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 JAGN1 84522 broad.mit.edu 37 3 9934929 9934930 + Frame_Shift_Ins INS - - G TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 - G - - Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr3:9934929_9934930insG ENST00000307768.4 + 2 589_590 c.420_421insG c.(421-423)ggtfs p.G141fs NM_032492.3 NP_115881.3 jagunal homolog 1 (Drosophila) 10 Medulloblastoma(99;0.227) GTTTCCTCTTTGGTTTTTCTGC 0.515000 0 SO:0001589 frameshift_variant ENST00000307768.4 0 1 hg19 CCDS2588.1 TCGA-S4-A8RP-01A-11D-A36O-08 JAGN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250335.1 1 0 0 116 483 0 93 0 1 1 230 0 93 2 0 0 0 0 0 0 1 1.000000 120 476 0 91 2 0 0 0 0 0 0 -3.418312 1 1 0 0 1 0 0 0 2.011262 0 0.520000 1.960000 0.517491 0.730000 0.620000 0.860000 0.740000 0.743700 0.730000 0 0.670000 0.800000 SGK1 6446 broad.mit.edu 37 6 134493456 134493460 + Splice_Site DEL TGTAA TGTAA - TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 TGTAA - TGTAA TGTAA Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr6:134493456_134493460delTGTAA ENST00000237305.7 - 8 751 c.e8-2 SGK1_ENST00000413996.3_Splice_Site|SGK1_ENST00000367858.5_Splice_Site|SGK1_ENST00000489458.2_Splice_Site|SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000367857.5_Splice_Site NM_005627.3 NP_005618.2 O00141 SGK1_HUMAN serum/glucocorticoid regulated kinase 1 46 Colorectal(23;0.221) TTTAAGTCTCTGTAAAAAAGTGAAT 0.356000 0 SO:0001630 splice_region_variant ENST00000237305.7 1 1 hg19 CCDS5170.1 TCGA-S4-A8RP-01A-11D-A36O-08 SGK1-009 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042312.2 1 0 0 72 303 0 65 1 9.999883e-01 3 69 0 65 2 0 0 0 0 0 0 1 1.000000 86 307 0 63 2 0 0 0 0 0 0 -2.974142 1 0 0 0 1 0 1 1 1.504111 1 0.520000 1.960000 0.351351 0.540000 0.430000 0.660000 0.540000 0.548407 0.540000 0 0.480000 0.600000 GTPBP4 23560 broad.mit.edu 37 10 1058521 1058521 + Silent SNP T T A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr10:1058521T>A ENST00000360803.4 + 14 1543 c.1461T>A c.(1459-1461)atT>atA p.I487I GTPBP4_ENST00000538293.1_Silent_p.I371I|GTPBP4_ENST00000545048.1_Silent_p.I440I NM_012341.2 NP_036473.2 Q9BZE4 NOG1_HUMAN GTP binding protein 4 21 all_epithelial(10;0.107)|Colorectal(49;0.14) OV - Ovarian serous cystadenocarcinoma(33;0.0814) CAAAGCAAATTCGAGAGAAAA 0.443000 0 SO:0001819 synonymous_variant ENST00000360803.4 1 1 hg19 CCDS31132.1 TCGA-S4-A8RP-01A-11D-A36O-08 GTPBP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046412.1 1 0 1 76 202 0 40 1 1 42 86 0 40 2 0 0 0 0 0 2 1 1.000000 73 200 0 38 2 0 0 0 0 40 2 -20.000000 1 1 0 0 1 1 2 3 2.027623 0 0.520000 1.960000 0.521245 0.990000 0.850000 1.000000 1.000000 0.981772 0.990000 1 0.940000 1.000000 PITPNM2 57605 broad.mit.edu 37 12 123480179 123480179 + Missense_Mutation SNP A A G TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr12:123480179A>G ENST00000542749.1 - 12 1874 c.1811T>C c.(1810-1812)cTg>cCg p.L604P PITPNM2_ENST00000280562.5_Missense_Mutation_p.L604P|PITPNM2_ENST00000320201.4_Missense_Mutation_p.L604P|PITPNM2_ENST00000392428.1_Missense_Mutation_p.L325P Q9BZ72 PITM2_HUMAN phosphatidylinositol transfer protein, membrane-associated 2 39 all_neural(191;0.101)|Medulloblastoma(191;0.163) TGCATTCATCAGGATGCCCGG 0.672000 0 SO:0001583 missense ENST00000542749.1 0 1 hg19 CCDS9242.1 . . . . . . . . . . A 7.514 0.655371 0.14580 . . ENSG00000090975 ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749 T;T;T;T 0.47528 1.16;1.16;0.84;1.16 4.83 2.46 0.29980 . 1.317200 0.05113 N 0.489206 T 0.38026 0.1025 L 0.29908 0.895 0.50813 D 0.999895 B;B 0.06786 0.001;0.001 B;B 0.09377 0.004;0.0 T 0.08764 -1.0706 10 0.52906 T 0.07 -2.8824 7.1979 0.25864 0.7029:0.0:0.2971:0.0 . 604;604 Q9BZ72-2;Q9BZ72 .;PITM2_HUMAN P 604;604;325;604 ENSP00000280562:L604P;ENSP00000322218:L604P;ENSP00000376223:L325P;ENSP00000437611:L604P ENSP00000280562:L604P L - 2 0 PITPNM2 122046132 1.000000 0.71417 0.067000 0.19924 0.223000 0.24884 2.220000 0.42908 0.223000 0.20920 0.459000 0.35465 CTG TCGA-S4-A8RP-01A-11D-A36O-08 PITPNM2-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401342.1 1 0 0 4 91 0 16 0 3.155902e-03 0 2 0 16 2 0 0 0 0 0 2 1 0.889405 4 90 0 15 2 0 0 0 0 16 2 -7.915158 1 1 0 0 1 0 0 0 2.002266 0 0.520000 1.960000 0.517491 0.170000 0.050000 0.370000 0.160000 0.195309 0.170000 0 0.100000 0.270000 DDX55 57696 broad.mit.edu 37 12 124103244 124103244 + Missense_Mutation SNP G G T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr12:124103244G>T ENST00000238146.4 + 12 1243 c.1193G>T c.(1192-1194)aGa>aTa p.R398I SNORA9_ENST00000384170.1_RNA|DDX55_ENST00000421670.3_Missense_Mutation_p.R5I|DDX55_ENST00000541259.1_Intron|DDX55_ENST00000538744.1_Missense_Mutation_p.R367I NM_020936.1 NP_065987.1 Q8NHQ9 DDX55_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 14 all_neural(191;0.101)|Medulloblastoma(191;0.163) AAGCCCCAGAGAAACACAGCG 0.527000 OREG0022230 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000238146.4 1 1 hg19 CCDS9251.1 . . . . . . . . . . G 10.18 1.279677 0.23307 . . ENSG00000111364 ENST00000238146;ENST00000538744;ENST00000421670 T;T;T 0.44482 4.02;3.74;0.92 6.06 -2.24 0.06909 Helicase, C-terminal (1); 38.690800 0.00644 U 0.000527 T 0.19525 0.0469 N 0.02916 -0.46 0.25732 N 0.985252 B;B 0.02656 0.0;0.0 B;B 0.04013 0.0;0.001 T 0.13282 -1.0515 10 0.34782 T 0.22 -21.4456 5.5124 0.16888 0.29:0.1477:0.4657:0.0966 . 398;367 Q8NHQ9;F5H5U2 DDX55_HUMAN;. I 398;367;5 ENSP00000238146:R398I;ENSP00000443114:R367I;ENSP00000442332:R5I ENSP00000238146:R398I R + 2 0 DDX55 122669197 0.014000 0.17966 0.001000 0.08648 0.636000 0.38137 0.389000 0.20751 -0.570000 0.06022 -0.290000 0.09829 AGA TCGA-S4-A8RP-01A-11D-A36O-08 DDX55-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400616.2 1 0 1 74 236 0 40 1 9.999631e-01 19 32 0 40 2 0 0 0 0 0 2 1 1.000000 72 232 0 38 2 0 0 0 0 40 2 -20.000000 1 1 0 0 1 0 0 0 2.002266 0 0.520000 1.960000 0.517491 0.900000 0.730000 1.000000 1.000000 0.907190 0.900000 1 0.810000 1.000000 GOLGA3 2802 broad.mit.edu 37 12 133384600 133384600 + Missense_Mutation SNP G G C TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr12:133384600G>C ENST00000450791.2 - 4 1238 c.1055C>G c.(1054-1056)gCg>gGg p.A352G GOLGA3_ENST00000545875.1_Missense_Mutation_p.A352G|GOLGA3_ENST00000204726.3_Missense_Mutation_p.A352G|GOLGA3_ENST00000456883.2_Missense_Mutation_p.A352G|GOLGA3_ENST00000537452.1_Missense_Mutation_p.A352G Q08378 GOGA3_HUMAN golgin A3 64 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0176)|Lung NSC(355;0.204) CAGGGTATCCGCAGGAATCTC 0.632000 0 SO:0001583 missense ENST00000450791.2 1 1 hg19 CCDS9281.1 . . . . . . . . . . g 9.288 1.049914 0.19827 . . ENSG00000090615 ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875 T;T;T;T;T 0.32023 1.47;1.47;1.47;1.47;1.47 5.43 1.61 0.23674 . 0.752409 0.13598 N 0.376048 T 0.25975 0.0633 L 0.56769 1.78 0.21355 N 0.999713 P;P;B 0.43352 0.804;0.553;0.394 B;B;B 0.35727 0.148;0.148;0.209 T 0.07868 -1.0750 10 0.45353 T 0.12 . 9.2674 0.37650 0.3553:0.0:0.6447:0.0 . 352;352;352 Q08378-4;Q08378-2;Q08378 .;.;GOGA3_HUMAN G 352 ENSP00000204726:A352G;ENSP00000410378:A352G;ENSP00000409303:A352G;ENSP00000442143:A352G;ENSP00000442603:A352G ENSP00000204726:A352G A - 2 0 GOLGA3 131894673 0.023000 0.18921 0.000000 0.03702 0.001000 0.01503 2.066000 0.41452 0.289000 0.22422 -0.232000 0.12228 GCG TCGA-S4-A8RP-01A-11D-A36O-08 GOLGA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000397569.2 1 0 1 75 271 0 61 1 9.569960e-01 7 14 0 61 2 0 0 0 0 0 2 1 1.000000 73 263 0 61 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 0 0 2.002266 0 0.520000 1.960000 0.517491 0.820000 0.660000 0.990000 0.830000 0.832338 0.820000 0 0.740000 0.910000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C G C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 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 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 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 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-S4-A8RP-01A-11D-A36O-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 80 278 0 46 1 8.213332e-01 2 11 0 46 2 1 1 70 334 0 355 2 1 1.000000 78 274 0 46 2 1 1 2314 5714 0 46 2 -20.000000 1 1 0 0 1 0 0 0 2.002266 0 0.520000 1.960000 0.517491 0.850000 0.690000 1.000000 1.000000 0.856722 0.850000 1 0.760000 0.940000 OR6C76 390326 broad.mit.edu 37 12 55820043 55820043 + Missense_Mutation SNP A A C TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr12:55820043A>C ENST00000328314.3 + 1 6 c.6A>C c.(4-6)aaA>aaC p.K2N NM_001005183.1 NP_001005183.1 A6NM76 O6C76_HUMAN olfactory receptor, family 6, subfamily C, member 76 14 CAGAAATGAAAAATAGAACAT 0.353000 0 SO:0001583 missense ENST00000328314.3 1 1 hg19 CCDS31823.1 . . . . . . . . . . a 14.40 2.524254 0.44866 . . ENSG00000185821 ENST00000328314 T 0.01455 4.87 4.35 0.417 0.16421 . 0.826740 0.10355 U 0.684675 T 0.01523 0.0049 N 0.25992 0.78 0.09310 N 1 B 0.16603 0.018 B 0.17098 0.017 T 0.47959 -0.9076 10 0.72032 D 0.01 . 2.9347 0.05810 0.518:0.2723:0.0781:0.1316 . 2 A6NM76 O6C76_HUMAN N 2 ENSP00000328402:K2N ENSP00000328402:K2N K + 3 2 OR6C76 54106310 0.003000 0.15002 0.105000 0.21289 0.688000 0.40055 1.295000 0.33377 -0.019000 0.14055 0.487000 0.48397 AAA TCGA-S4-A8RP-01A-11D-A36O-08 OR6C76-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406675.1 1 0 0 18 311 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 0.999982 18 308 0 41 2 0 0 0 0 41 2 -5.208442 1 1 0 0 1 0 0 0 2.002266 0 0.520000 1.960000 0.517491 0.210000 0.120000 0.320000 0.210000 0.219010 0.210000 0 0.160000 0.270000 CLSTN3 9746 broad.mit.edu 37 12 7301731 7301731 + Missense_Mutation SNP C C A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr12:7301731C>A ENST00000266546.6 + 13 2461 c.2011C>A c.(2011-2013)Caa>Aaa p.Q671K CLSTN3_ENST00000537408.1_Missense_Mutation_p.Q683K NM_014718.3 NP_055533.2 Q9BQT9 CSTN3_HUMAN calsyntenin 3 33 CCCTGATCTTCAAATCACCTG 0.562000 0 SO:0001583 missense ENST00000266546.6 1 1 hg19 CCDS8575.1 . . . . . . . . . . C 12.46 1.945190 0.34283 . . ENSG00000139182 ENST00000266546;ENST00000537408 T;T 0.36699 1.24;1.24 5.71 5.71 0.89125 . 0.121175 0.56097 D 0.000022 T 0.18299 0.0439 N 0.04959 -0.14 0.46901 D 0.999246 B;B 0.12013 0.005;0.002 B;B 0.09377 0.002;0.004 T 0.12477 -1.0546 10 0.09590 T 0.72 -14.034 14.6704 0.68939 0.1452:0.8548:0.0:0.0 . 683;671 Q5UE57;Q9BQT9 .;CSTN3_HUMAN K 671;683 ENSP00000266546:Q671K;ENSP00000440679:Q683K ENSP00000266546:Q671K Q + 1 0 CLSTN3 7192998 1.000000 0.71417 0.998000 0.56505 0.993000 0.82548 2.959000 0.49153 2.698000 0.92095 0.561000 0.74099 CAA TCGA-S4-A8RP-01A-11D-A36O-08 CLSTN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398560.2 1 0 1 19 166 0 31 1 9.993705e-01 12 96 0 31 2 0 0 0 0 0 2 1 0.999993 19 165 0 31 2 0 0 0 0 31 2 -20.000000 1 1 0 0 1 0 0 0 2.019861 0 0.520000 1.960000 0.520000 0.390000 0.240000 0.580000 0.400000 0.409300 0.390000 0 0.310000 0.490000 CRYL1 51084 broad.mit.edu 37 13 21006373 21006373 + Silent SNP C C A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr13:21006373C>A ENST00000298248.7 - 5 563 c.501G>T c.(499-501)acG>acT p.T167T CRYL1_ENST00000382812.1_Silent_p.T145T|MIR4499_ENST00000584834.1_RNA|CRYL1_ENST00000480748.1_5'UTR NM_015974.2 NP_057058.2 Q9Y2S2 CRYL1_HUMAN crystallin, lambda 1 14 all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244) TGTCCACTGTCGTAGGGGCCG 0.587000 0 SO:0001819 synonymous_variant ENST00000298248.7 1 0 hg19 CCDS41871.1 TCGA-S4-A8RP-01A-11D-A36O-08 CRYL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044071.1 1 0 0 9 218 0 37 0 9.866219e-01 0 186 0 37 2 0 0 0 0 0 2 1 0.993644 9 212 0 37 2 0 0 0 0 37 2 -3.318793 1 1 120936 1 35 1 0 0 0 2.010459 0 0.520000 1.960000 0.517491 0.150000 0.070000 0.270000 0.150000 0.166398 0.150000 0 0.110000 0.220000 SPPL2A 84888 broad.mit.edu 37 15 51012246 51012246 + Missense_Mutation SNP T T C TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr15:51012246T>C ENST00000261854.5 - 14 1653 c.1379A>G c.(1378-1380)aAg>aGg p.K460R SPPL2A_ENST00000559293.1_5'Flank NM_032802.3 NP_116191.2 Q8TCT8 SPP2A_HUMAN signal peptide peptidase like 2A 15 AGGTTGCCCCTTTTTCATCAG 0.408000 Melanoma(50;790 1209 4069 22965 33125) 0 SO:0001583 missense ENST00000261854.5 0 1 hg19 CCDS10138.1 . . . . . . . . . . T 5.356 0.250885 0.10130 . . ENSG00000138600 ENST00000261854 T 0.17054 2.3 5.66 4.52 0.55395 . 0.218396 0.51477 D 0.000088 T 0.06508 0.0167 N 0.04746 -0.17 0.20638 N 0.999871 P 0.41475 0.751 B 0.40982 0.345 T 0.14671 -1.0464 10 0.12766 T 0.61 -3.5127 1.9865 0.03437 0.2572:0.0784:0.1375:0.5268 . 460 Q8TCT8 PSL2_HUMAN R 460 ENSP00000261854:K460R ENSP00000261854:K460R K - 2 0 AC012100.1 48799538 1.000000 0.71417 0.976000 0.42696 0.949000 0.60115 2.041000 0.41213 0.955000 0.37878 0.477000 0.44152 AAG TCGA-S4-A8RP-01A-11D-A36O-08 SPPL2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254543.3 0 0 0 5 434 0 48 0 6.139203e-01 0 166 0 48 2 0 0 0 0 0 2 1 0.933217 5 422 0 48 2 0 0 0 0 48 2 -2.614492 1 1 0 0 1 1 2 3 2.395965 1 0.520000 1.960000 0.595687 0.060000 0.010000 1.000000 0.050000 0.243357 0.060000 0 0.030000 1.000000 TM6SF1 53346 broad.mit.edu 37 15 83776476 83776476 + Missense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr15:83776476C>T ENST00000322019.9 + 1 318 c.44C>T c.(43-45)tCg>tTg p.S15L TM6SF1_ENST00000564988.1_3'UTR|TM6SF1_ENST00000565774.1_Missense_Mutation_p.S15L|TM6SF1_ENST00000379390.6_Missense_Mutation_p.S15L|TM6SF1_ENST00000379386.4_Missense_Mutation_p.S15L Q9BZW5 TM6S1_HUMAN transmembrane 6 superfamily member 1 p.S15W(1) 15 CTGTCCCTCTCGGCCATCCCG 0.736000 1 Substitution - Missense(1) SO:0001583 missense ENST00000322019.9 0 1 hg19 CCDS10323.1 . . . . . . . . . . C 14.92 2.678630 0.47886 . . ENSG00000136404 ENST00000322019;ENST00000379386;ENST00000379384;ENST00000379390;ENST00000258909 T;T;T;T;T 0.36699 1.24;1.24;1.24;1.24;1.24 3.12 2.19 0.27852 . 0.244473 0.31847 U 0.006973 T 0.18551 0.0445 N 0.11927 0.2 0.28287 N 0.923729 B;B;B 0.16802 0.008;0.017;0.019 B;B;B 0.11329 0.002;0.002;0.006 T 0.12192 -1.0557 10 0.40728 T 0.16 -5.543 7.7752 0.29033 0.0:0.8663:0.0:0.1337 . 15;15;15 E9PD04;Q6P4D7;Q9BZW5 .;.;TM6S1_HUMAN L 15 ENSP00000317000:S15L;ENSP00000368696:S15L;ENSP00000368693:S15L;ENSP00000368700:S15L;ENSP00000258909:S15L ENSP00000258909:S15L S + 2 0 TM6SF1 81567480 1.000000 0.71417 0.998000 0.56505 0.959000 0.62525 3.405000 0.52630 0.318000 0.23185 0.306000 0.20318 TCG TCGA-S4-A8RP-01A-11D-A36O-08 TM6SF1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000304009.1 1 0 0 9 100 0 13 0 1.600310e-01 0 8 0 13 2 0 0 0 0 0 2 1 0.994635 9 99 0 12 2 0 0 0 0 13 2 -13.963460 1 1 121026 1 25 1 1 2 3 2.395965 1 0.520000 1.960000 0.595687 0.430000 0.200000 1.000000 0.380000 0.523283 0.430000 0 0.290000 1.000000 MCTP2 55784 broad.mit.edu 37 15 94945245 94945245 + Silent SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr15:94945245C>T ENST00000357742.4 + 16 2082 c.2082C>T c.(2080-2082)ttC>ttT p.F694F MCTP2_ENST00000451018.3_Silent_p.F694F|MCTP2_ENST00000557742.1_Silent_p.F282F|MCTP2_ENST00000331706.4_Silent_p.F282F NM_018349.3 NP_060819.3 Q6DN12 MCTP2_HUMAN multiple C2 domains, transmembrane 2 49 Lung NSC(78;0.0821)|all_lung(78;0.148) BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593) CAATAGCATTCGCGGTAAGCT 0.383000 0 SO:0001819 synonymous_variant ENST00000357742.4 1 1 hg19 CCDS32338.1 TCGA-S4-A8RP-01A-11D-A36O-08 MCTP2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415060.3 1 0 0 102 453 0 69 1 8.433548e-01 3 14 0 69 2 0 0 0 0 0 2 1 1.000000 102 448 0 68 2 0 0 0 0 69 2 -3.103181 1 1 121408 5 40 1 1 2 3 2.395965 1 0.520000 1.960000 0.595687 0.850000 0.700000 1.000000 0.840000 0.873107 0.850000 1 0.770000 1.000000 SRL 6345 broad.mit.edu 37 16 4245590 4245590 + Missense_Mutation SNP G G A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr16:4245590G>A ENST00000399609.3 - 5 586 c.574C>T c.(574-576)Cca>Tca p.P192S SRL_ENST00000537996.1_Missense_Mutation_p.P150S NM_001098814.1 NP_001092284.1 Q86TD4 SRCA_HUMAN sarcalumenin 21 ATGATGCCTGGTGTATCCACA 0.448000 0 SO:0001583 missense ENST00000399609.3 1 1 hg19 CCDS42113.1 . . . . . . . . . . G 29.2 4.989453 0.93106 . . ENSG00000185739 ENST00000399609;ENST00000330063;ENST00000537996 D;D 0.99769 -6.7;-6.7 5.1 5.1 0.69264 . 0.000000 0.85682 U 0.000000 D 0.99880 0.9943 H 0.97415 4 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.96581 0.9430 10 0.72032 D 0.01 -8.2552 19.0659 0.93110 0.0:0.0:1.0:0.0 . 192 Q86TD4-2 . S 192;650;150 ENSP00000382518:P192S;ENSP00000440350:P150S ENSP00000333285:P650S P - 1 0 SRL 4185591 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.567000 0.98161 2.797000 0.96272 0.655000 0.94253 CCA TCGA-S4-A8RP-01A-11D-A36O-08 SRL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438087.1 1 0 1 184 517 0 100 0 0 0 0 100 2 0 0 0 0 0 2 1 1.000000 182 509 0 100 2 0 0 0 0 100 2 -20.000000 1 1 0 0 1 1 2 3 2.041787 0 0.520000 1.960000 0.522483 0.990000 0.880000 1.000000 1.000000 0.981759 0.990000 1 0.940000 1.000000 XAF1 54739 broad.mit.edu 37 17 6674085 6674085 + Missense_Mutation SNP C C A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr17:6674085C>A ENST00000361842.3 + 6 870 c.631C>A c.(631-633)Cgt>Agt p.R211S XAF1_ENST00000441631.1_Missense_Mutation_p.R211S|XAF1_ENST00000346752.4_Missense_Mutation_p.R192S NM_017523.3 NP_059993.2 Q6GPH4 XAF1_HUMAN XIAP associated factor 1 6 GAAAGATGTTCGTCCAAAGAC 0.368000 0 SO:0001583 missense ENST00000361842.3 1 0 hg19 CCDS11080.1 . . . . . . . . . . C 16.42 3.119519 0.56505 . . ENSG00000132530 ENST00000361842;ENST00000441631;ENST00000346752;ENST00000431790 T;T;T 0.19394 4.15;2.15;2.17 4.79 3.82 0.43975 . 0.415576 0.23340 N 0.049260 T 0.27967 0.0689 N 0.20986 0.625 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.73380 0.98;0.98;0.98;0.956;0.956 T 0.02539 -1.1144 10 0.46703 T 0.11 -21.6281 9.3008 0.37845 0.0:0.9044:0.0:0.0956 . 211;109;192;211;151 C9K044;Q6GPH4-6;Q6GPH4-2;Q6GPH4;B3KPW1 .;.;.;XAF1_HUMAN;. S 211;211;192;109 ENSP00000354822:R211S;ENSP00000413199:R211S;ENSP00000341029:R192S ENSP00000341029:R192S R + 1 0 XAF1 6614809 0.720000 0.27996 0.918000 0.36340 0.039000 0.13416 0.503000 0.22610 1.626000 0.50381 0.655000 0.94253 CGT TCGA-S4-A8RP-01A-11D-A36O-08 XAF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439643.5 1 0 0 13 382 0 40 0 7.198409e-01 0 75 0 40 2 0 0 0 0 0 2 1 0.999504 13 376 0 39 2 0 0 0 0 40 2 -3.034592 1 1 0 0 1 1 2 3 2.035207 0 0.520000 1.960000 0.521245 0.120000 0.060000 0.210000 0.120000 0.135670 0.120000 0 0.090000 0.170000 GAS7 8522 broad.mit.edu 37 17 9923135 9923135 + Missense_Mutation SNP G G A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr17:9923135G>A ENST00000432992.2 - 2 423 c.263C>T c.(262-264)tCg>tTg p.S88L GAS7_ENST00000542249.1_Missense_Mutation_p.S24L|GAS7_ENST00000540214.1_Missense_Mutation_p.S24L|GAS7_ENST00000585266.1_Missense_Mutation_p.S28L|GAS7_ENST00000578655.1_5'UTR|GAS7_ENST00000323816.4_Missense_Mutation_p.S28L|GAS7_ENST00000437099.2_Missense_Mutation_p.S24L|GAS7_ENST00000579158.1_Missense_Mutation_p.S24L|GAS7_ENST00000396115.2_Missense_Mutation_p.S24L NM_201433.1 NP_958839.1 O60861 GAS7_HUMAN growth arrest-specific 7 39 GCCCTGAGGCGACAGGTAGCT 0.597000 T MLL AML* Dom yes 17 17p 8522 growth arrest-specific 7 L 0 SO:0001583 missense ENST00000432992.2 1 1 hg19 CCDS11152.1 . . . . . . . . . . G 25.2 4.610775 0.87258 . . ENSG00000007237 ENST00000323816;ENST00000396115;ENST00000437099;ENST00000540214;ENST00000537970 T;D;D 0.83250 2.04;-1.7;-1.7 5.02 5.02 0.67125 WW/Rsp5/WWP (6); 0.000000 0.85682 D 0.000000 D 0.90219 0.6942 M 0.79258 2.445 0.80722 D 1 D;D;D 0.89917 1.0;0.997;1.0 D;P;D 0.68765 0.96;0.901;0.96 D 0.90263 0.4302 9 . . . -21.8984 15.3829 0.74673 0.0:0.0:1.0:0.0 . 40;28;88 B7Z2L1;A8KAC2;O60861 .;.;GAS7_HUMAN L 88;28;27;24;28 ENSP00000322608:S88L;ENSP00000379421:S28L;ENSP00000446214:S24L . S - 2 0 GAS7 9863860 1.000000 0.71417 0.993000 0.49108 0.905000 0.53344 5.593000 0.67550 2.620000 0.88729 0.563000 0.77884 TCG TCGA-S4-A8RP-01A-11D-A36O-08 GAS7-017 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439883.1 1 0 1 47 171 0 41 0 9.012166e-01 0 17 0 41 2 0 0 0 0 0 2 1 1.000000 44 167 0 40 2 0 0 0 0 41 2 -20.000000 1 0 121412 3 36 1 1 2 3 2.035207 0 0.520000 1.960000 0.521245 0.820000 0.630000 1.000000 1.000000 0.834200 0.820000 0 0.720000 0.940000 CEP192 55125 broad.mit.edu 37 18 13100331 13100331 + Missense_Mutation SNP G G T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr18:13100331G>T ENST00000325971.8 + 36 6496 c.4903G>T c.(4903-4905)Gat>Tat p.D1635Y CEP192_ENST00000430049.2_Missense_Mutation_p.D1756Y|CEP192_ENST00000506447.1_Missense_Mutation_p.D2231Y|CEP192_ENST00000540847.2_3'UTR Q8TEP8 CE192_HUMAN centrosomal protein 192kDa 71 AATTCGAGAAGATTTAACTCA 0.338000 0 SO:0001583 missense ENST00000325971.8 0 1 hg19 . . . . . . . . . . G 21.1 4.101103 0.76983 . . ENSG00000101639 ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847 T;T;T 0.08458 3.09;3.09;3.1 5.52 5.52 0.82312 . 0.109070 0.64402 D 0.000005 T 0.29458 0.0734 M 0.68952 2.095 0.58432 D 0.999997 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.81914 0.995;0.991;0.988;0.995 T 0.00337 -1.1807 10 0.87932 D 0 -25.0451 18.5764 0.91157 0.0:0.0:1.0:0.0 . 1756;2231;235;833 C9JT09;E9PF99;F5GZ47;Q9HCK3 .;.;.;. Y 2231;1635;1635;1756;235 ENSP00000427550:D2231Y;ENSP00000317156:D1635Y;ENSP00000389190:D1756Y ENSP00000317156:D1635Y D + 1 0 CEP192 13090331 1.000000 0.71417 1.000000 0.80357 0.659000 0.38960 4.233000 0.58651 2.756000 0.94617 0.655000 0.94253 GAT TCGA-S4-A8RP-01A-11D-A36O-08 CEP192-201 KNOWN basic protein_coding protein_coding 0 0 0 9 380 0 46 0 7.207054e-02 0 17 0 46 2 0 0 0 0 0 2 1 0.994001 8 376 0 45 2 0 0 0 0 46 2 -8.899888 1 1 0 0 1 1 2 3 2.067673 0 0.520000 1.960000 0.526160 0.090000 0.040000 1.000000 0.090000 0.133610 0.090000 0 0.060000 0.140000 SMAD4 4089 broad.mit.edu 37 18 48591891 48591891 + Nonsense_Mutation SNP G G T rs121912581 TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr18:48591891G>T ENST00000342988.3 + 9 1592 c.1054G>T c.(1054-1056)Gga>Tga p.G352* SMAD4_ENST00000588745.1_Nonsense_Mutation_p.G256*|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.G352* 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) TACTGTTGATGGATACGTGGA 0.443000 38 Whole gene deletion(36)|Unknown(2) GRCh37 CM024126 SMAD4 M rs121912581 SO:0001587 stop_gained ENST00000342988.3 0 1 hg19 CCDS11950.1 . . . . . . . . . . G 43 10.484127 0.99413 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 . . . 5.86 5.86 0.93980 . 0.048668 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 . 18.9646 0.92691 0.0:0.0:1.0:0.0 . . . . X 352 . ENSP00000341551:G352X G + 1 0 SMAD4 46845889 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.676000 0.98643 2.771000 0.95319 0.563000 0.77884 GGA TCGA-S4-A8RP-01A-11D-A36O-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 125 234 0 68 1 1 9 42 0 68 2 1 1 222 489 0 924 2 1 1.000000 123 233 0 68 2 0 0 0 0 68 2 -13.232870 1 1 0 0 1 0 1 1 1.521161 1 0.520000 1.960000 0.351351 0.940000 0.830000 1.000000 0.990000 0.941564 0.940000 1 0.890000 0.990000 ZNF516 9658 broad.mit.edu 37 18 74154961 74154961 + Missense_Mutation SNP G G A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr18:74154961G>A ENST00000443185.2 - 3 367 c.50C>T c.(49-51)cCc>cTc p.P17L ZNF516_ENST00000524431.2_5'UTR NM_014643.3 NP_055458.1 Q92618 ZN516_HUMAN zinc finger protein 516 32 Prostate(75;0.0869)|Esophageal squamous(42;0.129) GGCCCTGGTGGGGCTGGGGCC 0.692000 0 SO:0001583 missense ENST00000443185.2 1 1 hg19 . . . . . . . . . . G 19.43 3.825265 0.71143 . . ENSG00000101493 ENST00000443185;ENST00000532857 T;T 0.11495 2.77;3.12 4.3 4.3 0.51218 . 0.095548 0.43919 D 0.000509 T 0.16514 0.0397 . . . 0.58432 D 0.999994 D 0.76494 0.999 D 0.64144 0.922 T 0.01757 -1.1280 9 0.02654 T 1 -13.6921 15.3131 0.74053 0.0:0.0:1.0:0.0 . 17 Q92618 ZN516_HUMAN L 17 ENSP00000394757:P17L;ENSP00000446211:P17L ENSP00000394757:P17L P - 2 0 ZNF516 72283949 1.000000 0.71417 0.992000 0.48379 0.981000 0.71138 5.885000 0.69736 2.106000 0.64143 0.561000 0.74099 CCC TCGA-S4-A8RP-01A-11D-A36O-08 ZNF516-201 KNOWN basic|appris_principal|exp_conf protein_coding protein_coding 1 0 0 22 52 0 12 1 7.362017e-01 3 5 0 12 2 0 0 0 0 0 2 1 1.000000 19 51 0 11 2 0 0 0 0 12 2 -20.000000 1 1 0 0 1 0 1 1 1.521161 1 0.520000 1.960000 0.351351 0.800000 0.550000 0.980000 0.830000 0.802709 0.800000 0 0.670000 0.920000 PPAN 56342 broad.mit.edu 37 19 10220315 10220315 + Silent SNP G G T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr19:10220315G>T ENST00000253107.7 + 6 628 c.522G>T c.(520-522)ctG>ctT p.L174L PPAN-P2RY11_ENST00000393796.4_Silent_p.L174L|P2RY11_ENST00000321826.4_5'Flank|PPAN_ENST00000556468.1_Silent_p.L174L|PPAN-P2RY11_ENST00000428358.1_Silent_p.L174L|PPAN_ENST00000393793.1_Silent_p.L121L|SNORD105_ENST00000386910.1_RNA|SNORD105B_ENST00000458770.1_RNA NM_020230.5 NP_064615.3 Q9NQ55 SSF1_HUMAN peter pan homolog (Drosophila) 15 OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05) AGGTGAACCTGAACACCATCA 0.577000 0 SO:0001819 synonymous_variant ENST00000253107.7 0 1 hg19 CCDS12225.1 TCGA-S4-A8RP-01A-11D-A36O-08 PPAN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316658.1 0 0 0 17 1437 0 267 0 2.556097e-01 0 79 0 267 2 0 0 0 0 0 2 1 0.999957 16 1411 0 266 2 0 0 0 0 267 2 -2.287386 0 1 0 0 1 1 2 3 2.033021 0 0.520000 1.960000 0.521245 0.040000 0.010000 0.080000 0.040000 0.047330 0.040000 0 0.020000 0.060000 PPAP2C 8612 broad.mit.edu 37 19 291323 291323 + Nonsense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr19:291323C>T ENST00000269812.3 - 1 63 c.14G>A c.(13-15)tGg>tAg p.W5* PPAP2C_ENST00000327790.3_5'Flank|PPAP2C_ENST00000434325.2_Intron NM_003712.2|NM_177526.1 NP_003703.1|NP_803545.1 O43688 LPP2_HUMAN phosphatidic acid phosphatase type 2C 5 all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228) CACGAAGACCCACCTCCGCTG 0.756000 0 SO:0001587 stop_gained ENST00000269812.3 0 1 hg19 CCDS12023.1 . . . . . . . . . . c 36 5.704477 0.96812 . . ENSG00000141934 ENST00000269812 . . . 3.51 2.13 0.27403 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.41790 T 0.15 . 6.8058 0.23777 0.0:0.8261:0.0:0.1739 . . . . X 5 . ENSP00000269812:W5X W - 2 0 PPAP2C 242323 0.980000 0.34600 1.000000 0.80357 0.754000 0.42855 -0.025000 0.12413 1.497000 0.48584 0.289000 0.19496 TGG TCGA-S4-A8RP-01A-11D-A36O-08 PPAP2C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451777.2 1 0 0 40 161 0 37 1 1 9 167 0 37 2 0 0 0 0 0 2 1 1.000000 40 158 0 37 2 0 0 0 0 37 2 -3.234261 1 1 0 0 1 1 2 3 2.168163 1 0.520000 1.960000 0.567256 0.890000 0.640000 1.000000 1.000000 0.885773 0.890000 1 0.750000 1.000000 NFKBIB 4793 broad.mit.edu 37 19 39398260 39398260 + Silent SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr19:39398260C>T ENST00000313582.5 + 5 964 c.930C>T c.(928-930)ccC>ccT p.P310P NFKBIB_ENST00000392079.3_Silent_p.P278P|NFKBIB_ENST00000572515.1_Silent_p.P310P NM_002503.4 NP_002494.2 Q15653 IKBB_HUMAN nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta 8 all_cancers(60;4.39e-06)|Ovarian(47;0.0454) Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554) AATCCGGCCCCTGCAGCAGCA 0.692000 Pancreas(165;1492 2005 6979 7739 34483) 0 SO:0001819 synonymous_variant ENST00000313582.5 1 1 hg19 CCDS12524.1 TCGA-S4-A8RP-01A-11D-A36O-08 NFKBIB-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438155.1 1 0 0 25 56 0 14 1 1 21 57 0 14 2 0 0 0 0 0 2 1 1.000000 24 53 0 14 2 0 0 0 0 14 2 -20.000000 1 1 0 0 1 1 2 3 2.033021 0 0.520000 1.960000 0.521245 0.990000 0.820000 1.000000 1.000000 0.985623 0.990000 1 0.990000 1.000000 LRRC4B 94030 broad.mit.edu 37 19 51021095 51021095 + Silent SNP G G T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr19:51021095G>T ENST00000599957.1 - 3 2072 c.1875C>A c.(1873-1875)ccC>ccA p.P625P LRRC4B_ENST00000389201.3_Silent_p.P625P Q9NT99 LRC4B_HUMAN leucine rich repeat containing 4B 30 all_neural(266;0.131) CCGAGGCGGCGGGCAGCTCGT 0.726000 0 SO:0001819 synonymous_variant ENST00000599957.1 1 1 hg19 CCDS42595.1 TCGA-S4-A8RP-01A-11D-A36O-08 LRRC4B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464907.1 1 0 0 39 108 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1.000000 39 107 0 28 2 0 0 0 0 30 2 -4.588884 1 1 120148 1 30 1 1 2 3 2.045623 0 0.520000 1.960000 0.522483 0.990000 0.760000 1.000000 1.000000 0.959530 0.990000 1 0.880000 1.000000 CELSR2 1952 broad.mit.edu 37 1 109812124 109812124 + Silent SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:109812124C>T ENST00000271332.3 + 21 6952 c.6891C>T c.(6889-6891)gcC>gcT p.A2297A NM_001408.2 NP_001399.1 Q9HCU4 CELR2_HUMAN cadherin, EGF LAG seven-pass G-type receptor 2 82 all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244) TGCCCCGGGCCCTGGACAAAC 0.597000 NSCLC(158;1285 2011 34800 34852 42084) 0 SO:0001819 synonymous_variant ENST00000271332.3 1 1 hg19 CCDS796.1 TCGA-S4-A8RP-01A-11D-A36O-08 CELSR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033200.1 0 0 1 66 201 0 40 1 9.641100e-01 8 11 0 40 2 0 0 0 0 0 2 1 1.000000 66 200 0 39 2 0 0 0 0 40 2 -20.000000 1 1 0 0 1 1 2 3 2.040192 0 0.520000 1.960000 0.522483 0.950000 0.760000 1.000000 1.000000 0.936397 0.950000 1 0.850000 1.000000 WNT2B 7482 broad.mit.edu 37 1 113059836 113059836 + Missense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:113059836C>T ENST00000369684.4 + 4 1260 c.775C>T c.(775-777)Cgc>Tgc p.R259C WNT2B_ENST00000256640.5_Missense_Mutation_p.R167C|WNT2B_ENST00000369686.5_Missense_Mutation_p.R240C|RP4-671G15.2_ENST00000608357.1_RNA NM_024494.2 NP_078613.1 Q93097 WNT2B_HUMAN wingless-type MMTV integration site family, member 2B 18 Lung SC(450;0.246) all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05) CTCAGATTTCCGCCGCACAGG 0.617000 0 SO:0001583 missense ENST00000369684.4 1 1 hg19 CCDS847.1 . . . . . . . . . . C 25.6 4.659360 0.88154 . . ENSG00000134245 ENST00000256640;ENST00000369686;ENST00000369684 T;T;T 0.78924 -1.22;-1.22;-1.22 5.53 5.53 0.82687 . 0.000000 0.85682 D 0.000000 D 0.91593 0.7344 H 0.95950 3.745 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.76071 0.987;0.987 D 0.93785 0.7087 10 0.87932 D 0 . 19.0601 0.93090 0.0:1.0:0.0:0.0 . 259;240 Q93097;Q93097-2 WNT2B_HUMAN;. C 167;240;259 ENSP00000256640:R167C;ENSP00000358700:R240C;ENSP00000358698:R259C ENSP00000256640:R167C R + 1 0 WNT2B 112861359 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.367000 0.52350 2.599000 0.87857 0.555000 0.69702 CGC TCGA-S4-A8RP-01A-11D-A36O-08 WNT2B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000030692.1 1 0 1 67 222 0 44 0 6.548984e-01 0 9 0 44 2 0 0 0 0 0 2 1 1.000000 65 219 0 43 2 0 0 0 0 44 2 -3.920221 1 1 0 0 1 1 2 3 2.040192 0 0.520000 1.960000 0.522483 0.890000 0.710000 1.000000 1.000000 0.893684 0.890000 1 0.800000 1.000000 PRAMEF1 65121 broad.mit.edu 37 1 12855916 12855916 + Missense_Mutation SNP G G A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:12855916G>A ENST00000332296.7 + 4 1299 c.1196G>A c.(1195-1197)cGc>cAc p.R399H PRAMEF1_ENST00000400814.3_Missense_Mutation_p.R154H NM_023013.2 NP_075389.1 O95521 PRAM1_HUMAN PRAME family member 1 35 Ovarian(185;0.249) Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731) GACCTGCTGCGCCACACCAGT 0.557000 0 SO:0001583 missense ENST00000332296.7 1 1 hg19 CCDS148.1 . . . . . . . . . . . 2.972 -0.212215 0.06140 . . ENSG00000116721 ENST00000332296;ENST00000400814 T;T 0.49432 0.78;0.78 1.56 -0.674 0.11369 . 1.571450 0.04233 N 0.335492 T 0.30008 0.0751 L 0.27053 0.805 0.09310 N 1 B 0.18166 0.026 B 0.11329 0.006 T 0.09357 -1.0678 10 0.12430 T 0.62 . 4.1186 0.10094 0.4747:0.0:0.5253:0.0 . 399 O95521 PRAM1_HUMAN H 399;154 ENSP00000332134:R399H;ENSP00000383616:R154H ENSP00000332134:R399H R + 2 0 PRAMEF1 12778503 0.000000 0.05858 0.003000 0.11579 0.017000 0.09413 -2.135000 0.01306 -0.196000 0.10366 0.205000 0.17691 CGC TCGA-S4-A8RP-01A-11D-A36O-08 PRAMEF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005458.1 1 0 0 133 297 0 109 0 0 0 0 109 2 0 0 0 0 0 2 1 1.000000 107 153 0 162 2 0 0 0 0 109 2 -10.785790 1 0 121386 7 36 1 0 1 1 1.561689 1 0.520000 1.960000 0.360341 0.880000 0.760000 1.000000 0.890000 0.888973 0.880000 1 0.820000 0.950000 CELF3 11189 broad.mit.edu 37 1 151681757 151681757 + Missense_Mutation SNP A A C TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:151681757A>C ENST00000290583.4 - 4 1138 c.345T>G c.(343-345)ttT>ttG p.F115L CELF3_ENST00000290585.4_Missense_Mutation_p.F115L|RIIAD1_ENST00000326413.3_5'Flank|CELF3_ENST00000392706.3_5'Flank|AL589765.1_ENST00000442233.2_5'Flank|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000470688.1_5'UTR NM_001172648.1|NM_007185.4 NP_001166119.1|NP_009116.3 Q5SZQ8 CELF3_HUMAN CUGBP, Elav-like family member 3 21 CGAAGGGCTCAAACATCTTCC 0.617000 0 SO:0001583 missense ENST00000290583.4 1 1 hg19 CCDS1002.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 18.12|18.12 3.553835|3.553835 0.65425|0.65425 .|. .|. ENSG00000159409|ENSG00000159409 ENST00000290585;ENST00000290583;ENST00000368833|ENST00000420342 T;T|. 0.43294|. 0.95;0.95|. 4.39|4.39 -2.57|-2.57 0.06248|0.06248 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.60521|0.60521 0.2275|0.2275 M|M 0.83774|0.83774 2.66|2.66 0.80722|0.80722 D|D 1|1 D;P;D;D;D|. 0.76494|. 0.977;0.945;0.999;0.985;0.981|. D;P;D;P;P|. 0.87578|. 0.962;0.7;0.998;0.843;0.756|. T|T 0.67345|0.67345 -0.5694|-0.5694 10|5 0.66056|. D|. 0.02|. -8.3106|-8.3106 9.4317|9.4317 0.38615|0.38615 0.5746:0.0:0.4254:0.0|0.5746:0.0:0.4254:0.0 .|. 115;115;114;115;114|. Q5SZQ7;Q5SZQ8-2;F8W6B7;Q5SZQ8;Q5SZQ8-3|. .;.;.;CELF3_HUMAN;.|. L|W 115;115;114|116 ENSP00000290585:F115L;ENSP00000290583:F115L|. ENSP00000290583:F115L|. F|L -|- 3|2 2|0 CELF3|CELF3 149948381|149948381 0.649000|0.649000 0.27322|0.27322 0.994000|0.994000 0.49952|0.49952 0.570000|0.570000 0.35934|0.35934 -0.097000|-0.097000 0.11042|0.11042 -0.328000|-0.328000 0.08539|0.08539 -0.624000|-0.624000 0.04008|0.04008 TTT|TTG TCGA-S4-A8RP-01A-11D-A36O-08 CELF3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036663.2 1 0 0 104 1167 0 178 0 6.412567e-01 0 26 0 178 2 0 0 0 0 0 2 1 1.000000 102 1150 0 177 2 0 0 0 0 178 2 -3.318794 1 1 0 0 1 0 4 4 2.346818 1 0.520000 1.960000 0.586635 0.370000 0.290000 1.000000 0.370000 0.498356 0.370000 0 0.330000 1.000000 TAS1R2 80834 broad.mit.edu 37 1 19166741 19166741 + Silent SNP C C T rs112760365 TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:19166741C>T ENST00000375371.3 - 6 1893 c.1872G>A c.(1870-1872)ccG>ccA p.P624P NM_152232.2 NP_689418.2 Q8TE23 TS1R2_HUMAN taste receptor, type 1, member 2 45 Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255) Aspartame(DB00168) AGACCTTGGGCGGCCCCACGT 0.617000 0 SO:0001819 synonymous_variant ENST00000375371.3 0 1 hg19 CCDS187.1 TCGA-S4-A8RP-01A-11D-A36O-08 TAS1R2-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000006953.1 0 0 0 7 230 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 0.980473 7 228 0 55 2 0 0 0 0 56 2 -2.860462 1 1 121412 3 37 1 0 1 1 1.525079 1 0.520000 1.960000 0.353622 0.080000 0.030000 0.160000 0.080000 0.094868 0.080000 0 0.050000 0.130000 KDM5B 10765 broad.mit.edu 37 1 202724554 202724554 + Missense_Mutation SNP C C A rs76768289 TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:202724554C>A ENST00000367265.3 - 11 2547 c.1383G>T c.(1381-1383)ttG>ttT p.L461F KDM5B_ENST00000456180.1_5'UTR|KDM5B_ENST00000367264.2_Missense_Mutation_p.L497F NM_006618.3 NP_006609.3 Q9UGL1 KDM5B_HUMAN lysine (K)-specific demethylase 5B 6 GCATGTTGTTCAAATTCCAGC 0.378000 0 SO:0001583 missense ENST00000367265.3 0 1 hg19 CCDS30974.1 . . . . . . . . . . C 18.80 3.700822 0.68501 . . ENSG00000117139 ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790 T;T;T 0.72505 -0.66;-0.66;-0.66 5.73 4.82 0.62117 Transcription factor jumonji/aspartyl beta-hydroxylase (2); 0.000000 0.85682 D 0.000000 D 0.86351 0.5912 M 0.93328 3.405 0.58432 D 0.999999 D;D 0.89917 0.999;1.0 D;D 0.91635 0.961;0.999 D 0.88022 0.2769 10 0.87932 D 0 -12.7178 9.1277 0.36826 0.0:0.7688:0.0:0.2312 . 497;461 Q9UGL1-2;Q9UGL1 .;KDM5B_HUMAN F 461;303;497;303 ENSP00000356234:L461F;ENSP00000356233:L497F;ENSP00000235790:L303F ENSP00000235790:L303F L - 3 2 KDM5B 200991177 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.022000 0.41030 1.425000 0.47237 0.655000 0.94253 TTG TCGA-S4-A8RP-01A-11D-A36O-08 KDM5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099184.2 0 0 0 20 642 0 70 0 4.654317e-01 1 49 0 70 2 0 0 0 0 0 2 1 0.999993 17 625 0 68 2 0 0 0 0 70 2 -1.775111 0 1 121390 23 41 1 0 5 5 2.415055 1 0.520000 1.960000 0.598326 0.140000 0.080000 1.000000 0.140000 0.298545 0.140000 0 0.110000 1.000000 MACF1 23499 broad.mit.edu 37 1 39951311 39951311 + Silent SNP T T C TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:39951311T>C ENST00000372915.3 + 97 22099 c.22012T>C c.(22012-22014)Tta>Cta p.L7338L MACF1_ENST00000564288.1_Silent_p.L7505L|MACF1_ENST00000289893.4_Silent_p.L5888L|MACF1_ENST00000361689.2_Silent_p.L5380L|MACF1_ENST00000539005.1_Silent_p.L5250L|MACF1_ENST00000567887.1_Silent_p.L7542L|MACF1_ENST00000317713.7_Silent_p.L5380L|MACF1_ENST00000545844.1_Silent_p.L5380L Q9UPN3 MACF1_HUMAN microtubule-actin crosslinking factor 1 203 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) CTTTGACCTCTTAGAGACGCA 0.587000 0 SO:0001819 synonymous_variant ENST00000372915.3 1 1 hg19 . . . . . . . . . . T 4.373 0.068714 0.08436 . . ENSG00000127603 ENST00000372925;ENST00000446276 T;T 0.67865 1.42;-0.29 5.28 -1.78 0.07957 . 0.000000 0.44483 D 0.000443 T 0.59622 0.2207 . . . 0.30229 N 0.796068 . . . . . . T 0.59925 -0.7362 6 . . . . 11.6204 0.51115 0.0:0.7097:0.0:0.2903 . . . . P 4383;404 ENSP00000362016:L4383P;ENSP00000391512:L404P . L + 2 0 MACF1 39723898 0.036000 0.19791 0.951000 0.38953 0.993000 0.82548 0.258000 0.18387 -0.143000 0.11334 0.533000 0.62120 CTT TCGA-S4-A8RP-01A-11D-A36O-08 MACF1-028 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding protein_coding OTTHUMT00000392096.1 0 0 0 71 208 1 44 1 1 99 221 1 44 22 1 1 310 915 0 1161 2 1 1.000000 69 206 1 44 19 0 0 0 1 44 2 -20.000000 1 1 0 0 1 1 2 3 2.040192 0 0.520000 1.960000 0.522483 0.980000 0.790000 1.000000 1.000000 0.953641 0.980000 1 0.880000 1.000000 DOCK7 85440 broad.mit.edu 37 1 62970389 62970389 + Missense_Mutation SNP C C A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr1:62970389C>A ENST00000340370.5 - 36 4600 c.4583G>T c.(4582-4584)cGa>cTa p.R1528L DOCK7_ENST00000251157.5_Missense_Mutation_p.R1550L NM_033407.2 NP_212132.2 Q96N67 DOCK7_HUMAN dedicator of cytokinesis 7 92 GCTACAGTGTCGGAGAAGCCT 0.413000 0 SO:0001583 missense ENST00000340370.5 1 0 hg19 CCDS30734.1 . . . . . . . . . . C 32 5.151238 0.94645 . . ENSG00000116641 ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441 T;T 0.64085 -0.08;-0.08 5.15 5.15 0.70609 . 0.000000 0.85682 D 0.000000 T 0.81555 0.4847 M 0.82323 2.585 0.80722 D 1 D;D;D;D;D;D 0.89917 0.998;0.999;1.0;1.0;0.974;0.973 D;D;D;D;P;P 0.91635 0.981;0.973;0.999;0.999;0.851;0.907 D 0.84445 0.0585 10 0.72032 D 0.01 . 18.6147 0.91299 0.0:1.0:0.0:0.0 . 1559;1550;1528;1519;1519;1550 Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6 DOCK7_HUMAN;.;.;.;.;. L 1559;1550;1528;289 ENSP00000251157:R1550L;ENSP00000340742:R1528L ENSP00000251157:R1550L R - 2 0 DOCK7 62742977 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 7.814000 0.86154 2.398000 0.81561 0.655000 0.94253 CGA TCGA-S4-A8RP-01A-11D-A36O-08 DOCK7-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000036806.1 1 0 0 12 288 0 37 0 3.826640e-01 0 31 0 37 2 0 0 0 0 0 2 1 0.999131 12 286 0 37 2 0 0 0 0 37 2 -4.228586 1 1 0 0 1 1 2 3 2.040192 0 0.520000 1.960000 0.522483 0.150000 0.080000 0.280000 0.160000 0.174088 0.150000 0 0.110000 0.210000 DCTN1 1639 broad.mit.edu 37 2 74597120 74597120 + Missense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr2:74597120C>T ENST00000361874.3 - 13 1681 c.1364G>A c.(1363-1365)cGc>cAc p.R455H DCTN1_ENST00000409240.1_Missense_Mutation_p.R418H|DCTN1_ENST00000407639.2_Missense_Mutation_p.R321H|DCTN1_ENST00000409567.3_Missense_Mutation_p.R435H|DCTN1_ENST00000409868.1_Missense_Mutation_p.R438H|DCTN1_ENST00000409438.1_Missense_Mutation_p.R321H|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.R448H NM_004082.4 NP_004073.2 Q14203 DCTN1_HUMAN dynactin 1 45 CCTCAACTCGCGCACTTTCTC 0.537000 0 SO:0001583 missense ENST00000361874.3 1 1 hg19 CCDS1939.1 . . . . . . . . . . C 34 5.327848 0.95733 . . ENSG00000204843 ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567 T;T;T;T;T;T;T 0.78707 -1.09;-1.09;-1.09;-1.09;-1.09;-1.2;-1.09 5.65 5.65 0.86999 . 0.000000 0.39615 N 0.001313 D 0.86062 0.5843 L 0.55834 1.745 0.80722 D 1 P;D;D;P;P;D 0.76494 0.745;0.999;0.999;0.522;0.678;0.999 B;P;D;B;B;D 0.78314 0.109;0.902;0.98;0.129;0.254;0.991 D 0.86070 0.1537 10 0.56958 D 0.05 -10.1178 18.4958 0.90864 0.0:1.0:0.0:0.0 . 435;418;455;448;321;321 E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4 .;.;DCTN1_HUMAN;.;.;. H 455;448;438;321;321;418;438;435 ENSP00000354791:R455H;ENSP00000377571:R448H;ENSP00000384844:R321H;ENSP00000387270:R321H;ENSP00000386406:R418H;ENSP00000387327:R438H;ENSP00000386843:R435H ENSP00000354791:R455H R - 2 0 DCTN1 74450628 1.000000 0.71417 0.997000 0.53966 0.984000 0.73092 7.615000 0.83006 2.659000 0.90383 0.655000 0.94253 CGC TCGA-S4-A8RP-01A-11D-A36O-08 DCTN1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252227.3 1 0 1 114 384 0 80 1 1 41 176 0 80 2 0 0 0 0 0 2 1 1.000000 112 372 0 80 2 0 0 0 0 80 2 -20.000000 1 0 121412 3 38 1 0 0 0 2.004695 0 0.520000 1.960000 0.517491 0.870000 0.730000 1.000000 1.000000 0.876787 0.870000 1 0.800000 0.950000 SETMAR 6419 broad.mit.edu 37 3 4345079 4345079 + Missense_Mutation SNP A A G TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr3:4345079A>G ENST00000358065.4 + 1 92 c.25A>G c.(25-27)Aca>Gca p.T9A SETMAR_ENST00000430981.1_Missense_Mutation_p.T9A|SETMAR_ENST00000425863.1_Missense_Mutation_p.T9A|SUMF1_ENST00000534863.1_Intron NM_006515.3 NP_006506.3 Q53H47 SETMR_HUMAN SET domain and mariner transposase fusion gene 9 Melanoma(143;0.0657) GGCAAAGACGACACGGCCTTG 0.647000 Chromatin Structure 0 SO:0001583 missense ENST00000358065.4 1 1 hg19 CCDS2563.2 . . . . . . . . . . A 10.03 1.238717 0.22711 . . ENSG00000170364 ENST00000358065;ENST00000430981;ENST00000425863 D;D;T 0.95001 -3.52;-3.58;0.6 2.53 1.28 0.21552 . . . . . D 0.85673 0.5751 N 0.22421 0.69 0.09310 N 1 . . . . . . T 0.71735 -0.4503 7 0.07644 T 0.81 . 5.2353 0.15443 0.6963:0.3037:0.0:0.0 . . . . A 9 ENSP00000373354:T9A;ENSP00000403000:T9A;ENSP00000403145:T9A ENSP00000373354:T9A T + 1 0 SETMAR 4320079 0.012000 0.17670 0.000000 0.03702 0.002000 0.02628 0.084000 0.14891 0.084000 0.17077 0.482000 0.46254 ACA TCGA-S4-A8RP-01A-11D-A36O-08 SETMAR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206587.4 1 0 1 12 37 0 10 0 6.162891e-01 1 7 0 10 2 0 0 0 0 0 2 1 0.999364 12 36 0 10 2 0 0 0 0 10 2 -19.999950 1 1 0 0 1 0 0 0 2.011262 0 0.520000 1.960000 0.517491 0.930000 0.540000 1.000000 1.000000 0.885546 0.930000 1 0.720000 1.000000 NEK1 4750 broad.mit.edu 37 4 170327820 170327820 + Missense_Mutation SNP G G T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr4:170327820G>T ENST00000439128.2 - 30 3857 c.3217C>A c.(3217-3219)Cgt>Agt p.R1073S NEK1_ENST00000512193.1_Missense_Mutation_p.R1004S|NEK1_ENST00000511633.1_Missense_Mutation_p.R1057S|NEK1_ENST00000510533.1_Missense_Mutation_p.R1029S|NEK1_ENST00000507142.1_Missense_Mutation_p.R1101S NM_012224.2 NP_036356.1 Q96PY6 NEK1_HUMAN NIMA-related kinase 1 45 Prostate(90;0.00601)|Renal(120;0.0183) TTGTCTTGACGAACATCTCCT 0.343000 0 SO:0001583 missense ENST00000439128.2 1 0 hg19 CCDS47162.1 . . . . . . . . . . G 5.931 0.355845 0.11239 . . ENSG00000137601 ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193 T;T;T;T;T 0.40225 1.04;1.04;1.04;1.04;1.04 5.03 2.21 0.28008 . 1.020820 0.07793 N 0.955279 T 0.29458 0.0734 L 0.36672 1.1 0.09310 N 1 B;B;B;B;B 0.31625 0.034;0.332;0.067;0.332;0.006 B;B;B;B;B 0.30495 0.054;0.116;0.054;0.116;0.015 T 0.24154 -1.0168 10 0.13108 T 0.6 . 6.2799 0.21001 0.2397:0.1331:0.6273:0.0 . 1004;1057;1101;1029;1073 Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6 .;.;.;.;NEK1_HUMAN S 1073;1057;1029;1101;1004 ENSP00000408020:R1073S;ENSP00000423332:R1057S;ENSP00000427653:R1029S;ENSP00000424757:R1101S;ENSP00000424938:R1004S ENSP00000408020:R1073S R - 1 0 NEK1 170564395 0.856000 0.29760 0.005000 0.12908 0.071000 0.16799 3.304000 0.51866 0.566000 0.29273 0.591000 0.81541 CGT TCGA-S4-A8RP-01A-11D-A36O-08 NEK1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000363157.3 1 0 0 8 201 0 27 0 9.396337e-02 0 12 0 27 2 0 0 0 0 0 2 1 0.988718 7 197 0 27 2 0 0 0 0 27 2 -2.924718 1 1 0 0 1 1 2 3 2.047020 0 0.520000 1.960000 0.522483 0.150000 0.060000 0.300000 0.140000 0.172375 0.150000 0 0.100000 0.220000 LIMCH1 22998 broad.mit.edu 37 4 41615603 41615603 + Missense_Mutation SNP G G T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr4:41615603G>T ENST00000313860.7 + 7 661 c.607G>T c.(607-609)Gac>Tac p.D203Y LIMCH1_ENST00000509638.1_Missense_Mutation_p.D44Y|LIMCH1_ENST00000514096.1_Missense_Mutation_p.D56Y|LIMCH1_ENST00000509454.1_Missense_Mutation_p.D51Y|LIMCH1_ENST00000509277.1_Missense_Mutation_p.D49Y|LIMCH1_ENST00000508501.1_Missense_Mutation_p.D203Y|LIMCH1_ENST00000396595.3_Missense_Mutation_p.D49Y|LIMCH1_ENST00000512820.1_Missense_Mutation_p.D203Y|LIMCH1_ENST00000512632.1_Missense_Mutation_p.D203Y|LIMCH1_ENST00000381753.4_Missense_Mutation_p.D49Y|LIMCH1_ENST00000512946.1_Missense_Mutation_p.D203Y|LIMCH1_ENST00000513024.1_Missense_Mutation_p.D44Y|LIMCH1_ENST00000503057.1_Missense_Mutation_p.D44Y|LIMCH1_ENST00000511496.1_Missense_Mutation_p.D44Y NM_014988.2 NP_055803.2 Q9UPQ0 LIMC1_HUMAN LIM and calponin homology domains 1 41 TGATTCCTTCGACAGCCTGGA 0.552000 0 SO:0001583 missense ENST00000313860.7 1 0 hg19 CCDS33977.1 . . . . . . . . . . G 33 5.197899 0.94997 . . ENSG00000064042 ENST00000513024;ENST00000509638;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000446625;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000509454;ENST00000396595;ENST00000381753 T;T;T;T;T;T;T;T;T;T;T;T 0.67171 -0.14;0.61;0.6;0.61;0.07;0.55;-0.25;0.01;-0.16;-0.16;0.01;-0.15 5.59 5.59 0.84812 . 0.044471 0.85682 D 0.000000 T 0.82240 0.4994 M 0.72894 2.215 0.80722 D 1 D;D;D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D;D;D 0.97110 0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.998;0.999;0.999 D 0.83535 0.0093 10 0.87932 D 0 -23.1392 19.5966 0.95541 0.0:0.0:1.0:0.0 . 49;203;49;49;51;44;44;203;203;203;203 E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;Q6NVB9;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0 .;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN Y 44;44;203;203;203;203;203;44;44;44;43;56;49;51;49;49 ENSP00000425222:D44Y;ENSP00000424825:D203Y;ENSP00000424645:D203Y;ENSP00000316891:D203Y;ENSP00000427045:D203Y;ENSP00000424437:D203Y;ENSP00000425631:D44Y;ENSP00000421242:D44Y;ENSP00000426334:D56Y;ENSP00000422864:D49Y;ENSP00000379840:D49Y;ENSP00000371172:D49Y ENSP00000316891:D203Y D + 1 0 LIMCH1 41310360 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.476000 0.97823 2.622000 0.88805 0.561000 0.74099 GAC TCGA-S4-A8RP-01A-11D-A36O-08 LIMCH1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000361249.2 1 0 0 15 288 0 45 0 1.865243e-01 0 15 0 45 2 0 0 0 0 0 2 1 0.999876 16 285 0 45 2 0 0 0 0 45 2 -4.867502 1 1 0 0 1 1 2 3 2.047020 0 0.520000 1.960000 0.522483 0.190000 0.110000 0.320000 0.190000 0.210020 0.190000 0 0.140000 0.250000 PHF15 0 broad.mit.edu 37 5 133914244 133914244 + Nonsense_Mutation SNP C C A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr5:133914244C>A ENST00000282605.4 + 12 1828 c.1742C>A c.(1741-1743)tCg>tAg p.S581* PHF15_ENST00000361895.2_Nonsense_Mutation_p.S538*|PHF15_ENST00000395003.1_Nonsense_Mutation_p.S537*|PHF15_ENST00000402835.1_3'UTR 22 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) CTGGCACAGTCGGTGCAGATC 0.607000 0 SO:0001587 stop_gained ENST00000282605.4 0 1 hg19 . . . . . . . . . . c 38 7.004263 0.97994 . . ENSG00000043143 ENST00000413974;ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000395003 . . . 5.07 5.07 0.68467 . 0.654761 0.14755 N 0.300363 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 18.4569 0.90724 0.0:1.0:0.0:0.0 . . . . X 581;597;581;538;538;537 . ENSP00000282605:S581X S + 2 0 PHF15 133942143 1.000000 0.71417 0.926000 0.36857 0.861000 0.49209 5.489000 0.66875 2.367000 0.80283 0.306000 0.20318 TCG TCGA-S4-A8RP-01A-11D-A36O-08 PHF15-003 NOVEL alternative_5_UTR|basic|appris_principal protein_coding protein_coding OTTHUMT00000251170.1 0 0 0 8 555 0 92 0 1.751833e-01 0 47 0 92 2 0 0 0 0 0 2 1 0.988736 7 548 0 92 2 0 0 0 0 92 2 -2.462800 0 1 0 0 1 0 3 3 2.192983 1 0.520000 1.960000 0.577167 0.070000 0.020000 1.000000 0.070000 0.294825 0.070000 0 0.040000 1.000000 HTR1A 3350 broad.mit.edu 37 5 63257207 63257207 + Missense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr5:63257207C>T ENST00000323865.3 - 1 573 c.340G>A c.(340-342)Gcc>Acc p.A114T RP11-158J3.2_ENST00000502882.1_RNA NM_000524.3 NP_000515.2 P08908 5HT1A_HUMAN 5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled 56 Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234) Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315) ACGTCGAGGGCGATGAACAGG 0.607000 0 SO:0001583 missense ENST00000323865.3 0 1 hg19 CCDS34168.1 . . . . . . . . . . C 15.15 2.747595 0.49257 . . ENSG00000178394 ENST00000323865 T 0.37752 1.18 5.12 1.64 0.23874 GPCR, rhodopsin-like superfamily (1); 0.060603 0.64402 D 0.000002 T 0.22044 0.0531 N 0.25426 0.745 0.41085 D 0.985551 P 0.41848 0.763 B 0.35655 0.207 T 0.03148 -1.1067 10 0.26408 T 0.33 . 12.99 0.58614 0.752:0.2479:0.0:0.0 . 114 P08908 5HT1A_HUMAN T 114 ENSP00000316244:A114T ENSP00000316244:A114T A - 1 0 HTR1A 63292963 0.996000 0.38824 0.989000 0.46669 0.928000 0.56348 2.510000 0.45468 0.399000 0.25367 0.561000 0.74099 GCC TCGA-S4-A8RP-01A-11D-A36O-08 HTR1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368397.1 1 0 1 15 82 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 0.999894 14 81 0 15 2 0 0 0 0 15 2 -19.999990 1 1 0 0 1 0 1 1 1.689880 1 0.520000 1.960000 0.418745 0.490000 0.290000 0.730000 0.480000 0.506042 0.490000 0 0.380000 0.620000 HBS1L 10767 broad.mit.edu 37 6 135300380 135300380 + Missense_Mutation SNP C C A TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr6:135300380C>A ENST00000367837.5 - 14 1830 c.1624G>T c.(1624-1626)Gac>Tac p.D542Y HBS1L_ENST00000445176.2_Missense_Mutation_p.D266Y|HBS1L_ENST00000367826.2_Missense_Mutation_p.D500Y|HBS1L_ENST00000527578.1_Missense_Mutation_p.D378Y|HBS1L_ENST00000415177.2_Missense_Mutation_p.D477Y|HBS1L_ENST00000367824.4_Missense_Mutation_p.D378Y NM_001145158.1|NM_006620.3 NP_001138630.1|NP_006611.1 Q9Y450 HBS1L_HUMAN HBS1-like translational GTPase 20 Colorectal(23;0.221) GCCGCCCAGTCGACAGGTTCA 0.428000 0 SO:0001583 missense ENST00000367837.5 1 0 hg19 CCDS5173.1 . . . . . . . . . . C 16.89 3.248542 0.59103 . . ENSG00000112339 ENST00000367837;ENST00000527578;ENST00000415177;ENST00000367826;ENST00000367824;ENST00000533274;ENST00000445176 T;T;T;T;T;T;T 0.68025 -0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3 5.72 5.72 0.89469 Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1); 0.088162 0.85682 D 0.000000 D 0.87605 0.6219 H 0.97186 3.955 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.79784 0.988;0.993 D 0.90934 0.4792 10 0.72032 D 0.01 -31.4881 19.8674 0.96824 0.0:1.0:0.0:0.0 . 500;542 Q9Y450-4;Q9Y450 .;HBS1L_HUMAN Y 542;378;477;500;378;412;266 ENSP00000356811:D542Y;ENSP00000436256:D378Y;ENSP00000389826:D477Y;ENSP00000356800:D500Y;ENSP00000356798:D378Y;ENSP00000434533:D412Y;ENSP00000415305:D266Y ENSP00000356798:D378Y D - 1 0 HBS1L 135342073 1.000000 0.71417 0.496000 0.27539 0.109000 0.19521 7.666000 0.83877 2.690000 0.91761 0.655000 0.94253 GAC TCGA-S4-A8RP-01A-11D-A36O-08 HBS1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042339.2 1 0 0 8 139 0 32 0 6.802806e-01 0 41 0 32 2 0 0 0 0 0 2 1 0.990001 10 137 0 31 2 0 0 0 0 32 2 -11.271480 1 0 0 0 1 0 1 1 1.504111 1 0.520000 1.960000 0.351351 0.150000 0.070000 0.280000 0.150000 0.169764 0.150000 0 0.110000 0.220000 ZNF451 26036 broad.mit.edu 37 6 57018799 57018799 + Silent SNP A A G TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr6:57018799A>G ENST00000370706.4 + 13 3268 c.3024A>G c.(3022-3024)ggA>ggG p.G1008G RP11-203B9.4_ENST00000586466.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|ZNF451_ENST00000491832.2_Silent_p.G1008G|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|ZNF451_ENST00000357489.3_Silent_p.G960G NM_001031623.2 NP_001026794.1 Q9Y4E5 ZN451_HUMAN zinc finger protein 451 32 Lung NSC(77;0.145) LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13) ACTTAGAGGGAGATATGATGT 0.458000 0 SO:0001819 synonymous_variant ENST00000370706.4 1 1 hg19 CCDS43477.1 TCGA-S4-A8RP-01A-11D-A36O-08 ZNF451-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041035.2 1 0 1 105 331 0 62 1 9.747737e-01 7 14 0 62 2 0 0 0 0 0 2 1 1.000000 104 324 0 62 2 0 0 0 0 62 2 -20.000000 1 1 0 0 1 0 0 0 2.004149 0 0.520000 1.960000 0.517491 0.910000 0.760000 1.000000 1.000000 0.916721 0.910000 1 0.840000 1.000000 RELN 5649 broad.mit.edu 37 7 103132427 103132427 + Missense_Mutation SNP A A G TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr7:103132427A>G ENST00000428762.1 - 58 9575 c.9416T>C c.(9415-9417)gTa>gCa p.V3139A RELN_ENST00000424685.2_Missense_Mutation_p.V3139A|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000343529.5_Missense_Mutation_p.V3139A NM_005045.3 NP_005036.2 P78509 RELN_HUMAN reelin 227 TTCCAGCATTACGGAATGAAG 0.363000 NSCLC(146;835 1944 15585 22231 52158) 0 SO:0001583 missense ENST00000428762.1 1 1 hg19 CCDS47680.1 . . . . . . . . . . A 25.6 4.658140 0.88154 . . ENSG00000189056 ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171 T;T;T 0.34472 1.36;1.36;1.36 5.93 5.93 0.95920 Neuraminidase (1); 0.000000 0.85682 D 0.000000 T 0.60011 0.2236 M 0.76170 2.325 0.58432 D 0.999999 D;B 0.55800 0.973;0.34 D;B 0.63957 0.92;0.224 T 0.63812 -0.6552 10 0.87932 D 0 . 16.3829 0.83481 1.0:0.0:0.0:0.0 . 3139;3139 P78509-2;P78509 .;RELN_HUMAN A 3139;3139;3139;656;3139 ENSP00000392423:V3139A;ENSP00000345694:V3139A;ENSP00000388446:V3139A ENSP00000345694:V3139A V - 2 0 RELN 102919663 1.000000 0.71417 0.843000 0.33291 0.866000 0.49608 8.558000 0.90704 2.271000 0.75665 0.459000 0.35465 GTA TCGA-S4-A8RP-01A-11D-A36O-08 RELN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000348148.1 1 0 0 54 179 0 36 0 1.398933e-01 0 3 0 36 2 0 0 0 0 0 2 1 1.000000 54 175 0 36 2 0 0 0 0 36 2 -20.000000 1 1 0 0 1 0 0 0 2.017447 0 0.520000 1.960000 0.520000 0.880000 0.690000 1.000000 1.000000 0.886732 0.880000 1 0.780000 1.000000 PRSS1 5644 broad.mit.edu 37 7 142458439 142458439 + Missense_Mutation SNP T T C TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr7:142458439T>C ENST00000311737.7 + 2 80 c.74T>C c.(73-75)gTt>gCt p.V25A PRSS1_ENST00000486171.1_Missense_Mutation_p.V25A NM_002769.4 NP_002760.1 P07477 TRY1_HUMAN protease, serine, 1 (trypsin 1) 38 Melanoma(164;0.047) all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165) all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189) Aprotinin(DB06692) GACAAGATCGTTGGGGGCTAC 0.547000 0 SO:0001583 missense ENST00000311737.7 1 1 hg19 CCDS5872.1 . . . . . . . . . . T 13.62 2.291402 0.40494 . . ENSG00000204983 ENST00000486171;ENST00000311737;ENST00000529243 D;D 0.94457 -3.43;-3.43 3.49 2.29 0.28610 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.057642 0.64402 D 0.000001 D 0.96457 0.8844 M 0.84773 2.715 0.42968 D 0.994423 P 0.38677 0.642 P 0.56960 0.81 D 0.95576 0.8642 10 0.87932 D 0 . 8.5187 0.33262 0.1739:0.0:0.0:0.8261 . 25 P07477 TRY1_HUMAN A 25 ENSP00000417854:V25A;ENSP00000308720:V25A ENSP00000308720:V25A V + 2 0 PRSS1 142138013 1.000000 0.71417 0.919000 0.36401 0.005000 0.04900 4.922000 0.63404 0.484000 0.27630 -0.794000 0.03295 GTT TCGA-S4-A8RP-01A-11D-A36O-08 PRSS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352538.2 1 0 0 99 955 0 129 1 1 28 2367 0 129 2 1 9.999197e-01 4 124 0 99 2 1 1.000000 45 756 0 138 2 0 0 0 0 129 2 -20.000000 1 0 121412 2 39 1 0 0 0 2.017447 0 0.520000 1.960000 0.520000 0.350000 0.290000 0.430000 0.360000 0.363888 0.350000 0 0.320000 0.400000 NUB1 51667 broad.mit.edu 37 7 151046243 151046243 + Missense_Mutation SNP A A G TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr7:151046243A>G ENST00000355851.4 + 3 279 c.202A>G c.(202-204)Att>Gtt p.I68V NUB1_ENST00000568733.1_Missense_Mutation_p.I92V|NUB1_ENST00000413040.2_Missense_Mutation_p.I92V|NUB1_ENST00000566856.1_Missense_Mutation_p.I68V NM_001243351.1 NP_001230280.1 Q9Y5A7 NUB1_HUMAN negative regulator of ubiquitin-like proteins 1 11 OV - Ovarian serous cystadenocarcinoma(82;0.00569) TTGCAAGGCAATTGAGCGTGG 0.368000 0 SO:0001583 missense ENST00000355851.4 1 1 hg19 . . . . . . . . . . A 11.23 1.576657 0.28092 . . ENSG00000013374 ENST00000413040;ENST00000355851;ENST00000470229;ENST00000490215;ENST00000483358 T;T;T 0.42900 0.96;0.96;0.96 5.95 2.18 0.27775 . 0.222920 0.47093 N 0.000249 T 0.23249 0.0562 N 0.25201 0.72 0.35458 D 0.7963 B;B;B 0.24092 0.097;0.002;0.004 B;B;B 0.18263 0.021;0.002;0.004 T 0.19976 -1.0289 10 0.14252 T 0.57 -16.5287 8.2332 0.31610 0.7526:0.0:0.2474:0.0 . 68;68;68 F8WDL9;Q9Y5A7;Q9Y5A7-2 .;NUB1_HUMAN;. V 68 ENSP00000348110:I68V;ENSP00000418234:I68V;ENSP00000420086:I68V ENSP00000348110:I68V I + 1 0 NUB1 150677176 0.995000 0.38212 0.991000 0.47740 0.997000 0.91878 1.119000 0.31258 0.131000 0.18576 0.533000 0.62120 ATT TCGA-S4-A8RP-01A-11D-A36O-08 NUB1-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 1 125 350 0 80 1 1 21 70 0 80 2 0 0 0 0 0 2 1 1.000000 125 344 0 78 2 0 0 0 0 80 2 -20.000000 1 1 0 0 1 1 2 3 2.043668 0 0.520000 1.960000 0.522483 0.990000 0.860000 1.000000 1.000000 0.977843 0.990000 1 0.930000 1.000000 SCRIB 23513 broad.mit.edu 37 8 144891881 144891881 + Missense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chr8:144891881C>T ENST00000320476.3 - 14 1544 c.1538G>A c.(1537-1539)cGg>cAg p.R513Q SCRIB_ENST00000356994.2_Missense_Mutation_p.R513Q|SCRIB_ENST00000377533.3_Missense_Mutation_p.R432Q NM_015356.4 NP_056171 Q14160 SCRIB_HUMAN scribbled planar cell polarity protein 42 all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18) GGCACTCAGCCGCTTCTCCTG 0.687000 Pancreas(51;966 1133 10533 14576 29674) 0 SO:0001583 missense ENST00000320476.3 1 1 hg19 CCDS6411.1 . . . . . . . . . . c 13.82 2.351523 0.41700 . . ENSG00000180900 ENST00000356994;ENST00000320476;ENST00000377533 T;T;T 0.78924 -1.22;-1.22;-1.22 4.54 3.64 0.41730 . . . . . T 0.80649 0.4663 L 0.47716 1.5 0.46396 D 0.999022 D;D 0.76494 0.999;0.999 D;D 0.79784 0.984;0.993 T 0.74722 -0.3569 9 0.11485 T 0.65 . 11.3811 0.49757 0.0:0.9096:0.0:0.0904 . 513;513 Q14160;Q14160-3 SCRIB_HUMAN;. Q 513;513;432 ENSP00000349486:R513Q;ENSP00000322938:R513Q;ENSP00000366756:R432Q ENSP00000322938:R513Q R - 2 0 SCRIB 144963869 1.000000 0.71417 0.892000 0.35008 0.125000 0.20455 4.335000 0.59298 2.249000 0.74217 0.401000 0.26515 CGG TCGA-S4-A8RP-01A-11D-A36O-08 SCRIB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000382215.1 1 0 1 59 255 0 50 1 9.999779e-01 17 54 0 50 2 0 0 0 0 0 2 1 1.000000 59 250 0 49 2 0 0 0 0 50 2 -20.000000 1 1 121316 13 40 1 0 3 3 2.531440 1 0.520000 1.960000 0.619048 0.900000 0.710000 1.000000 1.000000 0.903893 0.900000 1 0.800000 1.000000 NONO 4841 broad.mit.edu 37 X 70517747 70517747 + Missense_Mutation SNP C C T TCGA-S4-A8RP-01A-11D-A36O-08 TCGA-S4-A8RP-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 317e480a-3ba4-44b1-9920-557bc1b4c4ee 5f6753a1-efa7-4751-b4ae-2b230620b524 g.chrX:70517747C>T ENST00000276079.8 + 9 1295 c.1090C>T c.(1090-1092)Cgg>Tgg p.R364W NONO_ENST00000535149.1_Missense_Mutation_p.R275W|NONO_ENST00000490044.1_3'UTR|NONO_ENST00000373856.3_Missense_Mutation_p.R364W|NONO_ENST00000373841.1_Missense_Mutation_p.R364W NM_007363.4 NP_031389.3 Q15233 NONO_HUMAN non-POU domain containing, octamer-binding NONO/TFE3(2) 19 Renal(35;0.156) AGAAATGATGCGGCGACAGCA 0.512000 T TFE3 papillary renal cancer Dom yes X Xq13.1 4841 non-POU domain containing, octamer-binding E 0 SO:0001583 missense ENST00000276079.8 0 1 hg19 CCDS14410.1 . . . . . . . . . . c 16.85 3.235855 0.58886 . . ENSG00000147140 ENST00000535149;ENST00000276079;ENST00000373856;ENST00000373841 T;T;T;T 0.31510 1.54;1.49;1.49;1.49 5.23 4.35 0.52113 . 0.050066 0.85682 D 0.000000 T 0.50548 0.1622 M 0.75085 2.285 0.80722 D 1 D 0.76494 0.999 P 0.62089 0.898 T 0.54576 -0.8273 10 0.87932 D 0 -11.2943 11.2281 0.48897 0.5288:0.4712:0.0:0.0 . 364 Q15233 NONO_HUMAN W 275;364;364;364 ENSP00000441364:R275W;ENSP00000276079:R364W;ENSP00000362963:R364W;ENSP00000362947:R364W ENSP00000276079:R364W R + 1 2 NONO 70434472 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 3.256000 0.51492 1.145000 0.42336 0.529000 0.55759 CGG TCGA-S4-A8RP-01A-11D-A36O-08 NONO-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057138.1 0 0 0 5 133 0 19 1 9.992967e-01 4 471 0 19 2 0 0 0 0 0 2 1 0.936303 5 131 0 19 2 0 0 0 0 19 2 -2.908823 1 1 0 0 1 0 1 1 0.520000 1.960000 0.520000 0.140000 0.050000 0.300000 0.140000 0.163724 0.140000 0 0.090000 0.220000