677.2_Silent_p.Q3264Q NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2 NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1 P11532 DMD_HUMAN dystrophin 77 all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203) AACTTACAAATTGGAAGCAGC 0.383000 0 SO:0001819 synonymous_variant ENST00000357033.4 0 1 hg19 CCDS14233.1 . . . . . . . . . . T 9.064 0.995258 0.19043 5.22E-4 0.0 ENSG00000198947 ENST00000465285 . . . 5.11 -6.97 0.01616 . . . . . T 0.62221 0.2410 . . . 0.80722 D 1 . . . . . . T 0.66196 -0.5984 4 . . . . 15.5819 0.76448 0.1098:0.7325:0.0:0.1577 rs12690372;rs12690372 . . . V 997 . . I - 1 0 DMD 31132002 0.975000 0.34042 0.629000 0.29254 0.985000 0.73830 0.181000 0.16880 -2.089000 0.00860 -0.323000 0.08544 ATT TCGA-Q3-A5QY-01A-12D-A32N-08 DMD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056182.2 0 0 0 6 210 0 27 0 6.660461e-03 0 4 0 27 2 0 0 0 0 0 2 1 9.651049e-01 6 209 0 27 2 0 0 0 0 27 2 -7.907222 1 1 121410 44 46 1 0 1 1 0.090000 2.020000 0.090000 0.310000 0.130000 0.600000 0.300000 0.340105 0.310000 0 2.100000e-01 4.600000e-01