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 MUC6 4588 broad.mit.edu 37 11 1016412 1016414 + In_Frame_Del DEL GAG GAG - TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 GAG - GAG GAG Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr11:1016412_1016414delGAG ENST00000421673.2 - 31 6437_6439 c.6387_6389delCTC c.(6385-6390)tcctca>tca p.2129_2130SS>S NM_005961.2 NP_005952.2 Q6W4X9 MUC6_HUMAN mucin 6, oligomeric mucus/gel-forming p.S2130delS(1) 80 all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) GGGAGAAAATGAGGAGGACAGCT 0.522000 1 Deletion - In frame(1) SO:0001651 inframe_deletion ENST00000421673.2 1 1 hg19 CCDS44513.1 TCGA-2L-AAQA-01A-21D-A38G-08 MUC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382120.2 1 0 0 57 209 0 58 1 1 16 404 0 58 2 0 0 0 0 1 0.997701 67 210 5 62 35 0 0 0 0 0 0 -20.000000 1 0 0 0 1 0 0 0 2.071255 0 0.600000 1.890000 0.600000 0.710000 5.500000e-01 0.880000 0.720000 0.719562 0.710000 0 6.300000e-01 8.000000e-01 RNF43 54894 broad.mit.edu 37 17 56492904 56492908 + Frame_Shift_Del DEL AGGGC AGGGC - TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 AGGGC - AGGGC AGGGC Valid Somatic Phase_I WXS targeted Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr17:56492904_56492908delAGGGC ENST00000584437.1 - 1 1986_1990 c.31_35delGCCCT c.(31-36)gccctcfs p.AL11fs RNF43_ENST00000583753.1_Frame_Shift_Del_p.AL11fs|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000577716.1_Frame_Shift_Del_p.AL11fs|RNF43_ENST00000500597.2_Frame_Shift_Del_p.AL11fs|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Frame_Shift_Del_p.AL11fs|RNF43_ENST00000581868.1_Intron Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) CCAGGGCCAGAGGGCAGCCAGCTGC 0.556000 0 SO:0001589 frameshift_variant ENST00000584437.1 1 1 hg19 CCDS11607.1 TCGA-2L-AAQA-01A-21D-A38G-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 0 38 158 0 103 1 7.845042e-01 4 10 0 103 2 1 1 115 316 0 228 2 1 1.000000 50 165 0 103 2 0 0 0 0 0 0 -20.000000 1 0 0 0 1 0 1 1 1.475023 1 0.600000 1.890000 0.431010 0.450000 3.300000e-01 0.580000 0.450000 0.458472 0.450000 0 3.800000e-01 5.200000e-01 PMEPA1 56937 broad.mit.edu 37 20 56227349 56227349 + Frame_Shift_Del DEL G G - TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G - G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr20:56227349delG ENST00000341744.3 - 4 943 c.624delC c.(622-624)cccfs p.P208fs PMEPA1_ENST00000395814.1_Frame_Shift_Del_p.P158fs|PMEPA1_ENST00000347215.4_Frame_Shift_Del_p.P173fs|PMEPA1_ENST00000265626.4_Frame_Shift_Del_p.P158fs|PMEPA1_ENST00000395816.3_Frame_Shift_Del_p.P158fs NM_020182.4 NP_064567.2 Q969W9 PMEPA_HUMAN prostate transmembrane protein, androgen induced 1 16 AGTTACTGCTGGGGGGGCAGG 0.682000 0 SO:0001589 frameshift_variant ENST00000341744.3 1 0 hg19 CCDS13463.1 TCGA-2L-AAQA-01A-21D-A38G-08 PMEPA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079858.2 1 0 0 55 285 0 80 1 1 238 785 0 80 2 0 0 0 0 1 0.976157 77 278 6 80 40 0 0 0 0 0 0 -1.563211 0 1 0 0 1 0 0 0 2.045390 0 0.600000 1.890000 0.597586 0.530000 4.100000e-01 0.670000 0.530000 0.541462 0.530000 0 4.600000e-01 6.100000e-01 ARRDC1 92714 broad.mit.edu 37 9 140507340 140507354 + Splice_Site DEL CTTTGCAGCCATCCG CTTTGCAGCCATCCG - rs147183389 byFrequency TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 CTTTGCAGCCATCCG - CTTTGCAGCCATCCG CTTTGCAGCCATCCG Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr9:140507340_140507354delCTTTGCAGCCATCCG ENST00000371421.4 + 2 182_189 c.118_125delCTTTGCAGCCATCCG c.(118-126)ctttgcagc>c p.LCS40del C9orf37_ENST00000496793.1_5'Flank|ARRDC1_ENST00000491911.1_3'UTR NM_152285.2 NP_689498.1 Q8N5I2 ARRD1_HUMAN arrestin domain containing 1 13 all_cancers(76;0.106) CAGCCATCCCCTTTGCAGCCATCCGGGTGACCTGC 0.633000 0 SO:0001630 splice_region_variant ENST00000371421.4 1 1 hg19 CCDS7049.1 TCGA-2L-AAQA-01A-21D-A38G-08 ARRDC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055358.1 0 0 0 32 157 0 48 0 1 0 437 0 48 2 0 0 0 0 1 1.000000 39 162 0 48 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 2.067674 0 0.600000 1.890000 0.600000 0.560000 4.000000e-01 0.750000 0.560000 0.573886 0.560000 0 4.700000e-01 6.600000e-01 FAM178A 55719 broad.mit.edu 37 10 102672997 102672997 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr10:102672997C>T ENST00000238961.4 + 1 672 c.130C>T c.(130-132)Cct>Tct p.P44S FAM178A_ENST00000370271.3_Missense_Mutation_p.P44S|FAM178A_ENST00000609386.1_Missense_Mutation_p.P44S|FAM178A_ENST00000370269.3_Missense_Mutation_p.P44S|RP11-179B2.2_ENST00000608554.1_RNA NM_018121.3 NP_060591.3 Q8IX21 F178A_HUMAN family with sequence similarity 178, member A AACAGAGAGTCCTGGGGACAG 0.682000 0 SO:0001583 missense ENST00000238961.4 1 1 hg19 CCDS7500.1 . . . . . . . . . . C 24.6 4.545875 0.86022 . . ENSG00000119906 ENST00000370271;ENST00000238961;ENST00000370269 T;T;T 0.61392 0.11;0.85;0.81 5.25 5.25 0.73442 . 0.000000 0.53938 D 0.000044 T 0.63745 0.2537 N 0.24115 0.695 0.35168 D 0.771306 D;D;D 0.89917 0.995;0.995;1.0 D;D;D 0.87578 0.919;0.919;0.998 T 0.72204 -0.4361 10 0.72032 D 0.01 -15.2639 14.5237 0.67873 0.0:1.0:0.0:0.0 . 44;44;44 Q8IX21;B1AL17;B1AL16 F178A_HUMAN;.;. S 44 ENSP00000359294:P44S;ENSP00000238961:P44S;ENSP00000359292:P44S ENSP00000238961:P44S P + 1 0 FAM178A 102662987 1.000000 0.71417 1.000000 0.80357 0.954000 0.61252 3.254000 0.51477 2.890000 0.99128 0.585000 0.79938 CCT TCGA-2L-AAQA-01A-21D-A38G-08 FAM178A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000049897.3 1 0 1 16 30 0 19 1 9.857931e-01 11 6 0 19 2 0 0 0 0 0 2 1 0.999973 16 28 0 19 2 0 0 0 0 19 2 -20.000000 1 1 121232 2 25 1 1 2 3 2.117229 0 0.600000 1.890000 0.604743 0.990000 7.500000e-01 1.000000 1.000000 0.974213 0.990000 1 9.400000e-01 1 CRTAC1 55118 broad.mit.edu 37 10 99696061 99696061 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr10:99696061G>A ENST00000370597.3 - 3 642 c.287C>T c.(286-288)gCg>gTg p.A96V CRTAC1_ENST00000370591.2_Missense_Mutation_p.A96V|CRTAC1_ENST00000298819.4_Missense_Mutation_p.A96V NM_018058.6 NP_060528.3 Q9NQ79 CRAC1_HUMAN cartilage acidic protein 1 35 Colorectal(252;0.24) CTCATCGACCGCGATGTTCAC 0.662000 0 SO:0001583 missense ENST00000370597.3 1 1 hg19 CCDS31266.1 . . . . . . . . . . G 21.7 4.184476 0.78677 . . ENSG00000095713 ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591 T;T;T;T 0.20881 2.04;2.04;2.04;2.04 4.76 4.76 0.60689 . 0.000000 0.85682 D 0.000000 T 0.47875 0.1469 M 0.79475 2.455 0.80722 D 1 D;D 0.89917 0.996;1.0 P;D 0.91635 0.704;0.999 T 0.43523 -0.9386 10 0.27785 T 0.31 -10.778 17.7665 0.88480 0.0:0.0:1.0:0.0 . 96;96 Q9NQ79-2;Q9NQ79 .;CRAC1_HUMAN V 96;96;88;96 ENSP00000359629:A96V;ENSP00000298819:A96V;ENSP00000310810:A88V;ENSP00000359623:A96V ENSP00000298819:A96V A - 2 0 CRTAC1 99686051 1.000000 0.71417 0.892000 0.35008 0.640000 0.38277 9.725000 0.98778 2.204000 0.70986 0.313000 0.20887 GCG TCGA-2L-AAQA-01A-21D-A38G-08 CRTAC1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000049754.1 1 0 1 64 206 0 81 0 0 0 1 0 81 2 0 0 0 0 0 2 1 1.000000 63 203 0 81 2 0 0 0 0 81 2 -20.000000 1 1 121408 1 31 1 1 2 3 2.117229 0 0.600000 1.890000 0.604743 0.800000 6.300000e-01 1.000000 0.800000 0.809308 0.800000 0 7.100000e-01 9.000000e-01 HIPK3 10114 broad.mit.edu 37 11 33369721 33369721 + Missense_Mutation SNP G G C TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr11:33369721G>C ENST00000303296.4 + 12 2621 c.2316G>C c.(2314-2316)ttG>ttC p.L772F HIPK3_ENST00000525975.1_Intron|HIPK3_ENST00000379016.3_Intron|HIPK3_ENST00000456517.1_Intron NM_005734.3 NP_005725.3 Q9H422 HIPK3_HUMAN homeodomain interacting protein kinase 3 39 GAGGTATTTTGGTAAAACTAA 0.363000 0 SO:0001583 missense ENST00000303296.4 1 1 hg19 CCDS7884.1 . . . . . . . . . . G 11.03 1.517978 0.27211 . . ENSG00000110422 ENST00000303296 T 0.23348 1.91 5.74 5.74 0.90152 . 0.162090 0.29314 N 0.012518 T 0.13713 0.0332 N 0.14661 0.345 0.80722 D 1 P 0.35908 0.527 B 0.33042 0.157 T 0.12066 -1.0562 10 0.09843 T 0.71 . 13.1561 0.59518 0.0728:0.0:0.9272:0.0 . 772 Q9H422 HIPK3_HUMAN F 772 ENSP00000304226:L772F ENSP00000304226:L772F L + 3 2 HIPK3 33326297 1.000000 0.71417 1.000000 0.80357 0.894000 0.52154 3.785000 0.55424 2.707000 0.92482 0.557000 0.71058 TTG TCGA-2L-AAQA-01A-21D-A38G-08 HIPK3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000255358.1 1 0 1 72 136 0 59 1 9.977588e-01 11 10 0 59 2 0 0 0 0 0 2 1 1.000000 72 134 0 59 2 0 0 0 0 59 2 -9.530416 1 1 0 0 1 0 0 0 2.071255 0 0.600000 1.890000 0.600000 0.990000 9.400000e-01 1.000000 1.000000 0.996524 0.990000 1 9.900000e-01 1 PAMR1 25891 broad.mit.edu 37 11 35513689 35513689 + Nonsense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr11:35513689G>A ENST00000378880.2 - 3 728 c.283C>T c.(283-285)Cga>Tga p.R95* PAMR1_ENST00000532848.1_Nonsense_Mutation_p.R55*|PAMR1_ENST00000378878.3_Nonsense_Mutation_p.R95*|PAMR1_ENST00000278360.3_Nonsense_Mutation_p.R95*|PAMR1_ENST00000534803.1_5'UTR NM_001001991.1 NP_001001991.1 Q6UXH9 PAMR1_HUMAN peptidase domain containing associated with muscle regeneration 1 26 GAGCCATTTCGGCAGCTCTTG 0.522000 0 SO:0001587 stop_gained ENST00000378880.2 0 1 hg19 CCDS31460.1 . . . . . . . . . . G 41 9.063677 0.99053 2.27E-4 0.0 ENSG00000149090 ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605;ENST00000529303 . . . 5.05 3.08 0.35506 . 0.459441 0.22469 N 0.059650 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.87932 D 0 . 12.6536 0.56776 0.0:0.0:0.5742:0.4258 . . . . X 95;95;95;55;55;95 . ENSP00000278360:R95X R - 1 2 PAMR1 35470265 1.000000 0.71417 0.978000 0.43139 0.911000 0.54048 3.430000 0.52807 0.471000 0.27319 0.491000 0.48974 CGA TCGA-2L-AAQA-01A-21D-A38G-08 PAMR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389177.1 1 0 1 301 741 1 362 0 9.244735e-01 0 13 1 362 2 0 0 0 0 0 2 1 1.000000 300 732 1 357 12 0 0 0 1 362 2 -14.292280 1 1 121412 3 43 1 0 0 0 2.071255 0 0.600000 1.890000 0.600000 0.950000 8.600000e-01 1.000000 1.000000 0.957509 0.950000 1 9.100000e-01 1 PEX16 9409 broad.mit.edu 37 11 45936217 45936217 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr11:45936217C>T ENST00000378750.5 - 6 722 c.479G>A c.(478-480)gGc>gAc p.G160D PEX16_ENST00000532554.1_5'UTR|PEX16_ENST00000241041.3_Missense_Mutation_p.G160D|PEX16_ENST00000532681.1_Missense_Mutation_p.G65D Q9Y5Y5 PEX16_HUMAN peroxisomal biogenesis factor 16 7 CTCATGGTTGCCAGGGCTGTG 0.582000 0 SO:0001583 missense ENST00000378750.5 1 1 hg19 CCDS31472.1 . . . . . . . . . . C 3.698 -0.062097 0.07317 . . ENSG00000121680 ENST00000241041;ENST00000378750;ENST00000532681;ENST00000533151;ENST00000525192 T;T;T;T;T 0.21361 2.01;2.01;2.01;2.01;2.01 5.85 4.0 0.46444 . 0.670270 0.16493 N 0.212040 T 0.13756 0.0333 L 0.31294 0.92 0.09310 N 1 B;B 0.12630 0.004;0.006 B;B 0.12156 0.007;0.004 T 0.32161 -0.9917 10 0.15952 T 0.53 -5.9846 8.1875 0.31348 0.0:0.7141:0.139:0.1469 . 160;160 Q9Y5Y5;Q9Y5Y5-2 PEX16_HUMAN;. D 160;160;65;56;65 ENSP00000241041:G160D;ENSP00000368024:G160D;ENSP00000434654:G65D;ENSP00000433045:G56D;ENSP00000431309:G65D ENSP00000241041:G160D G - 2 0 PEX16 45892793 0.123000 0.22298 0.047000 0.18901 0.134000 0.20937 0.876000 0.28092 0.827000 0.34685 -0.291000 0.09656 GGC TCGA-2L-AAQA-01A-21D-A38G-08 PEX16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000392398.1 0 0 1 114 318 1 141 1 1 106 132 1 141 8 0 0 0 0 0 2 1 1.000000 110 308 0 139 2 0 0 0 1 141 2 -20.000000 1 1 0 0 1 0 0 0 2.071255 0 0.600000 1.890000 0.600000 0.870000 7.400000e-01 1.000000 1.000000 0.880302 0.870000 1 8.000000e-01 9.500000e-01 OR5D13 390142 broad.mit.edu 37 11 55541761 55541761 + Missense_Mutation SNP C C T rs140938722 by1000genomes TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr11:55541761C>T ENST00000361760.1 + 1 848 c.848C>T c.(847-849)gCg>gTg p.A283V NM_001001967.1 NP_001001967.1 Q8NGL4 OR5DD_HUMAN olfactory receptor, family 5, subfamily D, member 13 40 all_epithelial(135;0.196) TACACAGTGGCGATTCCAATG 0.363000 0 SO:0001583 missense ENST00000361760.1 1 0 hg19 CCDS31507.1 4 0.0018315018315018315 0 0.0 2 0.0055248618784530384 2 0.0034965034965034965 0 0.0 C 0 -2.801658 0.00075 . . ENSG00000198877 ENST00000361760 T 0.00013 9.25 3.68 1.18 0.20946 GPCR, rhodopsin-like superfamily (1); 0.960258 0.08414 N 0.949423 T 0.00012 0.0000 N 0.00006 -3.225 0.09310 N 1 B 0.02656 0.0 B 0.06405 0.002 T 0.49588 -0.8924 10 0.02654 T 1 -3.3382 3.6909 0.08346 0.1898:0.1116:0.0:0.6986 . 283 Q8NGL4 OR5DD_HUMAN V 283 ENSP00000354800:A283V ENSP00000354800:A283V A + 2 0 OR5D13 55298337 0.002000 0.14202 0.022000 0.16811 0.001000 0.01503 1.319000 0.33655 0.020000 0.15106 -1.495000 0.00966 GCG TCGA-2L-AAQA-01A-21D-A38G-08 OR5D13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391511.1 1 0 1 135 250 0 110 0 0 0 0 110 2 0 0 0 0 0 2 1 1.000000 134 246 0 110 2 0 0 0 0 110 2 -14.940370 1 1 121378 52 47 1 0 0 0 2.071255 0 0.600000 1.890000 0.600000 0.990000 9.900000e-01 1.000000 1.000000 0.999547 0.990000 1 9.900000e-01 1 FAM181B 220382 broad.mit.edu 37 11 82444594 82444594 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr11:82444594G>A ENST00000329203.3 - 1 312 c.178C>T c.(178-180)Cgc>Tgc p.R60C NM_175885.3 NP_787081.2 A6NEQ2 F181B_HUMAN family with sequence similarity 181, member B 4 GTGGCCTCGCGCACGTCCCCT 0.662000 0 SO:0001583 missense ENST00000329203.3 0 1 hg19 CCDS31648.1 . . . . . . . . . . G 12.73 2.025614 0.35701 . . ENSG00000182103 ENST00000329203 T 0.34275 1.37 3.79 1.62 0.23740 . 0.378309 0.21245 U 0.077752 T 0.41465 0.1160 L 0.43152 1.355 0.43919 D 0.996568 D 0.76494 0.999 D 0.63113 0.911 T 0.18366 -1.0339 9 . . . . 6.0139 0.19592 0.0:0.1346:0.4145:0.4508 . 60 A6NEQ2 F181B_HUMAN C 60 ENSP00000365295:R60C . R - 1 0 FAM181B 82122242 1.000000 0.71417 0.998000 0.56505 0.004000 0.04260 2.558000 0.45879 0.771000 0.33359 -0.519000 0.04390 CGC TCGA-2L-AAQA-01A-21D-A38G-08 FAM181B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391626.1 0 0 0 4 103 0 17 0 2.502085e-03 0 2 0 17 2 0 0 0 0 0 2 1 0.880154 3 99 0 17 2 0 0 0 0 17 2 -7.220390 1 0 0 0 1 0 0 0 2.073547 0 0.600000 1.890000 0.600000 0.130000 4.000000e-02 0.290000 0.120000 0.151943 0.130000 0 8.000000e-02 2.100000e-01 BTBD11 121551 broad.mit.edu 37 12 108013765 108013765 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr12:108013765G>A ENST00000280758.5 + 11 2983 c.2455G>A c.(2455-2457)Gtc>Atc p.V819I BTBD11_ENST00000490090.2_Missense_Mutation_p.V819I|BTBD11_ENST00000420571.2_Missense_Mutation_p.V700I|BTBD11_ENST00000357167.4_Missense_Mutation_p.V356I|RP11-128P10.1_ENST00000548473.1_RNA NM_001018072.1 NP_001018082.1 A6QL63 BTBDB_HUMAN BTB (POZ) domain containing 11 53 CGCTCCAGGCGTCCCGTGGAC 0.587000 0 SO:0001583 missense ENST00000280758.5 1 1 hg19 CCDS31893.1 . . . . . . . . . . G 27.8 4.868192 0.91587 2.27E-4 1.16E-4 ENSG00000151136 ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167 T;T;T;T 0.55052 0.65;0.65;0.67;0.54 5.15 5.15 0.70609 . 0.117935 0.56097 D 0.000021 T 0.72495 0.3467 M 0.70275 2.135 0.80722 D 1 D;P;D;D 0.71674 0.998;0.508;0.987;0.99 D;B;B;P 0.73708 0.981;0.073;0.403;0.496 T 0.75560 -0.3275 10 0.66056 D 0.02 . 18.6524 0.91435 0.0:0.0:1.0:0.0 . 700;356;819;819 A6QL63-2;E9PHS4;A6QL63;A6QL63-3 .;.;BTBDB_HUMAN;. I 819;700;819;356 ENSP00000280758:V819I;ENSP00000413889:V700I;ENSP00000447319:V819I;ENSP00000349690:V356I ENSP00000280758:V819I V + 1 0 BTBD11 106537895 1.000000 0.71417 1.000000 0.80357 0.727000 0.41649 7.975000 0.88055 2.398000 0.81561 0.650000 0.86243 GTC TCGA-2L-AAQA-01A-21D-A38G-08 BTBD11-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318003.1 0 0 1 32 101 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 1.000000 30 101 0 35 2 0 0 0 0 36 2 -3.017664 1 1 121406 35 41 1 0 0 0 2.008629 0 0.600000 1.890000 0.587629 0.770000 5.600000e-01 1.000000 1.000000 0.783994 0.770000 0 6.600000e-01 9.000000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2L-AAQA-01A-21D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 101 239 1 129 1 9.999856e-01 28 29 1 129 4 1 1 68 251 0 178 2 1 1.000000 101 236 0 128 2 1 1 2498 5510 1 129 146 -20.000000 1 1 0 0 1 0 0 0 2.008629 0 0.600000 1.890000 0.587629 0.950000 8.000000e-01 1.000000 1.000000 0.945562 0.950000 1 8.700000e-01 1 CPNE8 144402 broad.mit.edu 37 12 39117617 39117617 + Missense_Mutation SNP A A T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr12:39117617A>T ENST00000331366.5 - 13 967 c.871T>A c.(871-873)Ttg>Atg p.L291M CPNE8_ENST00000360449.3_Missense_Mutation_p.L279M|CPNE8_ENST00000538596.2_5'Flank NM_153634.2 NP_705898.1 Q86YQ8 CPNE8_HUMAN copine VIII 21 Esophageal squamous(101;0.187) Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157) GTTTCTACCAAGAAAGAGAGT 0.328000 0 SO:0001583 missense ENST00000331366.5 1 1 hg19 CCDS8733.1 . . . . . . . . . . A 15.26 2.781337 0.49891 . . ENSG00000139117 ENST00000331366;ENST00000360449 T;T 0.25085 1.82;1.82 4.51 0.923 0.19413 . 0.174644 0.38720 N 0.001594 T 0.20047 0.0482 L 0.35854 1.095 0.48762 D 0.999705 P 0.37207 0.587 B 0.42882 0.401 T 0.03534 -1.1027 10 0.59425 D 0.04 -5.3906 4.2841 0.10846 0.582:0.1718:0.2463:0.0 . 291 Q86YQ8 CPNE8_HUMAN M 291;279 ENSP00000329748:L291M;ENSP00000353633:L279M ENSP00000329748:L291M L - 1 2 CPNE8 37403884 0.989000 0.36119 0.997000 0.53966 0.989000 0.77384 0.619000 0.24388 0.317000 0.23160 0.460000 0.39030 TTG TCGA-2L-AAQA-01A-21D-A38G-08 CPNE8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403856.1 1 0 1 130 388 0 151 1 9.596372e-01 6 12 0 151 2 0 0 0 0 0 2 1 1.000000 130 383 0 149 2 0 0 0 0 151 2 -20.000000 1 1 0 0 1 0 0 0 2.008629 0 0.600000 1.890000 0.587629 0.800000 6.800000e-01 0.930000 0.810000 0.813416 0.800000 0 7.400000e-01 8.700000e-01 KCNA6 3742 broad.mit.edu 37 12 4920011 4920011 + Silent SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr12:4920011G>A ENST00000280684.3 + 1 1670 c.804G>A c.(802-804)acG>acA p.T268T RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Silent_p.T268T P17658 KCNA6_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 6 49 Dalfampridine(DB06637) TGGTGGAGACGCTGTGCATTG 0.562000 HNSCC(72;0.22) 0 SO:0001819 synonymous_variant ENST00000280684.3 1 1 hg19 CCDS8534.1 TCGA-2L-AAQA-01A-21D-A38G-08 KCNA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398909.1 1 0 1 143 324 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 141 322 0 146 2 0 0 0 0 147 2 -20.000000 1 1 0 0 1 0 0 0 2.042440 0 0.600000 1.890000 0.595142 0.990000 8.600000e-01 1.000000 1.000000 0.976558 0.990000 1 9.300000e-01 1 NCKAP5L 57701 broad.mit.edu 37 12 50191075 50191075 + Missense_Mutation SNP T T A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr12:50191075T>A ENST00000335999.6 - 8 769 c.568A>T c.(568-570)Att>Ttt p.I190F NM_001037806.3 NP_001032895.2 Q9HCH0 NCK5L_HUMAN NCK-associated protein 5-like 18 ACCTCCAGAATCTGGGCCTTC 0.682000 0 SO:0001583 missense ENST00000335999.6 1 1 hg19 CCDS41781.2 . . . . . . . . . . T 23.9 4.465970 0.84425 . . ENSG00000167566 ENST00000335999;ENST00000354423 T 0.63913 -0.07 4.3 4.3 0.51218 . . . . . T 0.71204 0.3312 L 0.42245 1.32 0.47153 D 0.999339 D 0.76494 0.999 D 0.87578 0.998 T 0.73372 -0.4003 9 0.59425 D 0.04 -4.9163 12.7587 0.57350 0.0:0.0:0.0:1.0 . 186 E2QRB5 . F 190;186 ENSP00000337998:I190F ENSP00000337998:I190F I - 1 0 NCKAP5L 48477342 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.480000 0.53172 1.717000 0.51406 0.379000 0.24179 ATT TCGA-2L-AAQA-01A-21D-A38G-08 NCKAP5L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346884.2 1 0 1 56 122 0 56 1 9.829473e-01 4 13 0 56 2 0 0 0 0 0 2 1 1.000000 56 122 0 53 2 0 0 0 0 56 2 -20.000000 1 1 0 0 1 0 0 0 2.008629 0 0.600000 1.890000 0.587629 0.990000 8.000000e-01 1.000000 1.000000 0.964849 0.990000 1 9.000000e-01 1 NCAPD2 9918 broad.mit.edu 37 12 6631057 6631057 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr12:6631057C>T ENST00000315579.5 + 15 2607 c.1808C>T c.(1807-1809)tCg>tTg p.S603L NCAPD2_ENST00000545962.1_Missense_Mutation_p.S558L NM_014865.3 NP_055680.3 Q15021 CND1_HUMAN non-SMC condensin I complex, subunit D2 48 CCCAATATGTCGGATCCTGAG 0.483000 0 SO:0001583 missense ENST00000315579.5 0 1 hg19 CCDS8548.1 . . . . . . . . . . C 6.832 0.522777 0.13066 . . ENSG00000010292 ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602 T;T;T 0.31769 2.49;1.48;2.22 4.69 0.379 0.16213 Armadillo-type fold (1); 0.958927 0.08648 N 0.914555 T 0.14917 0.0360 N 0.08118 0 0.09310 N 1 B;B;B 0.12013 0.005;0.0;0.001 B;B;B 0.06405 0.002;0.0;0.001 T 0.30179 -0.9987 10 0.29301 T 0.29 0.0031 7.6424 0.28300 0.1363:0.5837:0.0:0.28 . 558;564;603 F5GZJ1;B3KY03;Q15021 .;.;CND1_HUMAN L 603;475;558;475 ENSP00000325017:S603L;ENSP00000371895:S475L;ENSP00000444417:S558L ENSP00000325017:S603L S + 2 0 NCAPD2 6501318 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.426000 0.07008 -0.050000 0.13356 -1.736000 0.00690 TCG TCGA-2L-AAQA-01A-21D-A38G-08 NCAPD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399964.1 0 0 0 7 396 1 129 0 4.147525e-02 0 60 1 129 4 0 0 0 0 0 2 0 0.171051 6 394 1 129 12 0 0 0 1 129 2 -3.228614 1 1 0 0 1 0 0 0 2.042440 0 0.600000 1.890000 0.595142 0.050000 2.000000e-02 0.110000 0.060000 0.064975 0.050000 0 3.000000e-02 9.000000e-02 HECTD1 25831 broad.mit.edu 37 14 31576215 31576215 + Missense_Mutation SNP T T A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr14:31576215T>A ENST00000399332.1 - 38 7351 c.6863A>T c.(6862-6864)tAt>tTt p.Y2288F HECTD1_ENST00000553700.1_Missense_Mutation_p.Y2288F NM_015382.2 NP_056197.2 Q9ULT8 HECD1_HUMAN HECT domain containing E3 ubiquitin protein ligase 1 70 Hepatocellular(127;0.0877)|Breast(36;0.176) LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173) TCGTGACTCATAAATCAGTTT 0.368000 0 SO:0001583 missense ENST00000399332.1 1 1 hg19 CCDS41939.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 11.57|11.57 1.677590|1.677590 0.29783|0.29783 .|. .|. ENSG00000092148|ENSG00000092148 ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332 .|T;T .|0.39406 .|1.08;1.08 5.96|5.96 5.96|5.96 0.96718|0.96718 .|HECT (4); .|0.085238 .|0.49305 .|U .|0.000145 T|T 0.38161|0.38161 0.1030|0.1030 N|N 0.03608|0.03608 -0.345|-0.345 0.58432|0.58432 D|D 0.999996|0.999996 .|D .|0.57257 .|0.979 .|D .|0.71414 .|0.973 T|T 0.39563|0.39563 -0.9608|-0.9608 5|10 .|0.11794 .|T .|0.64 -10.4726|-10.4726 15.0049|15.0049 0.71504|0.71504 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. .|2288 .|Q9ULT8 .|HECD1_HUMAN L|F 654|2288;2290;2288 .|ENSP00000450697:Y2288F;ENSP00000382269:Y2288F .|ENSP00000261312:Y2290F M|Y -|- 1|2 0|0 HECTD1|HECTD1 30645966|30645966 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.994000|0.994000 0.84299|0.84299 7.694000|7.694000 0.84235|0.84235 2.270000|2.270000 0.75569|0.75569 0.533000|0.533000 0.62120|0.62120 ATG|TAT TCGA-2L-AAQA-01A-21D-A38G-08 HECTD1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409942.1 0 0 0 12 537 1 134 0 1.834330e-01 0 123 1 134 5 0 0 0 0 0 2 0 0.345185 12 536 1 132 15 0 0 0 1 134 2 -10.451700 1 1 120808 1 30 1 0 0 0 2.052130 0 0.600000 1.890000 0.597586 0.070000 3.000000e-02 0.120000 0.080000 0.078078 0.070000 0 5.000000e-02 1.000000e-01 MAGEL2 54551 broad.mit.edu 37 15 23890209 23890209 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr15:23890209G>A ENST00000532292.1 - 1 966 c.872C>T c.(871-873)gCc>gTc p.A291V NM_019066.4 NP_061939.3 Q9UJ55 MAGL2_HUMAN MAGE-like 2 7 all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14) GTCCTCTTGGGCTTCCAGATG 0.632000 0 SO:0001583 missense ENST00000532292.1 1 1 hg19 . . . . . . . . . . G 7.175 0.588375 0.13812 . . ENSG00000254585 ENST00000532292 . . . 4.22 3.3 0.37823 . . . . . T 0.18593 0.0446 N 0.08118 0 0.09310 N 1 . . . . . . T 0.19877 -1.0292 5 . . . . 7.8726 0.29576 0.1098:0.0:0.8901:0.0 . . . . S 323 . . P - 1 0 MAGEL2 21441302 0.001000 0.12720 0.002000 0.10522 0.299000 0.27559 0.810000 0.27183 1.364000 0.46038 0.655000 0.94253 CCC TCGA-2L-AAQA-01A-21D-A38G-08 MAGEL2-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000395182.2 1 0 0 16 232 0 118 0 0 0 1 0 118 2 0 0 0 0 0 2 1 0.999921 16 223 0 115 2 0 0 0 0 118 2 -19.366610 1 1 0 0 1 0 1 1 1.428970 1 0.600000 1.890000 0.428571 0.140000 8.000000e-02 0.230000 0.150000 0.157810 0.140000 0 1.100000e-01 1.900000e-01 ISLR2 57611 broad.mit.edu 37 15 74425848 74425848 + Silent SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr15:74425848C>T ENST00000361742.3 + 4 1522 c.753C>T c.(751-753)cgC>cgT p.R251R ISLR2_ENST00000453268.2_Silent_p.R251R|ISLR2_ENST00000565540.1_Silent_p.R251R|ISLR2_ENST00000435464.1_Silent_p.R251R|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000419208.1_Silent_p.R251R|ISLR2_ENST00000565159.1_Silent_p.R251R|ISLR2_ENST00000445793.1_Silent_p.R251R NM_001130136.1|NM_020851.2 NP_001123608.1|NP_065902.1 Q6UXK2 ISLR2_HUMAN immunoglobulin superfamily containing leucine-rich repeat 2 36 CCCCACTGCGCGCAGGACTGG 0.677000 0 SO:0001819 synonymous_variant ENST00000361742.3 1 1 hg19 CCDS10259.1 TCGA-2L-AAQA-01A-21D-A38G-08 ISLR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269046.1 1 0 1 90 188 0 94 0 2.475146e-01 0 3 0 94 2 0 0 0 0 0 2 1 1.000000 88 185 0 94 2 0 0 0 0 94 2 -20.000000 1 1 0 0 1 0.600000 1.890000 0 0 CCL8 6355 broad.mit.edu 37 17 32647821 32647821 + Splice_Site SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr17:32647821C>T ENST00000394620.1 + 3 661 c.195C>T c.(193-195)atC>atT p.I65I NM_005623.2 NP_005614.2 P80075 CCL8_HUMAN chemokine (C-C motif) ligand 8 4 Ovarian(249;0.0443)|Breast(31;0.151) TCCCCCACAGCTTCAAGACCA 0.512000 0 SO:0001630 splice_region_variant ENST00000394620.1 1 0 hg19 CCDS11280.1 TCGA-2L-AAQA-01A-21D-A38G-08 CCL8-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256376.2 1 0 1 40 78 0 72 0 0 0 1 0 72 2 0 0 0 0 0 2 1 1.000000 39 73 0 70 2 0 0 0 0 72 2 -20.000000 1 1 0 0 1 0 1 1 1.479540 1 0.600000 1.890000 0.431010 0.780000 5.900000e-01 0.960000 0.790000 0.787428 0.780000 0 6.800000e-01 8.800000e-01 RNF43 54894 broad.mit.edu 37 17 56492899 56492899 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr17:56492899G>A ENST00000584437.1 - 1 1995 c.40C>T c.(40-42)Ccc>Tcc p.P14S RNF43_ENST00000583753.1_Missense_Mutation_p.P14S|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000577716.1_Missense_Mutation_p.P14S|RNF43_ENST00000500597.2_Missense_Mutation_p.P14S|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Missense_Mutation_p.P14S|RNF43_ENST00000581868.1_Intron Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) AGCAGCCAGGGCCAGAGGGCA 0.552000 0 SO:0001583 missense ENST00000584437.1 1 0 hg19 CCDS11607.1 . . . . . . . . . . G 24.1 4.492626 0.84962 . . ENSG00000108375 ENST00000407977;ENST00000500597 T;T 0.23950 2.6;1.88 5.69 5.69 0.88448 . 0.000000 0.64402 D 0.000008 T 0.37237 0.0996 N 0.14661 0.345 0.52099 D 0.999941 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.997 T 0.32798 -0.9893 10 0.62326 D 0.03 -25.2822 19.1688 0.93569 0.0:0.0:1.0:0.0 . 14;14 Q68DV7-2;Q68DV7 .;RNF43_HUMAN S 14 ENSP00000385328:P14S;ENSP00000441969:P14S ENSP00000385328:P14S P - 1 0 RNF43 53847898 1.000000 0.71417 1.000000 0.80357 1.000000 0.99986 8.758000 0.91663 2.840000 0.97914 0.655000 0.94253 CCC TCGA-2L-AAQA-01A-21D-A38G-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 51 120 0 107 1 9.466499e-01 14 0 0 107 2 1 1 128 200 0 227 2 1 1.000000 51 119 0 107 2 0 0 0 0 107 2 -20.000000 1 0 0 0 1 0 1 1 1.475023 1 0.600000 1.890000 0.431010 0.690000 5.400000e-01 0.850000 0.690000 0.698904 0.690000 0 6.100000e-01 7.800000e-01 EXOC7 23265 broad.mit.edu 37 17 74097870 74097870 + Silent SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr17:74097870C>T ENST00000335146.7 - 3 254 c.201G>A c.(199-201)acG>acA p.T67T EXOC7_ENST00000467929.2_Silent_p.T26T|EXOC7_ENST00000332065.5_Silent_p.T67T|EXOC7_ENST00000589210.1_Silent_p.T67T|EXOC7_ENST00000405575.4_Silent_p.T67T|EXOC7_ENST00000411744.2_Silent_p.T67T|EXOC7_ENST00000607838.1_Silent_p.T67T|EXOC7_ENST00000406660.3_Silent_p.T67T Q9UPT5 EXOC7_HUMAN exocyst complex component 7 14 LUSC - Lung squamous cell carcinoma(166;0.187) GCAGATTCTCCGTCTGCTTGT 0.522000 0 SO:0001819 synonymous_variant ENST00000335146.7 1 1 hg19 CCDS45782.1 TCGA-2L-AAQA-01A-21D-A38G-08 EXOC7-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000319768.2 1 0 1 106 124 0 120 1 1 19 21 0 120 2 0 0 0 0 0 2 1 1.000000 103 123 0 118 2 0 0 0 0 120 2 -19.975330 1 1 121412 1 27 1 0 1 1 1.486540 1 0.600000 1.890000 0.431010 0.970000 8.700000e-01 1.000000 1.000000 0.969823 0.970000 1 9.300000e-01 1 TP53 7157 broad.mit.edu 37 17 7578406 7578406 + Missense_Mutation SNP C C T rs28934578 TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr17:7578406C>T ENST00000269305.4 - 5 713 c.524G>A c.(523-525)cGc>cAc p.R175H TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GTGGGGGCAGCGCCTCACAAC 0.652000 R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY) 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 980 Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3) GRCh37 CM062017|CM951224 TP53 M rs28934578 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 31 5.079737 0.94050 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 D;D;D;D;D;D;D;D 0.99889 -7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55 5.41 5.41 0.78517 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.101149 0.64402 D 0.000008 D 0.99908 0.9956 M 0.92784 3.345 0.80722 A 1 D;P;D;D;P;B;D 0.89917 0.999;0.578;1.0;0.998;0.632;0.213;0.999 D;B;D;D;B;B;D 0.91635 0.985;0.26;0.999;0.921;0.378;0.144;0.939 D 0.96278 0.9204 9 0.87932 D 0 -11.8679 17.0767 0.86588 0.0:1.0:0.0:0.0 rs28934578 136;175;175;82;175;175;175 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. H 175;175;175;175;175;175;164;82;43;82;43 ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H ENSP00000269305:R175H R - 2 0 TP53 7519131 1.000000 0.71417 0.989000 0.46669 0.795000 0.44927 6.042000 0.70996 2.702000 0.92279 0.655000 0.94253 CGC TCGA-2L-AAQA-01A-21D-A38G-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 134 159 0 152 1 1 47 15 0 152 2 1 1 330 366 0 514 2 1 1.000000 134 157 0 152 2 0 0 0 0 152 2 -20.000000 1 1 121412 1 41 1 0 1 1 1.491143 1 0.600000 1.890000 0.428571 0.970000 8.800000e-01 1.000000 0.990000 0.967531 0.970000 1 9.300000e-01 1 RAB40B 10966 broad.mit.edu 37 17 80616499 80616499 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr17:80616499C>T ENST00000571995.1 - 5 564 c.433G>A c.(433-435)Gcc>Acc p.A145T RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000269347.6_5'UTR|RAB40B_ENST00000538809.2_Intron NM_006822.2 NP_006813.1 Q12829 RB40B_HUMAN RAB40B, member RAS oncogene family 10 Breast(20;0.00132)|all_neural(118;0.0952) all_cancers(8;0.072)|all_epithelial(8;0.139) BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061) AGGCGCTCGGCGTAGGCCTGG 0.652000 0 SO:0001583 missense ENST00000571995.1 1 1 hg19 CCDS11816.1 . . . . . . . . . . C 34 5.306869 0.95629 . . ENSG00000141542 ENST00000269347;ENST00000538809 . . . 3.84 3.84 0.44239 Small GTP-binding protein domain (1); 0.000000 0.64402 D 0.000008 D 0.84804 0.5553 M 0.93678 3.445 0.80722 D 1 D 0.71674 0.998 D 0.63597 0.916 D 0.89908 0.4049 9 0.87932 D 0 . 16.2189 0.82244 0.0:1.0:0.0:0.0 . 145 Q12829 RB40B_HUMAN T 145;179 . ENSP00000269347:A145T A - 1 0 RAB40B 78209788 1.000000 0.71417 0.792000 0.32020 0.907000 0.53573 5.860000 0.69546 2.082000 0.62665 0.591000 0.81541 GCC TCGA-2L-AAQA-01A-21D-A38G-08 RAB40B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439007.1 1 0 1 78 154 0 100 1 9.985576e-01 16 7 0 100 2 0 0 0 0 0 2 1 1.000000 78 150 0 100 2 0 0 0 0 100 2 -20.000000 1 1 121400 1 29 1 0 1 1 1.486540 1 0.600000 1.890000 0.431010 0.770000 6.400000e-01 0.920000 0.780000 0.786322 0.770000 0 7.000000e-01 8.600000e-01 CDH2 1000 broad.mit.edu 37 18 25570188 25570188 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr18:25570188C>T ENST00000269141.3 - 10 1894 c.1471G>A c.(1471-1473)Gta>Ata p.V491I CDH2_ENST00000399380.3_Missense_Mutation_p.V460I NM_001792.3 NP_001783.2 P19022 CADH2_HUMAN cadherin 2, type 1, N-cadherin (neuronal) p.V491I(1) 82 TTTTCATTTACGTCAATAACT 0.468000 1 Substitution - Missense(1) SO:0001583 missense ENST00000269141.3 1 1 hg19 CCDS11891.1 . . . . . . . . . . C 19.67 3.871347 0.72065 0.0 1.16E-4 ENSG00000170558 ENST00000269141;ENST00000399380 T;T 0.62232 0.04;0.04 6.16 6.16 0.99307 Cadherin (3);Cadherin-like (1); 0.056760 0.64402 D 0.000001 T 0.61476 0.2350 L 0.49699 1.58 0.80722 D 1 B;B 0.17268 0.021;0.007 B;B 0.08055 0.003;0.001 T 0.53961 -0.8364 10 0.49607 T 0.09 . 20.8598 0.99761 0.0:1.0:0.0:0.0 . 460;491 A8MWK3;P19022 .;CADH2_HUMAN I 491;460 ENSP00000269141:V491I;ENSP00000382312:V460I ENSP00000269141:V491I V - 1 0 CDH2 23824186 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 7.487000 0.81328 2.937000 0.99478 0.650000 0.86243 GTA TCGA-2L-AAQA-01A-21D-A38G-08 CDH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000133246.3 1 0 1 154 181 0 158 0 9.413594e-01 0 8 0 158 2 0 0 0 0 0 2 1 1.000000 150 176 0 158 2 0 0 0 0 158 2 -20.000000 1 1 121412 3 40 1 0 1 1 1.506894 1 0.600000 1.890000 0.431010 0.980000 9.000000e-01 1.000000 1.000000 0.978490 0.980000 1 9.400000e-01 1 ALPK2 115701 broad.mit.edu 37 18 56246544 56246544 + Missense_Mutation SNP A A T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr18:56246544A>T ENST00000361673.3 - 4 1677 c.1464T>A c.(1462-1464)gaT>gaA p.D488E ALPK2_ENST00000587399.1_5'Flank NM_052947.3 NP_443179.3 Q86TB3 ALPK2_HUMAN alpha-kinase 2 84 TTACTGATTCATCCATGTTGA 0.493000 OREG0025011 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000361673.3 1 1 hg19 CCDS11966.2 . . . . . . . . . . A 10.08 1.251969 0.22880 . . ENSG00000198796 ENST00000361673 T 0.54479 0.57 5.34 -0.259 0.12971 . 0.515524 0.15105 N 0.280317 T 0.31231 0.0790 L 0.33485 1.01 0.09310 N 1 B 0.32829 0.386 B 0.24269 0.052 T 0.09122 -1.0689 10 0.35671 T 0.21 -8.4846 4.6008 0.12352 0.3972:0.4204:0.0685:0.1138 . 488 Q86TB3 ALPK2_HUMAN E 488 ENSP00000354991:D488E ENSP00000354991:D488E D - 3 2 ALPK2 54397524 0.027000 0.19231 0.028000 0.17463 0.004000 0.04260 0.054000 0.14205 -0.291000 0.09012 -0.313000 0.08912 GAT TCGA-2L-AAQA-01A-21D-A38G-08 ALPK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256126.1 1 0 1 169 223 0 228 0 0 0 0 228 2 0 0 0 0 0 2 1 1.000000 169 222 0 228 2 0 0 0 0 228 2 -20.000000 1 1 0 0 1 0 1 1 1.506894 1 0.600000 1.890000 0.431010 0.960000 8.700000e-01 1.000000 1.000000 0.964200 0.960000 1 9.200000e-01 1 RASAL3 64926 broad.mit.edu 37 19 15567402 15567402 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr19:15567402G>A ENST00000343625.7 - 10 1572 c.1487C>T c.(1486-1488)gCg>gTg p.A496V RASAL3_ENST00000608577.1_5'Flank NM_022904.1 NP_075055.1 Q86YV0 RASL3_HUMAN RAS protein activator like 3 18 GAACAGCAGCGCCTCACGGCC 0.617000 0 SO:0001583 missense ENST00000343625.7 1 1 hg19 CCDS46006.1 . . . . . . . . . . g 19.47 3.834497 0.71373 . . ENSG00000105122 ENST00000343625 T 0.79554 -1.28 4.37 4.37 0.52481 Rho GTPase activation protein (1);Ras GTPase-activating protein (4); 0.212338 0.22735 U 0.056263 T 0.82098 0.4963 L 0.49350 1.555 0.38814 D 0.955492 D 0.56968 0.978 P 0.54312 0.748 T 0.80476 -0.1366 10 0.23302 T 0.38 . 14.8191 0.70059 0.0:0.0:1.0:0.0 . 496 Q86YV0 RASL3_HUMAN V 496 ENSP00000341905:A496V ENSP00000341905:A496V A - 2 0 RASAL3 15428402 0.007000 0.16637 1.000000 0.80357 0.994000 0.84299 1.074000 0.30703 2.158000 0.67659 0.558000 0.71614 GCG TCGA-2L-AAQA-01A-21D-A38G-08 RASAL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461331.3 1 0 1 42 106 0 39 0 3.256585e-01 0 4 0 39 2 0 0 0 0 0 2 1 1.000000 43 106 0 38 2 0 0 0 0 39 2 -20.000000 1 1 0 0 1 0 0 0 2.067134 0 0.600000 1.890000 0.600000 0.940000 7.100000e-01 1.000000 1.000000 0.922540 0.940000 1 8.200000e-01 1 PDCD2L 84306 broad.mit.edu 37 19 34912428 34912428 + Missense_Mutation SNP T T C TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr19:34912428T>C ENST00000246535.3 + 6 849 c.802T>C c.(802-804)Tcc>Ccc p.S268P PDCD2L_ENST00000587065.2_5'UTR|RN7SL154P_ENST00000578043.1_RNA NM_032346.1 NP_115722.1 Q9BRP1 PDD2L_HUMAN programmed cell death 2-like 11 Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.211) TCCTAGGTATTCCTGGAGTGG 0.493000 0 SO:0001583 missense ENST00000246535.3 1 1 hg19 CCDS12438.1 . . . . . . . . . . T 17.84 3.486734 0.63962 . . ENSG00000126249 ENST00000246535 . . . 5.98 4.94 0.65067 Programmed cell death protein 2, C-terminal (1); 0.144113 0.64402 D 0.000004 T 0.81451 0.4825 M 0.91196 3.185 0.41755 D 0.989686 D 0.76494 0.999 D 0.73708 0.981 D 0.83431 0.0038 9 0.48119 T 0.1 -15.8635 11.5108 0.50492 0.1347:0.0:0.0:0.8653 . 268 Q9BRP1 PDD2L_HUMAN P 268 . ENSP00000246535:S268P S + 1 0 PDCD2L 39604268 1.000000 0.71417 0.999000 0.59377 0.749000 0.42624 3.088000 0.50175 1.048000 0.40298 0.477000 0.44152 TCC TCGA-2L-AAQA-01A-21D-A38G-08 PDCD2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459251.3 1 0 1 345 803 0 451 1 9.999897e-01 15 26 0 451 2 0 0 0 0 0 2 1 1.000000 341 785 0 448 2 0 0 0 0 451 2 -20.000000 1 1 0 0 1 0 0 0 2.067134 0 0.600000 1.890000 0.600000 0.990000 9.000000e-01 1.000000 1.000000 0.982919 0.990000 1 9.500000e-01 1 SBK2 646643 broad.mit.edu 37 19 56042597 56042597 + Silent SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr19:56042597G>A ENST00000413299.1 - 3 406 c.369C>T c.(367-369)taC>taT p.Y123Y SBK2_ENST00000344158.3_Silent_p.Y123Y NM_001101401.2 NP_001094871.2 P0C263 SBK2_HUMAN SH3 domain binding kinase family, member 2 9 TGCCAATGCCGTAGGCCGTCA 0.642000 0 SO:0001819 synonymous_variant ENST00000413299.1 1 1 hg19 CCDS42631.1 TCGA-2L-AAQA-01A-21D-A38G-08 SBK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341919.1 1 0 1 57 139 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1.000000 56 137 0 65 2 0 0 0 0 65 2 -6.138701 1 1 0 0 1 1 2 3 2.123521 0 0.600000 1.890000 0.605911 0.980000 7.700000e-01 1.000000 1.000000 0.951894 0.980000 1 8.700000e-01 1 ZNF787 126208 broad.mit.edu 37 19 56600294 56600294 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr19:56600294G>A ENST00000270459.3 - 3 365 c.247C>T c.(247-249)Cgg>Tgg p.R83W NM_001002836.2 NP_001002836 Q6DD87 ZN787_HUMAN zinc finger protein 787 5 Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157) CGCTGGTGCCGCGTCAGCTTG 0.721000 0 SO:0001583 missense ENST00000270459.3 1 1 hg19 CCDS42634.1 . . . . . . . . . . G 17.51 3.406781 0.62399 . . ENSG00000142409 ENST00000270459 T 0.56275 0.47 3.22 3.22 0.36961 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.73860 0.3641 M 0.88377 2.95 0.80722 D 1 D 0.89917 1.0 D 0.72075 0.976 T 0.78902 -0.2021 9 0.59425 D 0.04 -20.4997 12.27 0.54700 0.0:0.0:1.0:0.0 . 83 Q6DD87 ZN787_HUMAN W 83 ENSP00000270459:R83W ENSP00000270459:R83W R - 1 2 ZNF787 61292106 0.000000 0.05858 0.980000 0.43619 0.978000 0.69477 -0.893000 0.04127 1.812000 0.52913 0.462000 0.41574 CGG TCGA-2L-AAQA-01A-21D-A38G-08 ZNF787-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457498.1 1 0 0 43 133 0 51 1 9.999788e-01 30 25 0 51 2 0 0 0 0 0 2 1 1.000000 43 132 0 50 2 0 0 0 0 51 2 -20.000000 1 1 0 0 1 1 2 3 2.123521 0 0.600000 1.890000 0.605911 0.830000 6.200000e-01 1.000000 1.000000 0.836174 0.830000 0 7.200000e-01 9.600000e-01 MYO1F 4542 broad.mit.edu 37 19 8595429 8595429 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr19:8595429C>T ENST00000338257.8 - 20 2339 c.2072G>A c.(2071-2073)cGa>cAa p.R691Q NM_012335.3 NP_036467.2 O00160 MYO1F_HUMAN myosin IF 42 ATCGAACTTTCGCTCTCGCAC 0.647000 0 SO:0001583 missense ENST00000338257.8 1 1 hg19 CCDS42494.1 . . . . . . . . . . C 36 5.683094 0.96774 . . ENSG00000142347 ENST00000305795;ENST00000338257 D 0.95205 -3.64 5.36 5.36 0.76844 Myosin head, motor domain (1); 0.000000 0.85682 D 0.000000 D 0.96259 0.8780 M 0.81942 2.565 0.80722 D 1 D 0.63880 0.993 P 0.54174 0.744 D 0.95729 0.8773 10 0.41790 T 0.15 . 18.1619 0.89710 0.0:1.0:0.0:0.0 . 691 O00160 MYO1F_HUMAN Q 736;691 ENSP00000344871:R691Q ENSP00000304899:R736Q R - 2 0 MYO1F 8501429 1.000000 0.71417 0.952000 0.39060 0.951000 0.60555 7.748000 0.85085 2.532000 0.85374 0.555000 0.69702 CGA TCGA-2L-AAQA-01A-21D-A38G-08 MYO1F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342716.2 0 0 0 20 669 0 219 0 7.598679e-02 0 15 0 219 2 0 0 0 0 0 2 1 0.999994 20 654 0 218 2 0 0 0 0 219 2 -3.016125 1 1 0 0 1 0 0 0 2.067134 0 0.600000 1.890000 0.600000 0.090000 5.000000e-02 0.150000 0.100000 0.101187 0.090000 0 7.000000e-02 1.200000e-01 AGL 178 broad.mit.edu 37 1 100336383 100336383 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr1:100336383G>A ENST00000294724.4 + 7 1394 c.916G>A c.(916-918)Gtc>Atc p.V306I AGL_ENST00000370161.2_Missense_Mutation_p.V290I|AGL_ENST00000361522.4_Missense_Mutation_p.V289I|AGL_ENST00000361302.3_Missense_Mutation_p.V290I|AGL_ENST00000370165.3_Missense_Mutation_p.V306I|AGL_ENST00000361915.3_Missense_Mutation_p.V306I|AGL_ENST00000370163.3_Missense_Mutation_p.V306I NM_000028.2 NP_000019.2 P35573 GDE_HUMAN amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase 69 all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131) CCAAGTAGATGTCAACAAAGC 0.303000 0 SO:0001583 missense ENST00000294724.4 1 1 hg19 CCDS759.1 . . . . . . . . . . g 5.406 0.260007 0.10239 . . ENSG00000162688 ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522 D;D;D;D;D;D;D 0.85171 -1.95;-1.95;-1.95;-1.95;-1.95;-1.95;-1.95 5.34 1.41 0.22369 Glycoside hydrolase, superfamily (1); 0.273612 0.36101 N 0.002797 T 0.60843 0.2300 L 0.39898 1.24 0.09310 N 0.999996 B;B;B 0.06786 0.001;0.001;0.0 B;B;B 0.14578 0.011;0.011;0.007 T 0.53760 -0.8393 10 0.30078 T 0.28 . 9.6993 0.40175 0.2549:0.0:0.7451:0.0 . 289;290;306 P35573-2;P35573-3;P35573 .;.;GDE_HUMAN I 306;306;306;306;290;290;289 ENSP00000355106:V306I;ENSP00000359184:V306I;ENSP00000359182:V306I;ENSP00000294724:V306I;ENSP00000354971:V290I;ENSP00000359180:V290I;ENSP00000354635:V289I ENSP00000294724:V306I V + 1 0 AGL 100108971 0.990000 0.36364 0.001000 0.08648 0.123000 0.20343 2.092000 0.41700 0.073000 0.16731 -0.796000 0.03273 GTC TCGA-2L-AAQA-01A-21D-A38G-08 AGL-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029778.1 1 0 1 70 137 0 120 0 1.164730e-01 1 1 0 120 2 0 0 0 0 0 2 1 1.000000 70 136 0 119 2 0 0 0 0 120 2 -20.000000 1 1 121298 1 28 1 0 1 1 1.507771 1 0.600000 1.890000 0.431010 0.780000 6.400000e-01 0.930000 0.790000 0.790369 0.780000 0 7.000000e-01 8.600000e-01 AP4B1 10717 broad.mit.edu 37 1 114445373 114445373 + Silent SNP A A G TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr1:114445373A>G ENST00000369569.1 - 2 505 c.225T>C c.(223-225)taT>taC p.Y75Y AP4B1_ENST00000369567.1_Intron|AP4B1_ENST00000369566.3_Silent_p.Y75Y|AP4B1_ENST00000256658.4_Silent_p.Y75Y|AP4B1-AS1_ENST00000419536.1_RNA|DCLRE1B_ENST00000369563.3_5'Flank NM_001253852.1 NP_001240781.1 Q9Y6B7 AP4B1_HUMAN adaptor-related protein complex 4, beta 1 subunit 25 Lung SC(450;0.184) all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05) TCAGGGGAGCATATGTGCACA 0.498000 0 SO:0001819 synonymous_variant ENST00000369569.1 1 1 hg19 CCDS865.1 TCGA-2L-AAQA-01A-21D-A38G-08 AP4B1-009 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033037.1 1 0 0 135 158 0 149 1 9.999999e-01 33 1 0 149 2 0 0 0 0 0 2 1 1.000000 135 157 0 147 2 0 0 0 0 149 2 -20.000000 1 1 0 0 1 0 1 1 1.474776 1 0.600000 1.890000 0.440559 0.990000 9.200000e-01 1.000000 1.000000 0.990683 0.990000 1 9.700000e-01 1 ASTN1 460 broad.mit.edu 37 1 176833536 176833536 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr1:176833536C>T ENST00000367654.3 - 23 4004 c.3793G>A c.(3793-3795)Gag>Aag p.E1265K ASTN1_ENST00000367657.3_Intron|ASTN1_ENST00000361833.2_Missense_Mutation_p.E1257K NM_004319.1 NP_004310.1 O14525 ASTN1_HUMAN astrotactin 1 153 GGTTTGATCTCGCTGTAGCGG 0.587000 0 SO:0001583 missense ENST00000367654.3 1 1 hg19 . . . . . . . . . . C 25.1 4.600256 0.87055 . . ENSG00000152092 ENST00000361833;ENST00000367654 T;T 0.14022 2.55;2.54 4.61 4.61 0.57282 . 0.047461 0.85682 D 0.000000 T 0.09774 0.0240 L 0.27053 0.805 0.80722 D 1 P 0.50710 0.938 B 0.33454 0.164 T 0.12218 -1.0556 10 0.87932 D 0 -23.1216 17.4153 0.87498 0.0:1.0:0.0:0.0 . 1257 O14525-2 . K 1257;1265 ENSP00000354536:E1257K;ENSP00000356626:E1265K ENSP00000354536:E1257K E - 1 0 ASTN1 175100159 1.000000 0.71417 0.998000 0.56505 0.974000 0.67602 7.018000 0.76406 2.282000 0.76494 0.555000 0.69702 GAG TCGA-2L-AAQA-01A-21D-A38G-08 ASTN1-201 KNOWN basic protein_coding protein_coding 1 0 1 93 595 0 168 0 0 0 0 168 2 0 0 0 0 0 2 1 1.000000 92 586 0 164 2 0 0 0 0 168 2 -3.221886 1 1 121412 1 31 1 1 2 3 2.711459 1 0.600000 1.890000 0.692308 0.580000 4.700000e-01 0.700000 0.580000 0.589959 0.580000 0 5.200000e-01 6.500000e-01 COL24A1 255631 broad.mit.edu 37 1 86590761 86590761 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr1:86590761C>T ENST00000370571.2 - 3 1624 c.1258G>A c.(1258-1260)Gaa>Aaa p.E420K COL24A1_ENST00000436319.1_Missense_Mutation_p.E420K NM_152890.5 NP_690850.2 Q17RW2 COOA1_HUMAN collagen, type XXIV, alpha 1 p.E420*(1) 101 TCCATGAGTTCGTTAGTGTGT 0.358000 1 Substitution - Nonsense(1) SO:0001583 missense ENST00000370571.2 1 1 hg19 CCDS41353.1 . . . . . . . . . . C 9.195 1.026954 0.19512 . . ENSG00000171502 ENST00000370571;ENST00000436319 T;T 0.11821 2.74;2.74 5.45 3.24 0.37175 . 0.000000 0.40640 N 0.001059 T 0.02418 0.0074 N 0.19112 0.55 0.35766 D 0.820548 B;B 0.27791 0.189;0.046 B;B 0.25506 0.061;0.005 T 0.29119 -1.0022 10 0.07990 T 0.79 . 10.6098 0.45415 0.0:0.8214:0.0:0.1786 . 420;420 F8WDM8;Q17RW2 .;COOA1_HUMAN K 420 ENSP00000359603:E420K;ENSP00000392531:E420K ENSP00000359603:E420K E - 1 0 COL24A1 86363349 1.000000 0.71417 1.000000 0.80357 0.263000 0.26337 2.119000 0.41958 1.307000 0.44944 0.563000 0.77884 GAA TCGA-2L-AAQA-01A-21D-A38G-08 COL24A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029335.4 1 0 1 127 186 0 130 0 0 0 0 130 2 0 0 0 0 0 2 1 1.000000 126 182 0 130 2 0 0 0 0 130 2 -20.000000 1 1 120786 1 32 1 0 1 1 1.507771 1 0.600000 1.890000 0.431010 0.920000 8.100000e-01 1.000000 1.000000 0.929221 0.920000 1 8.700000e-01 9.800000e-01 TSHZ2 128553 broad.mit.edu 37 20 51871827 51871827 + Silent SNP G G A rs147016688 byFrequency TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr20:51871827G>A ENST00000371497.5 + 2 2717 c.1830G>A c.(1828-1830)gcG>gcA p.A610A TSHZ2_ENST00000603338.2_Silent_p.A607A|TSHZ2_ENST00000329613.6_Silent_p.A607A|RP4-678D15.1_ENST00000606932.1_RNA NM_001193421.1|NM_173485.5 NP_001180350.1|NP_775756.3 Q9NRE2 TSH2_HUMAN teashirt zinc finger homeobox 2 p.A610A(1) 84 STAD - Stomach adenocarcinoma(23;0.1) AAGATGAAGCGGTGAAGGAGT 0.502000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000371497.5 1 1 hg19 CCDS33490.1 TCGA-2L-AAQA-01A-21D-A38G-08 TSHZ2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080398.6 1 0 1 130 397 0 164 0 3.622207e-01 0 5 0 164 2 0 0 0 0 0 2 1 1.000000 130 395 0 160 2 0 0 0 0 164 2 -5.034111 1 1 121412 9 46 1 0 0 0 2.045390 0 0.600000 1.890000 0.597586 0.810000 6.900000e-01 0.940000 0.810000 0.819403 0.810000 0 7.500000e-01 8.800000e-01 DSCAM 1826 broad.mit.edu 37 21 41385178 41385178 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr21:41385178G>A ENST00000400454.1 - 33 6299 c.5822C>T c.(5821-5823)aCg>aTg p.T1941M NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) CTCCAGGACCGTGGGGCGCTT 0.627000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001583 missense ENST00000400454.1 1 1 hg19 CCDS42929.1 . . . . . . . . . . . 19.61 3.860756 0.71834 . . ENSG00000171587 ENST00000400454;ENST00000404019 T;T 0.59638 0.25;0.36 5.29 5.29 0.74685 . 0.345440 0.33180 N 0.005197 T 0.38585 0.1046 N 0.08118 0 0.43073 D 0.994714 P 0.48640 0.913 B 0.36666 0.23 T 0.52931 -0.8509 10 0.72032 D 0.01 . 18.9499 0.92637 0.0:0.0:1.0:0.0 . 1941 O60469 DSCAM_HUMAN M 1941;1675 ENSP00000383303:T1941M;ENSP00000385342:T1675M ENSP00000383303:T1941M T - 2 0 DSCAM 40307048 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 9.219000 0.95173 2.464000 0.83262 0.557000 0.71058 ACG TCGA-2L-AAQA-01A-21D-A38G-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 0 0 1 87 212 1 99 0 0 0 1 99 2 0 0 0 0 0 2 1 1.000000 87 208 1 97 12 0 0 0 1 99 2 -20.000000 1 1 120890 2 32 1 1 2 3 2.084981 0 0.600000 1.890000 0.601196 0.960000 8.000000e-01 1.000000 1.000000 0.951129 0.960000 1 8.800000e-01 1 TRIOBP 11078 broad.mit.edu 37 22 38153721 38153721 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr22:38153721G>A ENST00000406386.3 + 16 6044 c.5789G>A c.(5788-5790)cGg>cAg p.R1930Q TRIOBP_ENST00000403663.2_Missense_Mutation_p.R217Q|TRIOBP_ENST00000407319.2_Missense_Mutation_p.R217Q NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 12 Melanoma(58;0.0574) GTCATCAGCCGGGGTGGCCCT 0.701000 0 SO:0001583 missense ENST00000406386.3 0 1 hg19 CCDS43015.1 . . . . . . . . . . G 24.7 4.561208 0.86335 . . ENSG00000100106 ENST00000406386;ENST00000407319;ENST00000403663;ENST00000418339;ENST00000417857 T 0.26957 1.7 5.5 5.5 0.81552 . . . . . T 0.43055 0.1230 M 0.76574 2.34 0.31902 N 0.615782 D;D;D 0.71674 0.993;0.994;0.998 P;P;P 0.53760 0.713;0.734;0.608 T 0.56505 -0.7968 9 0.66056 D 0.02 . 13.1341 0.59399 0.0828:0.0:0.9172:0.0 . 217;217;1930 F8W6V6;F2Z2W0;Q9H2D6 .;.;TARA_HUMAN Q 1930;217;217;176;146 ENSP00000384312:R1930Q ENSP00000386026:R217Q R + 2 0 TRIOBP 36483667 0.999000 0.42202 0.997000 0.53966 0.785000 0.44390 3.643000 0.54374 2.580000 0.87095 0.555000 0.69702 CGG TCGA-2L-AAQA-01A-21D-A38G-08 TRIOBP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000319439.2 1 0 1 11 14 0 11 1 1 131 133 0 11 2 0 0 0 0 0 2 1 0.999115 11 12 0 11 2 0 0 0 0 11 2 -20.000000 1 1 119488 4 28 1 1 2 3 2.121955 0 0.600000 1.890000 0.605911 0.990000 8.700000e-01 1.000000 1.000000 0.992558 0.990000 1 9.900000e-01 1 TRIOBP 11078 broad.mit.edu 37 22 38165362 38165362 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr22:38165362C>T ENST00000406386.3 + 21 7084 c.6829C>T c.(6829-6831)Cgg>Tgg p.R2277W TRIOBP_ENST00000403663.2_Missense_Mutation_p.R564W NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 12 Melanoma(58;0.0574) CAGCAACGAGCGGAGTTCCTG 0.667000 0 SO:0001583 missense ENST00000406386.3 1 1 hg19 CCDS43015.1 . . . . . . . . . . C 16.69 3.193152 0.58017 . . ENSG00000100106 ENST00000406386;ENST00000403663 T 0.23950 1.88 4.96 0.994 0.19832 . . . . . T 0.44265 0.1285 L 0.53249 1.67 0.44711 D 0.997706 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.79784 0.993;0.971;0.989;0.976 T 0.48305 -0.9047 9 0.87932 D 0 . 14.7584 0.69588 0.5226:0.4774:0.0:0.0 . 2179;266;564;2277 Q9H2D6-2;Q8TCM3;F8W6V6;Q9H2D6 .;.;.;TARA_HUMAN W 2277;564 ENSP00000384312:R2277W ENSP00000386026:R564W R + 1 2 TRIOBP 36495308 1.000000 0.71417 0.989000 0.46669 0.459000 0.32528 0.925000 0.28791 0.428000 0.26173 0.462000 0.41574 CGG TCGA-2L-AAQA-01A-21D-A38G-08 TRIOBP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000319439.2 1 0 1 10 53 0 19 1 1 181 229 0 19 2 0 0 0 0 0 2 1 0.997463 9 53 0 18 2 0 0 0 0 19 2 -18.667730 1 1 120778 3 35 1 1 2 3 2.121955 0 0.600000 1.890000 0.605911 0.550000 2.900000e-01 1.000000 0.530000 0.582761 0.550000 0 4.100000e-01 7.500000e-01 UXS1 80146 broad.mit.edu 37 2 106710580 106710580 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr2:106710580G>A ENST00000409501.3 - 15 1222 c.1165C>T c.(1165-1167)Cac>Tac p.H389Y UXS1_ENST00000409032.1_Missense_Mutation_p.H221Y|UXS1_ENST00000283148.7_Missense_Mutation_p.H394Y|UXS1_ENST00000540130.1_Missense_Mutation_p.H332Y Q8NBZ7 UXS1_HUMAN UDP-glucuronate decarboxylase 1 17 CGGAAGTAGTGAATTGCTTTG 0.473000 0 SO:0001583 missense ENST00000409501.3 1 1 hg19 CCDS46378.1 . . . . . . . . . . G 17.04 3.287260 0.59867 . . ENSG00000115652 ENST00000283148;ENST00000540130;ENST00000409501;ENST00000409032 T;T;T;T 0.60548 0.18;0.18;0.18;0.18 5.68 5.68 0.88126 . 0.046027 0.85682 D 0.000000 T 0.54647 0.1871 L 0.43923 1.385 0.80722 D 1 B;B;B 0.19817 0.039;0.023;0.023 B;B;B 0.14578 0.011;0.005;0.008 T 0.51748 -0.8666 10 0.72032 D 0.01 -10.5314 19.7704 0.96361 0.0:0.0:1.0:0.0 . 394;389;394 Q8NBZ7-2;Q8NBZ7;A8K3Q3 .;UXS1_HUMAN;. Y 394;332;389;221 ENSP00000283148:H394Y;ENSP00000438265:H332Y;ENSP00000387019:H389Y;ENSP00000387096:H221Y ENSP00000283148:H394Y H - 1 0 UXS1 106077012 1.000000 0.71417 0.981000 0.43875 0.998000 0.95712 9.266000 0.95659 2.670000 0.90874 0.563000 0.77884 CAC TCGA-2L-AAQA-01A-21D-A38G-08 UXS1-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000329778.1 1 0 1 80 217 0 108 1 1 33 80 0 108 2 0 0 0 0 0 2 1 1.000000 80 214 0 108 2 0 0 0 0 108 2 -20.000000 1 1 0 0 1 0 0 0 2.070463 0 0.600000 1.890000 0.600000 0.890000 7.300000e-01 1.000000 1.000000 0.895344 0.890000 1 8.100000e-01 9.800000e-01 INHBB 3625 broad.mit.edu 37 2 121106698 121106698 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr2:121106698C>T ENST00000295228.3 + 2 518 c.472C>T c.(472-474)Cgc>Tgc p.R158C NM_002193.2 NP_002184.2 P09529 INHBB_HUMAN inhibin, beta B 15 Prostate(154;0.122) CTCCCGGGTCCGCCTATACTT 0.557000 0 SO:0001583 missense ENST00000295228.3 1 1 hg19 CCDS2132.1 . . . . . . . . . . C 16.25 3.070536 0.55539 . . ENSG00000163083 ENST00000295228 T 0.66995 -0.24 5.09 5.09 0.68999 Transforming growth factor-beta, N-terminal (1); 0.216528 0.39210 N 0.001426 T 0.61751 0.2372 L 0.54323 1.7 0.47698 D 0.999492 B 0.17667 0.023 B 0.12837 0.008 T 0.60667 -0.7218 10 0.59425 D 0.04 -3.9508 12.8184 0.57679 0.1636:0.8364:0.0:0.0 . 158 P09529 INHBB_HUMAN C 158 ENSP00000295228:R158C ENSP00000295228:R158C R + 1 0 INHBB 120823168 1.000000 0.71417 1.000000 0.80357 0.871000 0.50021 1.726000 0.38085 2.804000 0.96469 0.655000 0.94253 CGC TCGA-2L-AAQA-01A-21D-A38G-08 INHBB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254234.1 1 0 1 109 283 0 155 0 8.852491e-01 0 12 0 155 2 0 0 0 0 0 2 1 1.000000 109 281 0 153 2 0 0 0 0 155 2 -7.065246 1 1 121410 1 32 1 0 0 0 2.070463 0 0.600000 1.890000 0.600000 0.920000 7.700000e-01 1.000000 1.000000 0.921713 0.920000 1 8.400000e-01 1 TRIB2 28951 broad.mit.edu 37 2 12858610 12858610 + Silent SNP T T G TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr2:12858610T>G ENST00000405331.3 + 1 247 c.177T>G c.(175-177)tcT>tcG p.S59S TRIB2_ENST00000155926.4_Silent_p.S59S|TRIB2_ENST00000381465.2_Intron|RP11-333O1.1_ENST00000569860.1_lincRNA tribbles pseudokinase 2 19 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) ATTGCGTTTCTTGTATCGGGA 0.567000 OREG0014450 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000405331.3 1 1 hg19 TCGA-2L-AAQA-01A-21D-A38G-08 TRIB2-004 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000323585.1 1 0 1 146 370 0 151 1 1 26 51 0 151 2 0 0 0 0 0 2 1 1.000000 143 366 0 150 2 0 0 0 0 151 2 -20.000000 1 1 0 0 1 0 0 0 2.066531 0 0.600000 1.890000 0.600000 0.930000 8.100000e-01 1.000000 1.000000 0.937002 0.930000 1 8.700000e-01 1 ITGA6 3655 broad.mit.edu 37 2 173333979 173333979 + Missense_Mutation SNP T T A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr2:173333979T>A ENST00000264106.6 + 4 717 c.514T>A c.(514-516)Tgg>Agg p.W172R ITGA6_ENST00000409532.1_Missense_Mutation_p.W58R|ITGA6_ENST00000264107.7_Missense_Mutation_p.W172R|ITGA6_ENST00000409080.1_Missense_Mutation_p.W172R|ITGA6_ENST00000375221.2_Missense_Mutation_p.W172R|ITGA6_ENST00000343713.4_Missense_Mutation_p.W172R P23229 ITA6_HUMAN integrin, alpha 6 44 OV - Ovarian serous cystadenocarcinoma(117;0.0979) TGGGGGAGATTGGAGCTTTTG 0.448000 0 SO:0001583 missense ENST00000264106.6 1 1 hg19 . . . . . . . . . . T 18.32 3.597715 0.66332 . . ENSG00000091409 ENST00000412899;ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358 T;T;T;T;T;T;T;T;T 0.54675 0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56 6.17 6.17 0.99709 . 0.000000 0.85682 D 0.000000 T 0.68943 0.3056 M 0.77406 2.37 0.80722 D 1 B;B;P 0.43578 0.313;0.448;0.811 B;P;P 0.54346 0.279;0.55;0.749 T 0.66748 -0.5845 10 0.33141 T 0.24 . 16.8222 0.85835 0.0:0.0:0.0:1.0 . 172;172;172 P23229-4;G5E9H1;P23229-2 .;.;. R 58;58;172;172;172;172;172;172;172 ENSP00000413470:W58R;ENSP00000386614:W58R;ENSP00000264107:W172R;ENSP00000264106:W172R;ENSP00000364369:W172R;ENSP00000341078:W172R;ENSP00000386896:W172R;ENSP00000406694:W172R;ENSP00000394169:W172R ENSP00000264106:W172R W + 1 0 ITGA6 173042225 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 8.040000 0.89188 2.371000 0.80710 0.533000 0.62120 TGG TCGA-2L-AAQA-01A-21D-A38G-08 ITGA6-201 KNOWN basic protein_coding protein_coding 1 0 1 225 514 0 249 1 1 43 103 0 249 2 0 0 0 0 0 2 1 1.000000 223 501 0 247 2 0 0 0 0 249 2 -14.468880 1 1 0 0 1 0 0 0 2.070463 0 0.600000 1.890000 0.600000 0.990000 9.000000e-01 1.000000 1.000000 0.984398 0.990000 1 9.500000e-01 1 PPM1G 5496 broad.mit.edu 37 2 27607706 27607706 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr2:27607706C>T ENST00000344034.4 - 5 923 c.659G>A c.(658-660)cGt>cAt p.R220H PPM1G_ENST00000350803.4_Missense_Mutation_p.R220H NM_177983.2 NP_817092.1 O15355 PPM1G_HUMAN protein phosphatase, Mg2+/Mn2+ dependent, 1G 19 Acute lymphoblastic leukemia(172;0.155) CTCAGTCCCACGTTCCGAGTT 0.572000 0 SO:0001583 missense ENST00000344034.4 1 1 hg19 CCDS1752.1 . . . . . . . . . . C 10.38 1.335465 0.24253 . . ENSG00000115241 ENST00000344034;ENST00000350803;ENST00000544412 T;T 0.44083 0.93;0.93 5.75 2.95 0.34219 Protein phosphatase 2C-like (3); 0.608394 0.16245 N 0.222966 T 0.27663 0.0680 L 0.36672 1.1 0.27600 N 0.948996 B 0.02656 0.0 B 0.01281 0.0 T 0.21245 -1.0251 10 0.21014 T 0.42 0.2289 5.1636 0.15073 0.0:0.5481:0.1408:0.3111 . 220 O15355 PPM1G_HUMAN H 220;220;203 ENSP00000342778:R220H;ENSP00000264714:R220H ENSP00000342778:R220H R - 2 0 PPM1G 27461210 0.997000 0.39634 0.997000 0.53966 0.986000 0.74619 1.019000 0.30014 0.348000 0.23949 0.655000 0.94253 CGT TCGA-2L-AAQA-01A-21D-A38G-08 PPM1G-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215032.1 1 0 0 16 398 0 113 1 9.996773e-01 11 322 0 113 2 0 0 0 0 0 2 1 0.999922 16 388 0 112 2 0 0 0 0 113 2 -4.127870 1 1 0 0 1 0 0 0 2.066531 0 0.600000 1.890000 0.600000 0.120000 7.000000e-02 0.200000 0.130000 0.135982 0.120000 0 9.000000e-02 1.700000e-01 FANCD2 2177 broad.mit.edu 37 3 10107621 10107621 + Silent SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr3:10107621C>T ENST00000419585.1 + 25 2504 c.2343C>T c.(2341-2343)ttC>ttT p.F781F FANCD2_ENST00000287647.3_Silent_p.F781F|FANCD2_ENST00000383806.1_Silent_p.F781F|FANCD2_ENST00000383807.1_Silent_p.F781F Q9BXW9 FACD2_HUMAN Fanconi anemia, complementation group D2 51 AGCGTTCATTCATGTGTTCTC 0.393000 D, Mis, N, F AML, leukemia Involved in tolerance or repair of DNA crosslinks Fanconi Anemia yes Rec Fanconi anaemia D2 3 3p26 2177 Fanconi anemia, complementation group D2 L 0 SO:0001819 synonymous_variant Familial Cancer Database Pancytopenia Dysmelia, FA (several complementation groups) ENST00000419585.1 1 1 hg19 CCDS33696.1 TCGA-2L-AAQA-01A-21D-A38G-08 FANCD2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000339873.1 1 0 1 62 218 0 90 1 9.137255e-01 6 11 0 90 2 0 0 0 0 0 2 1 1.000000 60 217 0 90 2 0 0 0 0 90 2 -20.000000 1 1 0 0 1 0 0 0 2.047777 0 0.600000 1.890000 0.597586 0.730000 5.700000e-01 0.890000 0.730000 0.738402 0.730000 0 6.500000e-01 8.200000e-01 GPR156 165829 broad.mit.edu 37 3 119962542 119962542 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr3:119962542C>T ENST00000464295.1 - 3 623 c.178G>A c.(178-180)Gga>Aga p.G60R GPR156_ENST00000461057.1_Missense_Mutation_p.G60R|GPR156_ENST00000315843.3_Missense_Mutation_p.G60R Q8NFN8 GP156_HUMAN G protein-coupled receptor 156 32 AGCAGAAGTCCACAGCTGAGA 0.433000 0 SO:0001583 missense ENST00000464295.1 1 1 hg19 CCDS2997.1 . . . . . . . . . . C 20.2 3.949646 0.73787 . . ENSG00000175697 ENST00000464295;ENST00000315843;ENST00000461057 D;D;D 0.91945 -2.94;-2.94;-2.94 5.2 4.31 0.51392 GPCR, family 3, C-terminal (2); 0.089971 0.46758 D 0.000261 D 0.95974 0.8689 M 0.88512 2.96 0.58432 D 0.999998 D;D 0.89917 1.0;1.0 D;D 0.75020 0.985;0.985 D 0.95894 0.8909 9 . . . -13.3173 10.9026 0.47059 0.187:0.813:0.0:0.0 . 60;60 E9PFZ4;Q8NFN8 .;GP156_HUMAN R 60 ENSP00000417261:G60R;ENSP00000324553:G60R;ENSP00000418758:G60R . G - 1 0 GPR156 121445232 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 4.539000 0.60657 1.385000 0.46445 0.650000 0.86243 GGA TCGA-2L-AAQA-01A-21D-A38G-08 GPR156-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000355139.1 1 0 1 118 273 0 127 0 0 0 1 0 127 2 0 0 0 0 0 2 1 1.000000 118 271 0 122 2 0 0 0 0 127 2 -8.936694 1 1 0 0 1 0 0 0 2.047777 0 0.600000 1.890000 0.597586 0.990000 8.400000e-01 1.000000 1.000000 0.970078 0.990000 1 9.100000e-01 1 PIK3CA 5290 broad.mit.edu 37 3 178936074 178936074 + Missense_Mutation SNP C C G rs121913285 TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr3:178936074C>G ENST00000263967.3 + 10 1773 c.1616C>G c.(1615-1617)cCt>cGt p.P539R NM_006218.2 NP_006209.2 P42336 PK3CA_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha p.P539R(17) 5269 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) Caffeine(DB00201) ACACGAGATCCTCTCTCTGAA 0.328000 P539R(BT20_BREAST)|P539R(MFE296_ENDOMETRIUM) 57 Mis colorectal, gastric, gliobastoma, breast HNSCC(19;0.045)|TSP Lung(28;0.18) Colon(199;1504 1750 3362 26421 31210 32040) Dom yes 3 3q26.3 5290 phosphoinositide-3-kinase, catalytic, alpha polypeptide E, O 17 Substitution - Missense(17) SO:0001583 missense ENST00000263967.3 1 1 hg19 CCDS43171.1 . . . . . . . . . . C 29.2 4.987372 0.93106 . . ENSG00000121879 ENST00000263967 D 0.89270 -2.49 5.78 5.78 0.91487 Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 D 0.94466 0.8219 M 0.80332 2.49 0.80722 D 1 D 0.59357 0.985 D 0.63192 0.912 D 0.94197 0.7446 10 0.59425 D 0.04 -26.0829 20.0024 0.97423 0.0:1.0:0.0:0.0 . 539 P42336 PK3CA_HUMAN R 539 ENSP00000263967:P539R ENSP00000263967:P539R P + 2 0 PIK3CA 180418768 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 7.487000 0.81328 2.722000 0.93159 0.467000 0.42956 CCT TCGA-2L-AAQA-01A-21D-A38G-08 PIK3CA-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000348409.2 1 0 1 87 251 0 103 1 9.932764e-01 9 16 0 103 2 0 0 0 0 0 2 1 1.000000 82 242 0 105 2 0 0 0 0 103 2 -5.078832 1 1 0 0 1 1 2 3 2.084391 0 0.600000 1.890000 0.601196 0.850000 7.000000e-01 1.000000 1.000000 0.862002 0.850000 1 7.700000e-01 9.400000e-01 TOP2B 7155 broad.mit.edu 37 3 25674236 25674236 + Missense_Mutation SNP A A G TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr3:25674236A>G ENST00000264331.4 - 9 1075 c.1076T>C c.(1075-1077)aTt>aCt p.I359T TOP2B_ENST00000435706.2_Missense_Mutation_p.I354T NM_001068.2 NP_001059.2 Q02880 TOP2B_HUMAN topoisomerase (DNA) II beta 180kDa 36 Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773) AACTACTTCAATCAGTTTACC 0.328000 0 SO:0001583 missense ENST00000264331.4 0 1 hg19 . . . . . . . . . . A 17.51 3.408676 0.62399 . . ENSG00000077097 ENST00000435706;ENST00000264331;ENST00000424225 T;T 0.46063 0.88;0.88 5.4 5.4 0.78164 . 0.000000 0.85682 D 0.000000 T 0.43233 0.1238 L 0.53561 1.675 0.80722 D 1 B 0.25048 0.117 B 0.29440 0.102 T 0.37337 -0.9710 10 0.54805 T 0.06 -15.1386 15.4062 0.74881 1.0:0.0:0.0:0.0 . 354 Q02880-2 . T 354;359;354 ENSP00000396704:I354T;ENSP00000264331:I359T ENSP00000264331:I359T I - 2 0 TOP2B 25649240 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.059000 0.93902 2.032000 0.59987 0.528000 0.53228 ATT TCGA-2L-AAQA-01A-21D-A38G-08 TOP2B-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 0 11 657 0 209 0 1.635157e-01 0 40 0 209 2 0 0 0 0 0 2 1 0.998218 11 648 0 205 2 0 0 0 0 209 2 -3.327245 1 1 120794 1 34 1 0 0 0 2.047777 0 0.600000 1.890000 0.597586 0.050000 2.000000e-02 0.100000 0.060000 0.059260 0.050000 0 3.000000e-02 8.000000e-02 ITPR1 3708 broad.mit.edu 37 3 4722339 4722339 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr3:4722339G>A ENST00000443694.2 + 22 3025 c.3025G>A c.(3025-3027)Gga>Aga p.G1009R ITPR1_ENST00000354582.6_Missense_Mutation_p.G1024R|ITPR1_ENST00000357086.4_Missense_Mutation_p.G1015R|ITPR1_ENST00000423119.2_Missense_Mutation_p.G1015R|ITPR1_ENST00000456211.2_Missense_Mutation_p.G1000R|ITPR1_ENST00000302640.8_Missense_Mutation_p.G1009R|ITPR1_ENST00000544951.1_Intron Q14643 ITPR1_HUMAN inositol 1,4,5-trisphosphate receptor, type 1 106 Caffeine(DB00201) AACATCCTCCGGAAACAGCAG 0.433000 0 SO:0001583 missense ENST00000443694.2 1 1 hg19 CCDS54551.1 . . . . . . . . . . G 14.99 2.700462 0.48307 . . ENSG00000150995 ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694 T;T;T;T;T;T 0.54866 0.55;0.55;0.55;0.55;0.55;0.55 5.56 5.56 0.83823 . 0.236966 0.43260 D 0.000598 T 0.50735 0.1633 M 0.69358 2.11 0.80722 D 1 B;B;P 0.36837 0.308;0.311;0.571 B;B;B 0.32090 0.027;0.02;0.14 T 0.50320 -0.8842 10 0.26408 T 0.33 . 17.7004 0.88293 0.0:0.0:1.0:0.0 . 1009;1024;1015 E7EPX7;Q14643;G5E9P1 .;ITPR1_HUMAN;. R 1024;1009;1024;1015;1015;1000;1009 ENSP00000306253:G1009R;ENSP00000346595:G1024R;ENSP00000405934:G1015R;ENSP00000349597:G1015R;ENSP00000397885:G1000R;ENSP00000401671:G1009R ENSP00000306253:G1009R G + 1 0 ITPR1 4697339 1.000000 0.71417 0.968000 0.41197 0.959000 0.62525 6.688000 0.74557 2.599000 0.87857 0.591000 0.81541 GGA TCGA-2L-AAQA-01A-21D-A38G-08 ITPR1-004 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000337982.3 0 0 1 65 128 1 67 0 1.156986e-01 0 2 1 67 2 0 0 0 0 0 2 1 1.000000 65 126 1 67 11 0 0 0 1 67 2 -20.000000 1 1 0 0 1 0 0 0 2.047777 0 0.600000 1.890000 0.597586 0.990000 8.900000e-01 1.000000 1.000000 0.992010 0.990000 1 9.900000e-01 1 DCHS2 54798 broad.mit.edu 37 4 155156138 155156138 + Silent SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr4:155156138C>T ENST00000357232.4 - 25 8300 c.8301G>A c.(8299-8301)acG>acA p.T2767T NM_017639.3 NP_060109.2 Q6V1P9 PCD23_HUMAN dachsous cadherin-related 2 176 all_hematologic(180;0.208) Renal(120;0.0854) GATCAGAGGTCGTCTGAGTTG 0.418000 0 SO:0001819 synonymous_variant ENST00000357232.4 1 1 hg19 CCDS3785.1 TCGA-2L-AAQA-01A-21D-A38G-08 DCHS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365281.2 0 0 0 12 301 0 151 0 0 0 0 151 2 0 0 0 0 0 2 1 0.999129 12 299 0 150 2 0 0 0 0 151 2 -3.831311 1 1 121408 1 36 1 0 1 1 1.574951 1 0.600000 1.890000 0.454297 0.090000 4.000000e-02 0.160000 0.090000 0.100455 0.090000 0 6.000000e-02 1.300000e-01 CTNND2 1501 broad.mit.edu 37 5 10973809 10973809 + Missense_Mutation SNP A A C TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:10973809A>C ENST00000304623.8 - 22 3623 c.3434T>G c.(3433-3435)gTc>gGc p.V1145G CTNND2_ENST00000503622.1_Missense_Mutation_p.V808G|CTNND2_ENST00000458100.2_Missense_Mutation_p.V712G|CTNND2_ENST00000511377.1_Missense_Mutation_p.V1054G|CTNND2_ENST00000359640.2_Missense_Mutation_p.V1087G|CTNND2_ENST00000495388.2_5'UTR NM_001332.2 NP_001323.1 Q9UQB3 CTND2_HUMAN catenin (cadherin-associated protein), delta 2 136 CTCCTGTGGGACTGGCTGTGC 0.522000 0 SO:0001583 missense ENST00000304623.8 1 1 hg19 CCDS3881.1 . . . . . . . . . . A 6.986 0.551943 0.13374 . . ENSG00000169862 ENST00000304623;ENST00000359640;ENST00000511377;ENST00000538638;ENST00000458100;ENST00000503622 T;T;T;T;T 0.78595 -1.08;-1.15;-1.07;-1.19;-1.19 5.93 2.29 0.28610 . 0.757929 0.12479 N 0.465306 T 0.57021 0.2025 N 0.08118 0 0.80722 D 1 B;B;B 0.26318 0.002;0.035;0.146 B;B;B 0.24974 0.004;0.012;0.057 T 0.35943 -0.9768 10 0.26408 T 0.33 -15.0539 9.4259 0.38578 0.8:0.0:0.2:0.0 . 808;737;1145 B4DRK2;B4DG58;Q9UQB3 .;.;CTND2_HUMAN G 1145;1087;1054;240;712;808 ENSP00000307134:V1145G;ENSP00000352661:V1087G;ENSP00000426510:V1054G;ENSP00000391155:V712G;ENSP00000426887:V808G ENSP00000307134:V1145G V - 2 0 CTNND2 11026809 1.000000 0.71417 0.990000 0.47175 0.996000 0.88848 4.062000 0.57492 0.162000 0.19483 0.533000 0.62120 GTC TCGA-2L-AAQA-01A-21D-A38G-08 CTNND2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206999.1 0 0 1 85 209 0 111 0 0 0 0 111 2 0 0 0 0 0 2 1 1.000000 83 206 0 110 2 0 0 0 0 111 2 -20.000000 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.950000 7.900000e-01 1.000000 1.000000 0.943457 0.950000 1 8.700000e-01 1 SRFBP1 153443 broad.mit.edu 37 5 121362757 121362757 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:121362757G>A ENST00000339397.4 + 8 1298 c.1226G>A c.(1225-1227)aGg>aAg p.R409K SRFBP1_ENST00000504881.1_Intron NM_152546.2 NP_689759.2 serum response factor binding protein 1 15 all_cancers(142;0.0124)|Prostate(80;0.0322) KIRC - Kidney renal clear cell carcinoma(527;0.206) GCAAGCAGAAGGCGAAAAGAA 0.368000 0 SO:0001583 missense ENST00000339397.4 1 1 hg19 CCDS43354.1 . . . . . . . . . . G 11.20 1.569176 0.28003 . . ENSG00000151304 ENST00000339397 . . . 5.76 -0.243 0.13035 Bud-site selection protein, BUD22 (1); 0.337294 0.36303 N 0.002678 T 0.30479 0.0766 N 0.16368 0.405 0.34634 D 0.719936 B 0.17038 0.02 B 0.17433 0.018 T 0.29366 -1.0014 9 0.13853 T 0.58 -6.0429 11.318 0.49403 0.5482:0.0:0.4518:0.0 . 409 Q8NEF9 SRFB1_HUMAN K 409 . ENSP00000341324:R409K R + 2 0 SRFBP1 121390656 1.000000 0.71417 0.984000 0.44739 0.962000 0.63368 1.433000 0.34947 0.003000 0.14656 0.655000 0.94253 AGG TCGA-2L-AAQA-01A-21D-A38G-08 SRFBP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371200.1 1 0 1 130 228 0 121 1 9.999987e-01 27 12 0 121 2 0 0 0 0 0 2 1 1.000000 129 222 0 120 2 0 0 0 0 121 2 -20.000000 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.990000 9.900000e-01 1.000000 1.000000 0.999849 0.990000 1 9.900000e-01 1 DND1 373863 broad.mit.edu 37 5 140052939 140052939 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:140052939G>A ENST00000542735.1 - 2 102 c.59C>T c.(58-60)gCg>gTg p.A20V HARS_ENST00000504156.1_3'UTR NM_194249.2 NP_919225.1 Q8IYX4 DND1_HUMAN DND microRNA-mediated repression inhibitor 1 5 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CTCCAGCGCCGCCTTGTTCTC 0.642000 0 SO:0001583 missense ENST00000542735.1 1 1 hg19 CCDS4236.1 . . . . . . . . . . G 13.62 2.290610 0.40494 . . ENSG00000256453 ENST00000542735 T 0.34859 1.34 4.58 4.58 0.56647 . 0.209202 0.33457 N 0.004895 T 0.20333 0.0489 N 0.20574 0.59 0.80722 D 1 P 0.35401 0.499 B 0.23716 0.048 T 0.06516 -1.0822 10 0.37606 T 0.19 -6.6743 12.0698 0.53609 0.0868:0.0:0.9132:0.0 . 20 Q8IYX4 DND1_HUMAN V 20 ENSP00000445366:A20V ENSP00000445366:A20V A - 2 0 DND1 140033123 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 2.251000 0.43187 2.358000 0.79984 0.462000 0.41574 GCG TCGA-2L-AAQA-01A-21D-A38G-08 DND1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251669.2 1 0 0 86 331 0 125 1 9.943920e-01 12 21 0 125 2 0 0 0 0 0 2 1 1.000000 84 327 0 122 2 0 0 0 0 125 2 -20.000000 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.680000 5.500000e-01 0.810000 0.680000 0.688942 0.680000 0 6.100000e-01 7.500000e-01 PCDHGA5 56110 broad.mit.edu 37 5 140745619 140745619 + Silent SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:140745619C>T ENST00000518069.1 + 1 1722 c.1722C>T c.(1720-1722)ggC>ggT p.G574G PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron NM_018918.2|NM_032054.1 NP_061741.1|NP_114443.1 Q9Y5G8 PCDG5_HUMAN protocadherin gamma subfamily A, 5 18 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GTTCCACGGGCGTGGAGCTGG 0.622000 0 SO:0001819 synonymous_variant ENST00000518069.1 1 1 hg19 CCDS54925.1 TCGA-2L-AAQA-01A-21D-A38G-08 PCDHGA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374742.1 1 0 1 286 609 0 295 0 6.197435e-01 1 5 0 295 2 0 0 0 0 0 2 1 1.000000 283 598 0 293 2 0 0 0 0 295 2 -20.000000 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.990000 9.500000e-01 1.000000 1.000000 0.997153 0.990000 1 9.900000e-01 1 FAT2 2196 broad.mit.edu 37 5 150885588 150885588 + Silent SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:150885588G>A ENST00000261800.5 - 23 12600 c.12588C>T c.(12586-12588)tcC>tcT p.S4196S NM_001447.2 NP_001438.1 Q9NYQ8 FAT2_HUMAN FAT atypical cadherin 2 196 Medulloblastoma(196;0.0912)|all_hematologic(541;0.104) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) GAGTCACTTCGGAGTGGGGGT 0.622000 0 SO:0001819 synonymous_variant ENST00000261800.5 1 1 hg19 CCDS4317.1 . . . . . . . . . . G 0.702 -0.790312 0.02884 . . ENSG00000086570 ENST00000520200 . . . 5.02 -5.86 0.02304 . . . . . . . . . . . 0.29771 N 0.83475 . . . . . . . . . . . . . . 7.4588 0.27283 0.3167:0.2335:0.4498:0.0 . . . . X 969 . . R - 1 2 FAT2 150865781 0.000000 0.05858 0.001000 0.08648 0.120000 0.20174 -2.499000 0.00968 -0.718000 0.04949 -0.459000 0.05422 CGA TCGA-2L-AAQA-01A-21D-A38G-08 FAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252434.1 1 0 1 162 409 0 249 0 0 0 1 0 249 2 0 0 0 0 0 2 1 1.000000 161 399 0 248 2 0 0 0 0 249 2 -9.212538 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.930000 8.100000e-01 1.000000 1.000000 0.937584 0.930000 1 8.700000e-01 1 FAT2 2196 broad.mit.edu 37 5 150923873 150923873 + Missense_Mutation SNP A A G TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:150923873A>G ENST00000261800.5 - 9 6827 c.6815T>C c.(6814-6816)tTt>tCt p.F2272S NM_001447.2 NP_001438.1 Q9NYQ8 FAT2_HUMAN FAT atypical cadherin 2 196 Medulloblastoma(196;0.0912)|all_hematologic(541;0.104) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) CAATTGGGAAAAAGTGGGAGG 0.517000 0 SO:0001583 missense ENST00000261800.5 0 1 hg19 CCDS4317.1 . . . . . . . . . . A 17.95 3.513047 0.64522 . . ENSG00000086570 ENST00000261800 T 0.32023 1.47 5.68 5.68 0.88126 Cadherin (2);Cadherin-like (1); 0.000000 0.64402 D 0.000002 T 0.69860 0.3158 H 0.96604 3.85 0.80722 D 1 D 0.76494 0.999 D 0.83275 0.996 T 0.81348 -0.0973 10 0.87932 D 0 . 15.938 0.79729 1.0:0.0:0.0:0.0 . 2272 Q9NYQ8 FAT2_HUMAN S 2272 ENSP00000261800:F2272S ENSP00000261800:F2272S F - 2 0 FAT2 150904066 1.000000 0.71417 1.000000 0.80357 0.920000 0.55202 9.252000 0.95491 2.167000 0.68274 0.459000 0.35465 TTT TCGA-2L-AAQA-01A-21D-A38G-08 FAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252434.1 0 0 0 9 430 1 137 0 0 0 1 1 137 2 0 0 0 0 0 2 0 0.314426 8 424 1 136 12 0 0 0 1 137 2 -8.826884 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.060000 2.000000e-02 0.130000 0.070000 0.075243 0.060000 0 4.000000e-02 1.000000e-01 SGCD 6444 broad.mit.edu 37 5 155771526 155771526 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:155771526C>T ENST00000435422.3 + 2 515 c.28C>T c.(28-30)Cgg>Tgg p.R10W SGCD_ENST00000447401.1_Missense_Mutation_p.R11W|SGCD_ENST00000517913.1_Missense_Mutation_p.R11W|SGCD_ENST00000337851.4_Missense_Mutation_p.R11W NM_001128209.1 NP_001121681.1 Q92629 SGCD_HUMAN sarcoglycan, delta (35kDa dystrophin-associated glycoprotein) 24 Renal(175;0.00488) Medulloblastoma(196;0.0378)|all_neural(177;0.106) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) CACTCACCACCGGAGCACCAT 0.478000 0 SO:0001583 missense ENST00000435422.3 1 1 hg19 CCDS47327.1 . . . . . . . . . . C 21.9 4.212095 0.79240 . . ENSG00000170624 ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401 T;D;D;T 0.86694 1.41;-2.15;-2.16;1.41 5.59 2.34 0.29019 . 0.051785 0.64402 D 0.000001 D 0.91297 0.7256 L 0.60455 1.87 0.58432 D 0.999998 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.99;0.996;0.999 D 0.91387 0.5132 10 0.72032 D 0.01 0.2039 14.2572 0.66060 0.5847:0.4153:0.0:0.0 . 10;11;11 Q92629;Q92629-2;Q92629-3 SGCD_HUMAN;.;. W 11;10;11;11 ENSP00000429378:R11W;ENSP00000403003:R10W;ENSP00000338343:R11W;ENSP00000408324:R11W ENSP00000338343:R11W R + 1 2 SGCD 155704104 1.000000 0.71417 1.000000 0.80357 0.980000 0.70556 1.486000 0.35530 0.624000 0.30286 0.655000 0.94253 CGG TCGA-2L-AAQA-01A-21D-A38G-08 SGCD-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000373469.3 1 0 1 83 231 0 132 0 5.914051e-01 0 7 0 132 2 0 0 0 0 0 2 1 1.000000 83 225 0 132 2 0 0 0 0 132 2 -5.335612 1 1 120894 5 37 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.870000 7.100000e-01 1.000000 1.000000 0.878408 0.870000 1 7.900000e-01 9.600000e-01 HK3 3101 broad.mit.edu 37 5 176318141 176318141 + Missense_Mutation SNP C C T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:176318141C>T ENST00000292432.5 - 4 402 c.311G>A c.(310-312)cGt>cAt p.R104H NM_002115.2 NP_002106.2 P52790 HXK3_HUMAN hexokinase 3 (white cell) 47 all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115) Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) CCACAAAACACGCAGTGAGGC 0.602000 0 SO:0001583 missense ENST00000292432.5 1 1 hg19 CCDS4407.1 . . . . . . . . . . C 24.2 4.504410 0.85176 . . ENSG00000160883 ENST00000292432 D 0.99724 -6.54 4.96 4.96 0.65561 Hexokinase, N-terminal (1); 0.000000 0.51477 D 0.000081 D 0.99664 0.9875 M 0.87900 2.915 0.32374 N 0.55541 D 0.71674 0.998 D 0.62955 0.909 D 0.97938 1.0324 10 0.62326 D 0.03 -7.6649 17.1545 0.86787 0.0:1.0:0.0:0.0 . 104 P52790 HXK3_HUMAN H 104 ENSP00000292432:R104H ENSP00000292432:R104H R - 2 0 HK3 176250747 0.996000 0.38824 0.984000 0.44739 0.870000 0.49936 4.152000 0.58111 2.460000 0.83146 0.561000 0.74099 CGT TCGA-2L-AAQA-01A-21D-A38G-08 HK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253428.1 1 0 1 103 254 0 95 0 6.460933e-01 0 7 0 95 2 0 0 0 0 0 2 1 1.000000 102 249 0 94 2 0 0 0 0 95 2 -20.000000 1 1 121410 7 39 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.950000 8.000000e-01 1.000000 1.000000 0.944724 0.950000 1 8.700000e-01 1 OR2Y1 134083 broad.mit.edu 37 5 180166545 180166545 + Nonsense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:180166545G>A ENST00000307832.2 - 1 554 c.514C>T c.(514-516)Cga>Tga p.R172* NM_001001657.1 NP_001001657.1 Q8NGV0 OR2Y1_HUMAN olfactory receptor, family 2, subfamily Y, member 1 20 all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114) all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) TGATTCAGTCGATGGCCACAG 0.542000 0 SO:0001587 stop_gained ENST00000307832.2 0 1 hg19 CCDS34323.1 . . . . . . . . . . g 17.19 3.327676 0.60743 0.0 1.16E-4 ENSG00000174339 ENST00000307832 . . . 4.41 2.59 0.31030 . 3.529880 0.00714 N 0.000849 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 7.0741 0.25195 0.0936:0.0:0.7351:0.1713 . . . . X 172 . ENSP00000312403:R172X R - 1 2 OR2Y1 180099151 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -1.967000 0.01508 0.572000 0.29383 0.511000 0.50034 CGA TCGA-2L-AAQA-01A-21D-A38G-08 OR2Y1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368059.2 1 0 1 79 147 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 1.000000 79 146 0 80 2 0 0 0 0 80 2 -20.000000 1 1 121412 1 28 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.990000 9.500000e-01 1.000000 1.000000 0.997567 0.990000 1 9.900000e-01 1 PPWD1 23398 broad.mit.edu 37 5 64868000 64868000 + Missense_Mutation SNP G G A rs150307628 TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:64868000G>A ENST00000261308.5 + 5 928 c.856G>A c.(856-858)Gta>Ata p.V286I PPWD1_ENST00000535264.1_Missense_Mutation_p.V256I|PPWD1_ENST00000538977.1_Missense_Mutation_p.V130I NM_015342.3 NP_056157.1 Q96BP3 PPWD1_HUMAN peptidylprolyl isomerase domain and WD repeat containing 1 19 Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186) TCCAACCAGCGTATGTTTTTC 0.348000 0 SO:0001583 missense ENST00000261308.5 1 1 hg19 CCDS3985.1 . . . . . . . . . . A 8.826 0.938643 0.18206 2.27E-4 3.49E-4 ENSG00000113593 ENST00000261308;ENST00000535264;ENST00000538977;ENST00000505380 T;T;T;T 0.61040 0.14;0.14;0.14;0.14 5.59 5.59 0.84812 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.098404 0.64402 N 0.000003 T 0.44095 0.1277 L 0.38838 1.175 0.09310 N 0.999997 B;B 0.02656 0.0;0.0 B;B 0.04013 0.001;0.001 T 0.28808 -1.0032 10 0.09338 T 0.73 . 11.6254 0.51142 0.9304:0.0:0.0695:0.0 . 256;286 F5H7P7;Q96BP3 .;PPWD1_HUMAN I 286;256;130;205 ENSP00000261308:V286I;ENSP00000442371:V256I;ENSP00000444496:V130I;ENSP00000423234:V205I ENSP00000261308:V286I V + 1 0 PPWD1 64903756 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 4.661000 0.61518 0.955000 0.37878 -0.361000 0.07541 GTA TCGA-2L-AAQA-01A-21D-A38G-08 PPWD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253970.2 0 0 1 156 414 1 204 1 9.989898e-01 7 23 1 204 2 0 0 0 0 0 2 1 1.000000 155 412 1 202 12 0 0 0 1 204 2 -20.000000 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.900000 7.800000e-01 1.000000 1.000000 0.908774 0.900000 1 8.400000e-01 9.700000e-01 TNPO1 3842 broad.mit.edu 37 5 72195908 72195908 + Splice_Site SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr5:72195908G>A ENST00000337273.5 + 21 2840 c.2414G>A c.(2413-2415)tGg>tAg p.W805* TNPO1_ENST00000454282.1_Splice_Site_p.W755*|TNPO1_ENST00000523768.1_Splice_Site_p.W755*|TNPO1_ENST00000506351.2_Splice_Site_p.W797* NM_002270.3 NP_002261.3 Q92973 TNPO1_HUMAN transportin 1 p.W797*(1)|p.W797L(1) 36 Lung NSC(167;0.0053)|Ovarian(174;0.0175) ATAAGACCCTGGTGTGTATTA 0.348000 2 Substitution - Nonsense(1)|Substitution - Missense(1) SO:0001630 splice_region_variant ENST00000337273.5 0 0 hg19 CCDS43329.1 . . . . . . . . . . G 38 6.879768 0.97904 . . ENSG00000083312 ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351;ENST00000519220 . . . 5.58 5.58 0.84498 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -5.5419 19.1767 0.93605 0.0:0.0:1.0:0.0 . . . . X 805;755;755;797;316 . ENSP00000336712:W805X W + 2 0 TNPO1 72231664 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.476000 0.97823 2.619000 0.88677 0.467000 0.42956 TGG TCGA-2L-AAQA-01A-21D-A38G-08 TNPO1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000218577.3 1 0 1 166 364 0 206 0 1 1 59 0 206 2 0 0 0 0 0 2 1 1.000000 163 359 0 205 2 0 0 0 0 206 2 -12.030340 1 1 0 0 1 0 1 1 2.058923 0 0.600000 1.890000 0.598796 0.990000 9.000000e-01 1.000000 1.000000 0.989269 0.990000 1 9.600000e-01 1 PHF1 5252 broad.mit.edu 37 6 33382134 33382134 + Silent SNP C C A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr6:33382134C>A ENST00000374516.3 + 9 1138 c.867C>A c.(865-867)ctC>ctA p.L289L PHF1_ENST00000374512.3_Silent_p.L289L NM_024165.2 NP_077084.1 O43189 PHF1_HUMAN PHD finger protein 1 19 Ovarian(999;0.0443) ACAGTTTGCTCCTGGGGGAGG 0.498000 OREG0017346 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000374516.3 1 1 hg19 CCDS4777.1 TCGA-2L-AAQA-01A-21D-A38G-08 PHF1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076175.3 1 0 1 139 261 0 131 1 1 39 66 0 131 2 0 0 0 0 0 2 1 1.000000 136 256 0 130 2 0 0 0 0 131 2 -14.824100 1 1 0 0 1 0 0 0 1.902920 0 0.600000 1.890000 0.563319 0.990000 9.100000e-01 1.000000 1.000000 0.992118 0.990000 1 9.800000e-01 1 CBLL1 79872 broad.mit.edu 37 7 107398626 107398626 + Missense_Mutation SNP G G A TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr7:107398626G>A ENST00000440859.3 + 6 946 c.479G>A c.(478-480)cGa>cAa p.R160Q CBLL1_ENST00000415884.2_3'UTR|CBLL1_ENST00000222597.2_Missense_Mutation_p.R159Q NM_001284291.1|NM_024814.2 NP_001271220.1|NP_079090.2 Q75N03 HAKAI_HUMAN Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase 21 CAGTGTACACGAGGTTCTCTC 0.378000 0 SO:0001583 missense ENST00000440859.3 1 1 hg19 CCDS5747.1 . . . . . . . . . . G 19.61 3.860457 0.71834 . . ENSG00000105879 ENST00000440859;ENST00000535365;ENST00000222597;ENST00000420796;ENST00000417616 T;T;T 0.32753 1.45;1.44;1.48 5.14 4.24 0.50183 . 0.000000 0.85682 D 0.000000 T 0.48241 0.1489 L 0.52759 1.655 0.80722 D 1 D;D 0.89917 1.0;0.996 D;P 0.77004 0.989;0.755 T 0.36432 -0.9748 10 0.28530 T 0.3 -2.0467 15.7175 0.77681 0.0:0.1374:0.8626:0.0 . 159;160 B7ZM03;Q75N03 .;HAKAI_HUMAN Q 160;39;159;110;106 ENSP00000401277:R160Q;ENSP00000222597:R159Q;ENSP00000410615:R110Q ENSP00000222597:R159Q R + 2 0 CBLL1 107185862 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.543000 0.98089 1.259000 0.44117 0.655000 0.94253 CGA TCGA-2L-AAQA-01A-21D-A38G-08 CBLL1-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000337156.2 1 0 1 124 295 0 160 1 9.995125e-01 14 16 0 160 2 0 0 0 0 0 2 1 1.000000 123 291 0 158 2 0 0 0 0 160 2 -8.710860 1 1 121412 6 39 1 0 1 1 2.061758 0 0.600000 1.890000 0.598796 0.970000 8.300000e-01 1.000000 1.000000 0.962309 0.970000 1 9.000000e-01 1 FIGNL1 63979 broad.mit.edu 37 7 50513641 50513641 + Missense_Mutation SNP G G T TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr7:50513641G>T ENST00000419119.1 - 2 2898 c.1345C>A c.(1345-1347)Cta>Ata p.L449I FIGNL1_ENST00000395556.2_Missense_Mutation_p.L449I|FIGNL1_ENST00000356889.4_Missense_Mutation_p.L449I|FIGNL1_ENST00000433017.1_Missense_Mutation_p.L449I Q6PIW4 FIGL1_HUMAN fidgetin-like 1 p.L449L(1) 29 Glioma(55;0.08)|all_neural(89;0.245) Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06) TTGCCAATTAGAGTTTTACCA 0.458000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000419119.1 0 1 hg19 CCDS5510.1 . . . . . . . . . . G 20.7 4.031312 0.75504 . . ENSG00000132436 ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119 D;D;D;D 0.95342 -3.68;-3.68;-3.68;-3.68 5.99 4.18 0.49190 ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1); 0.000000 0.64402 D 0.000001 D 0.97573 0.9205 M 0.92970 3.365 0.80722 D 1 D 0.64830 0.994 D 0.76071 0.987 D 0.98137 1.0434 10 0.72032 D 0.01 -9.5128 12.3571 0.55182 0.1376:0.0:0.8624:0.0 . 449 Q6PIW4 FIGL1_HUMAN I 449 ENSP00000349356:L449I;ENSP00000378924:L449I;ENSP00000399997:L449I;ENSP00000410811:L449I ENSP00000349356:L449I L - 1 2 FIGNL1 50481135 1.000000 0.71417 0.899000 0.35326 0.997000 0.91878 6.779000 0.75057 1.538000 0.49270 0.655000 0.94253 CTA TCGA-2L-AAQA-01A-21D-A38G-08 FIGNL1-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342579.1 0 0 0 5 377 0 118 0 7.323079e-03 0 8 0 118 2 0 0 0 0 0 2 1 0.934399 5 369 0 118 2 0 0 0 0 118 2 -5.581852 1 1 0 0 1 0 1 1 2.061758 0 0.600000 1.890000 0.598796 0.040000 0 0.100000 0.040000 0.051722 0.040000 0 2.000000e-02 7.000000e-02 ZNF3 7551 broad.mit.edu 37 7 99669508 99669508 + Missense_Mutation SNP T T C TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr7:99669508T>C ENST00000424697.1 - 6 905 c.599A>G c.(598-600)cAt>cGt p.H200R ZNF3_ENST00000303915.6_Missense_Mutation_p.H200R|ZNF3_ENST00000299667.4_Missense_Mutation_p.H200R|ZNF3_ENST00000413658.2_Intron NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3 NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3 P17036 ZNF3_HUMAN zinc finger protein 3 25 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029) STAD - Stomach adenocarcinoma(171;0.129) ATCACACTTATGGGGTCTGTC 0.433000 0 SO:0001583 missense ENST00000424697.1 1 1 hg19 CCDS43619.1 . . . . . . . . . . T 16.68 3.189385 0.57909 . . ENSG00000166526 ENST00000424697;ENST00000303915;ENST00000299667 T;T;T 0.35421 1.31;1.31;1.31 4.6 4.6 0.57074 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.53938 D 0.000041 T 0.51584 0.1683 L 0.60845 1.875 0.37016 D 0.895972 D;D 0.63880 0.993;0.982 P;P 0.62491 0.824;0.903 T 0.61783 -0.6992 10 0.87932 D 0 -15.5748 12.2643 0.54668 0.0:0.0:0.0:1.0 . 183;200 B3KRP4;P17036 .;ZNF3_HUMAN R 200 ENSP00000415358:H200R;ENSP00000306372:H200R;ENSP00000299667:H200R ENSP00000299667:H200R H - 2 0 ZNF3 99507444 0.001000 0.12720 1.000000 0.80357 0.998000 0.95712 0.261000 0.18442 2.075000 0.62263 0.533000 0.62120 CAT TCGA-2L-AAQA-01A-21D-A38G-08 ZNF3-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336247.3 1 0 1 153 379 0 183 1 9.996521e-01 12 20 0 183 2 0 0 0 0 0 2 1 1.000000 152 376 0 183 2 0 0 0 0 183 2 -20.000000 1 1 121164 5 39 1 0 1 1 2.061758 0 0.600000 1.890000 0.598796 0.950000 8.200000e-01 1.000000 1.000000 0.946925 0.950000 1 8.800000e-01 1 GPSM1 26086 broad.mit.edu 37 9 139228944 139228944 + Missense_Mutation SNP C C T rs140085951 TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr9:139228944C>T ENST00000440944.1 + 2 329 c.109C>T c.(109-111)Cgt>Tgt p.R37C GPSM1_ENST00000392945.3_Missense_Mutation_p.R37C NM_001145638.1 NP_001139110 Q86YR5 GPSM1_HUMAN G-protein signaling modulator 1 9 Myeloproliferative disorder(178;0.0821) GGAGGGCGAGCGTCTGTGCAA 0.652000 0 SO:0001583 missense ENST00000440944.1 1 1 hg19 CCDS48055.1 . . . . . . . . . . c 19.82 3.899125 0.72754 . . ENSG00000160360 ENST00000392945;ENST00000440944;ENST00000354753 T;T;T 0.75477 -0.94;-0.94;-0.0 4.66 3.65 0.41850 . 0.000000 0.64402 U 0.000001 D 0.84397 0.5463 M 0.69523 2.12 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.999;1.0 D 0.86778 0.1977 10 0.87932 D 0 -12.3547 14.5162 0.67821 0.1569:0.8431:0.0:0.0 . 37;37 Q86YR5;Q86YR5-3 GPSM1_HUMAN;. C 37;37;14 ENSP00000376674:R37C;ENSP00000392828:R37C;ENSP00000346797:R14C ENSP00000346797:R14C R + 1 0 GPSM1 138348765 1.000000 0.71417 0.996000 0.52242 0.939000 0.58152 1.805000 0.38883 2.113000 0.64589 0.556000 0.70494 CGT TCGA-2L-AAQA-01A-21D-A38G-08 GPSM1-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 24 100 0 39 1 3.407763e-01 2 4 0 39 2 0 0 0 0 0 2 1 1.000000 24 98 0 39 2 0 0 0 0 39 2 -20.000000 1 1 121256 1 35 1 0 0 0 2.067674 0 0.600000 1.890000 0.600000 0.640000 4.300000e-01 0.880000 0.640000 0.657670 0.640000 0 5.300000e-01 7.700000e-01 KIF24 347240 broad.mit.edu 37 9 34256761 34256761 + Silent SNP A A G TCGA-2L-AAQA-01A-21D-A38G-08 TCGA-2L-AAQA-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 33208690-91c9-4811-8043-6659815440e9 a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8 g.chr9:34256761A>G ENST00000402558.2 - 10 2868 c.2844T>C c.(2842-2844)taT>taC p.Y948Y KIF24_ENST00000345050.2_Silent_p.Y814Y|KIF24_ENST00000379166.2_Silent_p.Y948Y|KIF24_ENST00000379174.3_Silent_p.Y814Y Q5T7B8 KIF24_HUMAN kinesin family member 24 32 LUSC - Lung squamous cell carcinoma(29;0.0107) TTTCCTGTCTATATATGAAAT 0.527000 0 SO:0001819 synonymous_variant ENST00000402558.2 1 1 hg19 CCDS6551.2 TCGA-2L-AAQA-01A-21D-A38G-08 KIF24-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052150.5 1 0 1 140 315 0 136 1 2.273725e-01 2 1 0 136 2 0 0 0 0 0 2 1 1.000000 136 306 0 134 2 0 0 0 0 136 2 -20.000000 1 1 0 0 1 0 1 1 2.060315 0 0.600000 1.890000 0.598796 0.990000 8.800000e-01 1.000000 1.000000 0.981744 0.990000 1 9.400000e-01 1