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 DHX30 22907 broad.mit.edu 37 3 47889357 47889358 + Frame_Shift_Del DEL AT AT - TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 AT - AT AT Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr3:47889357_47889358delAT ENST00000445061.1 + 14 2604_2605 c.2197_2198delAT c.(2197-2199)attfs p.I733fs DHX30_ENST00000446256.2_Frame_Shift_Del_p.I694fs|DHX30_ENST00000348968.4_Frame_Shift_Del_p.I705fs|MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000457607.1_Frame_Shift_Del_p.I761fs NM_138615.2 NP_619520.1 Q7L2E3 DHX30_HUMAN DEAH (Asp-Glu-Ala-His) box helicase 30 37 GGCCACCAACATTGCTGAGACT 0.535000 0 SO:0001589 frameshift_variant ENST00000445061.1 0 1 hg19 CCDS2759.1 TCGA-IB-A5SO-01A-11D-A32N-08 DHX30-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000257495.2 1 0 0 18 249 0 59 1 9.925499e-01 2 110 0 59 2 0 0 0 0 0 0 1 0.999986 20 249 0 59 2 0 0 0 0 0 0 -19.996020 1 1 0 0 1 0 1 1 1.887303 1 0.230000 1.870000 0.168826 0.540000 0.330000 0.800000 0.530000 0.558479 0.540000 0 0.430000 0.680000 C10orf2 56652 broad.mit.edu 37 10 102748967 102748967 + Nonsense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr10:102748967C>T ENST00000311916.2 + 1 1185 c.1000C>T c.(1000-1002)Cga>Tga p.R334* MRPL43_ENST00000299179.5_5'Flank|C10orf2_ENST00000473656.1_Intron|MRPL43_ENST00000318325.2_5'Flank|C10orf2_ENST00000370228.1_Nonsense_Mutation_p.R334*|MRPL43_ENST00000493646.1_5'Flank|MRPL43_ENST00000370241.3_5'Flank|MRPL43_ENST00000318364.8_5'Flank|MRPL43_ENST00000342071.1_5'Flank|MRPL43_ENST00000370242.4_5'Flank|MRPL43_ENST00000477279.1_5'Flank|MRPL43_ENST00000370234.4_5'Flank|MRPL43_ENST00000370236.1_5'Flank NM_001163813.1|NM_021830.4 NP_001157285.1|NP_068602.2 Q96RR1 PEO1_HUMAN chromosome 10 open reading frame 2 24 Colorectal(252;0.122)|all_hematologic(284;0.152) CTTCTTGGTGCGACCAGGAGA 0.572000 0 SO:0001587 stop_gained ENST00000311916.2 0 1 hg19 CCDS7506.1 . . . . . . . . . . c 22.300000 4.269486 0.804690 . . ENSG00000107815 ENST00000311916;ENST00000370228 . . . 5.9 2.63 0.31362 . 0.176895 0.49916 D 0.000131 . . . . . . 0.807220 A 1.000000 . . . . . . . . . . 0.02654 T 1 -21.1322 10.4927 0.44760 0.2696:0.6067:0.1237:0.0 . . . . X 334 . ENSP00000309595:R334X R + 1 2 C10orf2 102738957 1 0.714170 1 0.803570 0.332000 0.286340 2.501000 0.453890 1.443000 0.475860 0.457000 3.337800e-01 CGA TCGA-IB-A5SO-01A-11D-A32N-08 C10orf2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049886.1 1 0 0 23 283 0 65 1 2.401563e-01 2 10 0 65 2 0 0 0 0 0 2 1 0.999999 23 280 0 65 2 0 0 0 0 65 2 -3.142713 1 1 121412 2 38 1 1 2 3 2.064678 0 0.230000 1.870000 0.238754 0.680000 0.430000 1.000000 0.650000 0.703523 0.680000 0 0.540000 0.870000 ADAMTS15 170689 broad.mit.edu 37 11 130319167 130319167 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:130319167G>A ENST00000299164.2 + 1 299 c.299G>A c.(298-300)cGc>cAc p.R100H NM_139055.2 NP_620686.1 Q8TE58 ATS15_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 15 36 all_hematologic(175;0.0429) Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837) GACCTGCGACGCTGCTTCTAT 0.677000 0 SO:0001583 missense ENST00000299164.2 1 1 hg19 CCDS8488.1 . . . . . . . . . . G 9.717000 1.158526 0.214540 . . ENSG00000166106 ENST00000299164 T 0.04551 3.6 4.63 3.69 0.42338 Peptidase M12B, propeptide (1); . . . . T 0.02047 0.0064 N 0.03154 -0.405 0.220960 N 0.999367 B 0.19817 0.039 B 0.16722 0.016 T 0.47598 -0.9105 9 0.17369 T 0.5 . 4.0747 0.09899 0.2047:0.2129:0.5824:0.0 . 100 Q8TE58 ATS15_HUMAN H 100 ENSP00000299164:R100H ENSP00000299164:R100H R + 2 0 ADAMTS15 129824377 7.700000e-02 0.213120 7.170000e-01 0.305850 0.993000 0.825480 0.552000 0.233760 1.245000 0.438850 0.561000 7.409900e-01 CGC TCGA-IB-A5SO-01A-11D-A32N-08 ADAMTS15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385638.1 1 0 0 45 383 0 114 0 0 0 0 114 2 0 0 0 0 0 2 1 1.000000 44 380 0 112 2 0 0 0 0 114 2 -15.607740 1 1 0 0 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.880000 0.660000 1.000000 1.000000 0.881192 0.880000 1 0.760000 1.000000 PTPN5 84867 broad.mit.edu 37 11 18754215 18754215 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:18754215G>A ENST00000358540.2 - 12 1683 c.1253C>T c.(1252-1254)gCg>gTg p.A418V PTPN5_ENST00000396170.1_Missense_Mutation_p.A386V|PTPN5_ENST00000396167.2_Missense_Mutation_p.A386V|PTPN5_ENST00000477854.1_Missense_Mutation_p.A222V|PTPN5_ENST00000396166.3_5'Flank|PTPN5_ENST00000396171.4_Missense_Mutation_p.A418V|PTPN5_ENST00000396168.1_Missense_Mutation_p.A394V|RP11-1081L13.4_ENST00000527285.1_RNA NM_006906.1 NP_008837.1 P54829 PTN5_HUMAN protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched) 27 ACCGTCGTACGCCACCTGCTC 0.572000 OREG0020824 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000358540.2 1 1 hg19 CCDS7845.1 . . . . . . . . . . g 6.138000 0.393746 0.116380 . . ENSG00000110786 ENST00000477854;ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168 D;D;D;D;D;D 0.83419 -1.72;-1.72;-1.72;-1.72;-1.72;-1.72 5.55 3.19 0.36642 Protein-tyrosine phosphatase, receptor/non-receptor type (3); 0.490245 0.20026 N 0.100810 T 0.56819 0.2011 N 0.04746 -0.17 0.214160 N 0.999693 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.47446 -0.9117 10 0.02654 T 1 . 4.3729 0.11256 0.6621:0.0:0.1925:0.1454 . 418;386 P54829;B3KXG7 PTN5_HUMAN;. V 222;418;386;418;386;394 ENSP00000435056:A222V;ENSP00000351342:A418V;ENSP00000379473:A386V;ENSP00000379474:A418V;ENSP00000379470:A386V;ENSP00000379471:A394V ENSP00000351342:A418V A - 2 0 PTPN5 18710791 4.530000e-01 0.257210 5.450000e-01 0.281530 0.995000 0.863560 1.154000 0.316880 0.372000 0.245910 -0.285000 9.966000e-02 GCG TCGA-IB-A5SO-01A-11D-A32N-08 PTPN5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000259196.2 1 0 0 25 415 0 93 0 9.618080e-02 0 9 0 93 2 0 0 0 0 0 2 1 1.000000 24 409 0 93 2 0 0 0 0 93 2 -3.221177 1 1 121412 2 38 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.480000 0.310000 0.680000 0.480000 0.493100 0.480000 0 0.390000 0.580000 SLC5A12 159963 broad.mit.edu 37 11 26725427 26725427 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:26725427G>A ENST00000396005.3 - 5 902 c.593C>T c.(592-594)aCg>aTg p.T198M SLC5A12_ENST00000280467.6_Missense_Mutation_p.T198M NM_178498.3 NP_848593.2 Q1EHB4 SC5AC_HUMAN solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12 35 AATGAGAACCGTTAAGAAGCC 0.403000 0 SO:0001583 missense ENST00000396005.3 0 1 hg19 CCDS7860.2 . . . . . . . . . . G 21.500000 4.161956 0.782260 . . ENSG00000148942 ENST00000396005;ENST00000280467;ENST00000533617 D;D;D 0.88046 -2.33;-2.33;-2.33 5.16 5.16 0.70880 . 0.058040 0.64402 D 0.000003 D 0.91212 0.7231 L 0.46670 1.46 0.395320 D 0.968674 D;D 0.69078 0.978;0.997 P;D 0.67725 0.707;0.953 D 0.92534 0.6036 10 0.72032 D 0.01 . 18.6369 0.91382 0.0:0.0:1.0:0.0 . 198;198 Q1EHB4-2;Q1EHB4 .;SC5AC_HUMAN M 198;198;10 ENSP00000379326:T198M;ENSP00000280467:T198M;ENSP00000435053:T10M ENSP00000280467:T198M T - 2 0 SLC5A12 26682003 1 0.714170 9.360000e-01 0.375960 0.978000 0.694770 7.957000 0.878700 2.412000 0.818960 0.484000 4.762100e-01 ACG TCGA-IB-A5SO-01A-11D-A32N-08 SLC5A12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319681.1 0 0 0 7 529 0 141 0 0 0 0 141 2 0 0 0 0 0 2 1 0.979798 6 523 0 141 2 0 0 0 0 141 2 -2.139137 0 1 0 0 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.110000 0.040000 0.220000 0.110000 0.124844 0.110000 0 0.070000 0.170000 FOSL1 8061 broad.mit.edu 37 11 65661489 65661489 + Missense_Mutation SNP T T A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:65661489T>A ENST00000312562.2 - 3 587 c.401A>T c.(400-402)cAg>cTg p.Q134L FOSL1_ENST00000448083.2_Intron|FOSL1_ENST00000531493.1_Intron|FOSL1_ENST00000532401.1_Silent_p.A132A NM_005438.3 NP_005429.1 P15407 FOSL1_HUMAN FOS-like antigen 1 10 GCTCACCGCCTGCAGGAAGTC 0.657000 0 SO:0001583 missense ENST00000312562.2 0 1 hg19 CCDS8121.1 . . . . . . . . . . T 27.000000 4.791078 0.903670 . . ENSG00000175592 ENST00000312562 T 0.56444 0.46 4.26 4.26 0.50523 Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1); 0.120965 0.56097 D 0.000025 T 0.69278 0.3093 M 0.75777 2.31 0.807220 D 1.000000 D 0.71674 0.998 D 0.70487 0.969 T 0.73512 -0.3959 10 0.87932 D 0 -19.5225 11.6688 0.51389 0.0:0.0:0.0:1.0 . 134 P15407 FOSL1_HUMAN L 134 ENSP00000310170:Q134L ENSP00000310170:Q134L Q - 2 0 FOSL1 65418065 1 0.714170 1 0.803570 0.990000 0.784780 7.533000 0.819940 1.931000 0.559610 0.528000 5.322800e-01 CAG TCGA-IB-A5SO-01A-11D-A32N-08 FOSL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391168.2 0 0 0 3 38 0 10 0 9.791946e-01 0 110 0 10 2 0 0 0 0 0 2 1 0.804735 2 38 0 10 2 0 0 0 0 10 2 -8.245490 1 0 0 0 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.660000 0.200000 1.000000 1.000000 0.669880 0.660000 0 0.380000 1.000000 KLC2 64837 broad.mit.edu 37 11 66029444 66029444 + Splice_Site SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:66029444G>A ENST00000417856.1 + 3 702 c.e3+1 RP11-867G23.1_ENST00000530805.1_RNA|KLC2_ENST00000316924.5_Splice_Site|KLC2_ENST00000394066.2_Intron|KLC2_ENST00000394065.2_Splice_Site|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394078.1_Splice_Site|KLC2_ENST00000394067.2_Splice_Site|KLC2_ENST00000421552.1_Intron NM_001134775.1 NP_001128247.1 Q9H0B6 KLC2_HUMAN kinesin light chain 2 p.?(1) 24 CTCCCCTAACGTGAGCTCCTA 0.632000 1 Unknown(1) SO:0001630 splice_region_variant ENST00000417856.1 0 1 hg19 CCDS8130.1 . . . . . . . . . . G 14.190000 2.461432 0.437360 . . ENSG00000174996 ENST00000417856;ENST00000440228;ENST00000394067;ENST00000316924;ENST00000394078;ENST00000475757;ENST00000394065 . . . 4.15 3.19 0.36642 . . . . . . . . . . . 0.807220 D 1.000000 . . . . . . . . . . . . . . 10.7987 0.46476 0.0:0.1934:0.8066:0.0 . . . . . -1 . . . + . . KLC2 65786020 3.520000e-01 0.248950 7.150000e-01 0.305520 0.343000 0.289850 2.337000 0.439470 0.897000 0.363920 0.561000 7.409900e-01 . TCGA-IB-A5SO-01A-11D-A32N-08 KLC2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258200.1 0 0 0 4 132 0 27 0 1.563966e-03 1 1 0 27 2 0 0 0 0 0 2 1 0.891506 4 132 0 27 2 0 0 0 0 27 2 -6.702899 1 1 121408 1 33 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.270000 0.090000 0.570000 0.240000 0.297849 0.270000 0 0.160000 0.420000 EPS8L2 64787 broad.mit.edu 37 11 722406 722406 + Silent SNP C C T rs146372566 TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:722406C>T ENST00000533256.1 + 14 1440 c.1065C>T c.(1063-1065)gtC>gtT p.V355V AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Silent_p.V371V|EPS8L2_ENST00000530636.1_Silent_p.V355V|EPS8L2_ENST00000318562.8_Silent_p.V355V Q9H6S3 ES8L2_HUMAN EPS8-like 2 13 all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136) CCCAGATCGTCAACACCTGCA 0.657000 0 SO:0001819 synonymous_variant ENST00000533256.1 1 1 hg19 CCDS31328.1 TCGA-IB-A5SO-01A-11D-A32N-08 EPS8L2-003 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382344.1 1 0 0 19 228 0 69 1 9.999998e-01 155 194 0 69 2 0 0 0 0 0 2 1 0.999992 20 225 0 69 2 0 0 0 0 69 2 -19.999970 1 1 0 0 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.650000 0.410000 0.950000 0.640000 0.667567 0.650000 0 0.520000 0.800000 FAT3 120114 broad.mit.edu 37 11 92523233 92523233 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr11:92523233G>A ENST00000298047.6 + 7 4477 c.4460G>A c.(4459-4461)aGa>aAa p.R1487K FAT3_ENST00000525166.1_Missense_Mutation_p.R1337K|FAT3_ENST00000409404.2_Missense_Mutation_p.R1487K Q8TDW7 FAT3_HUMAN FAT atypical cadherin 3 85 Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858) GCCACAGATAGAGATGAGAAG 0.473000 TCGA Ovarian(4;0.039) 0 SO:0001583 missense ENST00000298047.6 1 1 hg19 . . . . . . . . . . G 12.620000 1.991286 0.351310 . . ENSG00000165323 ENST00000298047;ENST00000409404;ENST00000525166 T;T;T 0.01685 4.69;4.69;4.69 6.17 5.27 0.74061 . . . . . T 0.01189 0.0039 N 0.11927 0.2 0.807220 D 1.000000 B 0.21753 0.06 B 0.19666 0.026 T 0.41893 -0.9483 9 0.02654 T 1 . 11.64 0.51227 0.1347:0.0:0.8653:0.0 . 1487 Q8TDW7-3 . K 1487;1487;1337 ENSP00000298047:R1487K;ENSP00000387040:R1487K;ENSP00000432586:R1337K ENSP00000298047:R1487K R + 2 0 FAT3 92162881 1 0.714170 5.620000e-01 0.283700 0.866000 0.496080 4.904000 0.632790 1.636000 0.505260 0.655000 9.425300e-01 AGA TCGA-IB-A5SO-01A-11D-A32N-08 FAT3-201 KNOWN basic protein_coding protein_coding 1 0 0 40 403 0 113 0 0 0 0 113 2 0 0 0 0 0 2 1 1.000000 40 400 0 112 2 0 0 0 0 113 2 -11.542060 1 1 0 0 1 0 0 0 1.979230 0 0.230000 1.870000 0.208145 0.760000 0.550000 0.990000 0.760000 0.770774 0.760000 0 0.650000 0.880000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.400000 4.409094 0.833400 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.807220 D 1.000000 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1 0.714170 1 0.803570 0.998000 0.957120 7.743000 0.850200 2.668000 0.907890 0.563000 7.788400e-01 GGT TCGA-IB-A5SO-01A-11D-A32N-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 9 77 0 26 1 9.356873e-01 13 31 0 26 2 1 1 34 461 0 283 2 1 0.994775 9 76 0 26 2 1 1 901 7113 0 26 2 -6.860924 1 1 121404 2 44 1 1 2 3 2.077328 0 0.230000 1.870000 0.240481 0.970000 0.480000 1.000000 1.000000 0.880578 0.970000 1 0.690000 1.000000 POU6F1 5463 broad.mit.edu 37 12 51586202 51586202 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr12:51586202G>A ENST00000389243.4 - 9 1241 c.302C>T c.(301-303)gCc>gTc p.A101V POU6F1_ENST00000550824.1_Missense_Mutation_p.A101V|POU6F1_ENST00000333640.10_Missense_Mutation_p.A101V Q14863 PO6F1_HUMAN POU class 6 homeobox 1 11 AGCTGGGCTGGCAATGACCAC 0.612000 0 SO:0001583 missense ENST00000389243.4 0 1 hg19 CCDS31803.1 . . . . . . . . . . G 14.580000 2.577348 0.459020 . . ENSG00000184271 ENST00000389243;ENST00000333640;ENST00000550824 D;D;D 0.86230 -2.09;-2.09;-2.09 5.69 4.75 0.60458 . 0.553568 0.20789 N 0.085655 T 0.81302 0.4794 L 0.34521 1.04 0.254960 N 0.987598 B 0.14438 0.01 B 0.04013 0.001 T 0.70342 -0.4898 10 0.40728 T 0.16 . 15.0878 0.72167 0.0:0.1424:0.8576:0.0 . 101 Q14863 PO6F1_HUMAN V 101 ENSP00000373895:A101V;ENSP00000330190:A101V;ENSP00000448389:A101V ENSP00000330190:A101V A - 2 0 POU6F1 49872469 1 0.714170 9.970000e-01 0.539660 0.980000 0.705560 3.445000 0.529210 2.695000 0.919700 0.655000 9.425300e-01 GCC TCGA-IB-A5SO-01A-11D-A32N-08 POU6F1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405126.1 0 0 0 5 480 1 128 0 8.125651e-03 0 30 1 128 3 0 0 0 0 0 2 0 0.027485 5 472 1 125 14 0 0 0 1 128 2 -2.500785 1 1 0 0 1 1 2 3 2.077328 0 0.230000 1.870000 0.240481 0.100000 0.030000 1.000000 0.090000 0.194134 0.100000 0 0.060000 0.180000 ESPL1 9700 broad.mit.edu 37 12 53663505 53663505 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr12:53663505G>A ENST00000257934.4 + 3 870 c.779G>A c.(778-780)cGt>cAt p.R260H ESPL1_ENST00000552462.1_Missense_Mutation_p.R260H NM_012291.4 NP_036423.4 Q14674 ESPL1_HUMAN extra spindle pole bodies homolog 1 (S. cerevisiae) 70 GAACACTGCCGTCGCTTTTGC 0.572000 Colon(53;1069 1201 2587 5382) 0 SO:0001583 missense ENST00000257934.4 0 1 hg19 CCDS8852.1 . . . . . . . . . . G 23.500000 4.429533 0.837760 . . ENSG00000135476 ENST00000257934;ENST00000552462 T;T 0.15256 2.44;2.44 5.41 4.5 0.54988 . 0.131175 0.50627 D 0.000102 T 0.36663 0.0975 M 0.72118 2.19 0.376320 D 0.921717 D 0.89917 1.0 D 0.63283 0.913 T 0.18116 -1.0347 9 . . . . 13.5552 0.61756 0.0776:0.0:0.9224:0.0 . 260 Q14674 ESPL1_HUMAN H 260 ENSP00000257934:R260H;ENSP00000449831:R260H . R + 2 0 ESPL1 51949772 1 0.714170 1 0.803570 0.892000 0.519520 4.064000 0.575060 2.815000 0.969180 0.561000 7.409900e-01 CGT TCGA-IB-A5SO-01A-11D-A32N-08 ESPL1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406899.2 0 0 0 6 417 0 107 0 3.093068e-04 0 2 0 107 2 0 0 0 0 0 2 1 0.964453 6 414 0 107 2 0 0 0 0 107 2 -2.885850 1 1 121412 5 38 1 1 2 3 2.077328 0 0.230000 1.870000 0.240481 0.140000 0.050000 1.000000 0.130000 0.226845 0.140000 0 0.080000 0.230000 COL4A1 1282 broad.mit.edu 37 13 110857876 110857876 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr13:110857876C>T ENST00000375820.4 - 16 989 c.868G>A c.(868-870)Gga>Aga p.G290R COL4A1_ENST00000543140.1_Missense_Mutation_p.G290R NM_001845.4 NP_001836.2 P02462 CO4A1_HUMAN collagen, type IV, alpha 1 105 all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604) Breast(118;0.2) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145) CCATCTTTTCCGGGTTTGCCC 0.473000 0 SO:0001583 missense ENST00000375820.4 0 1 hg19 CCDS9511.1 . . . . . . . . . . C 14.190000 2.460326 0.437360 . . ENSG00000187498 ENST00000375815;ENST00000375820;ENST00000397198;ENST00000543140 D;D 0.99353 -5.77;-5.77 4.61 4.61 0.57282 . 0.000000 0.85682 D 0.000000 D 0.99677 0.9879 H 0.98199 4.17 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 D 0.97186 0.9854 10 0.87932 D 0 . 17.8452 0.88728 0.0:1.0:0.0:0.0 . 290 P02462 CO4A1_HUMAN R 279;290;290;290 ENSP00000364979:G290R;ENSP00000443348:G290R ENSP00000364973:G279R G - 1 0 COL4A1 109655877 1 0.714170 1 0.803570 0.287000 0.271600 6.226000 0.722770 2.280000 0.763070 0.551000 6.891000e-01 GGA TCGA-IB-A5SO-01A-11D-A32N-08 COL4A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045759.3 0 0 0 9 596 0 148 0 9.952571e-01 0 629 0 148 2 0 0 0 0 0 2 1 0.993819 9 586 0 148 2 0 0 0 0 148 2 -2.185200 0 1 121412 1 31 1 1 2 3 2.119712 0 0.230000 1.870000 0.248157 0.140000 0.060000 1.000000 0.130000 0.280539 0.140000 0 0.090000 0.300000 DYNC1H1 1778 broad.mit.edu 37 14 102493761 102493761 + Silent SNP A A G rs8010870 byFrequency TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr14:102493761A>G ENST00000360184.4 + 46 9092 c.8928A>G c.(8926-8928)ctA>ctG p.L2976L NM_001376.4 NP_001367.2 Q14204 DYHC1_HUMAN dynein, cytoplasmic 1, heavy chain 1 166 ATGAAGATCTACGGACAGTGT 0.418000 0 SO:0001819 synonymous_variant ENST00000360184.4 1 0 hg19 CCDS9966.1 TCGA-IB-A5SO-01A-11D-A32N-08 DYNC1H1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414574.1 0 0 1 28 240 0 62 1 9.999934e-01 26 139 0 62 2 0 0 0 0 0 2 1 1.000000 27 237 0 62 2 0 0 0 0 62 2 -2.443248 0 1 121412 16837 76 1 1 2 3 2.063149 0 0.230000 1.870000 0.237888 0.930000 0.630000 1.000000 1.000000 0.902137 0.930000 1 0.770000 1.000000 EFS 10278 broad.mit.edu 37 14 23829227 23829227 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr14:23829227C>T ENST00000216733.3 - 4 1067 c.460G>A c.(460-462)Gcc>Acc p.A154T EFS_ENST00000351354.3_Missense_Mutation_p.A61T|EFS_ENST00000429593.2_Missense_Mutation_p.A61T NM_005864.2 NP_005855.1 O43281 EFS_HUMAN embryonal Fyn-associated substrate 16 all_cancers(95;7.12e-06) ACCCGGAGGGCGGTGGGGGGC 0.637000 0 SO:0001583 missense ENST00000216733.3 0 1 hg19 CCDS9595.1 . . . . . . . . . . C 16.740000 3.207479 0.583430 . . ENSG00000100842 ENST00000216733;ENST00000351354;ENST00000429593 T;T;T 0.57907 0.37;0.67;0.8 5.32 4.42 0.53409 . 0.471664 0.23237 N 0.050387 T 0.47377 0.1442 M 0.62723 1.935 0.332550 D 0.558962 P;P;P 0.52577 0.94;0.954;0.923 B;B;B 0.41619 0.259;0.361;0.198 T 0.60449 -0.7261 10 0.26408 T 0.33 -7.6625 10.4055 0.44254 0.0:0.907:0.0:0.093 . 61;61;154 B4DJ56;O43281-2;O43281 .;.;EFS_HUMAN T 154;61;61 ENSP00000216733:A154T;ENSP00000340607:A61T;ENSP00000416684:A61T ENSP00000216733:A154T A - 1 0 EFS 22899067 9.810000e-01 0.347290 9.030000e-01 0.355200 0.393000 0.305370 1.155000 0.317000 1.450000 0.477170 0.563000 7.788400e-01 GCC TCGA-IB-A5SO-01A-11D-A32N-08 EFS-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071770.2 0 0 0 5 345 0 102 0 1.256457e-01 0 35 0 102 2 0 0 0 0 0 2 1 0.936553 5 342 0 101 2 0 0 0 0 102 2 -3.035067 1 1 0 0 1 0 1 1 1.891540 1 0.230000 1.870000 0.165719 0.120000 0.040000 0.250000 0.110000 0.134837 0.120000 0 0.070000 0.190000 AKAP6 9472 broad.mit.edu 37 14 33290803 33290803 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr14:33290803G>A ENST00000280979.4 + 13 3954 c.3784G>A c.(3784-3786)Gac>Aac p.D1262N AKAP6_ENST00000557272.1_Intron NM_004274.4 NP_004265.3 Q13023 AKAP6_HUMAN A kinase (PRKA) anchor protein 6 122 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) CCCTGGTTATGACGAGGAGGC 0.448000 Melanoma(49;821 1200 7288 13647 42351) 0 SO:0001583 missense ENST00000280979.4 0 1 hg19 CCDS9644.1 . . . . . . . . . . G 13.870000 2.367025 0.419020 . . ENSG00000151320 ENST00000280979 T 0.05319 3.46 6.03 6.03 0.97812 . 0.414559 0.26828 N 0.022293 T 0.05273 0.0140 N 0.14661 0.345 0.807220 D 1.000000 B 0.32245 0.361 B 0.21360 0.034 T 0.45026 -0.9289 10 0.66056 D 0.02 -10.2954 18.7374 0.91761 0.0:0.0:1.0:0.0 . 1262 Q13023 AKAP6_HUMAN N 1262 ENSP00000280979:D1262N ENSP00000280979:D1262N D + 1 0 AKAP6 32360554 1 0.714170 1 0.803570 0.876000 0.504520 5.563000 0.673520 2.861000 0.982270 0.655000 9.425300e-01 GAC TCGA-IB-A5SO-01A-11D-A32N-08 AKAP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276617.2 0 0 0 5 192 0 38 0 1.055276e-03 0 2 0 38 2 0 0 0 0 0 2 1 0.937509 5 191 0 37 2 0 0 0 0 38 2 -6.859260 1 1 0 0 1 0 1 1 1.891540 1 0.230000 1.870000 0.165719 0.210000 0.080000 0.430000 0.200000 0.235827 0.210000 0 0.130000 0.320000 RTF1 23168 broad.mit.edu 37 15 41763442 41763442 + Silent SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr15:41763442G>A ENST00000389629.4 + 8 1110 c.1098G>A c.(1096-1098)cgG>cgA p.R366R NM_015138.4 NP_055953.3 Q92541 RTF1_HUMAN Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) p.R241R(1) 18 all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143) GATTATCACGGCATAAGCTAG 0.458000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000389629.4 0 1 hg19 CCDS32200.2 TCGA-IB-A5SO-01A-11D-A32N-08 RTF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258111.1 0 0 0 5 474 0 117 0 3.054074e-01 0 90 0 117 2 0 0 0 0 0 2 1 0.935401 5 467 0 116 2 0 0 0 0 117 2 -1.625385 0 1 0 0 1 1 2 3 2.072761 0 0.230000 1.870000 0.239619 0.100000 0.030000 1.000000 0.090000 0.188290 0.100000 0 0.060000 0.180000 SEMA6D 80031 broad.mit.edu 37 15 48063190 48063190 + Silent SNP G G A rs144939945 TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr15:48063190G>A ENST00000316364.5 + 19 2869 c.2430G>A c.(2428-2430)ccG>ccA p.P810P SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000358066.4_Silent_p.P748P|SEMA6D_ENST00000389428.3_Silent_p.P735P|SEMA6D_ENST00000389433.2_Silent_p.P791P|SEMA6D_ENST00000537942.1_Silent_p.P748P|SEMA6D_ENST00000389432.2_Silent_p.P767P|SEMA6D_ENST00000536845.2_Silent_p.P810P|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000558014.1_Silent_p.P748P|SEMA6D_ENST00000354744.4_Silent_p.P754P NM_153618.1 NP_705871.1 Q8NFY4 SEM6D_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D p.P748P(1)|p.P810P(1) 77 all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18) AGTTTTTTCCGTCTAGTCCGC 0.507000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000316364.5 1 1 hg19 CCDS32225.1 TCGA-IB-A5SO-01A-11D-A32N-08 SEMA6D-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416868.1 1 0 0 26 391 1 98 0 9.123163e-02 0 8 1 98 2 0 0 0 0 0 2 1 0.955465 25 387 1 94 16 0 0 0 1 98 2 -6.657005 1 1 121412 5 40 1 1 2 3 2.072761 0 0.230000 1.870000 0.239619 0.560000 0.370000 1.000000 0.550000 0.601943 0.560000 0 0.450000 0.720000 UNC13C 440279 broad.mit.edu 37 15 54916007 54916007 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr15:54916007G>A ENST00000260323.11 + 31 6214 c.6214G>A c.(6214-6216)Gac>Aac p.D2072N UNC13C_ENST00000537900.1_Missense_Mutation_p.D2070N|UNC13C_ENST00000539562.2_5'UTR|UNC13C_ENST00000545554.1_Missense_Mutation_p.D2072N NM_001080534.1 NP_001074003.1 Q8NB66 UN13C_HUMAN unc-13 homolog C (C. elegans) 121 TGCTATTAATGACCTAAACTG 0.368000 0 SO:0001583 missense ENST00000260323.11 1 1 hg19 CCDS45264.1 . . . . . . . . . . G 8.260000 0.811040 0.165370 . . ENSG00000137766 ENST00000260323;ENST00000545554;ENST00000537900 T;T;T 0.75367 -0.93;-0.93;-0.93 5.53 4.55 0.56014 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.344021 0.33419 N 0.004929 T 0.57227 0.2039 N 0.20357 0.565 0.342890 D 0.683087 B 0.06786 0.001 B 0.04013 0.001 T 0.59915 -0.7364 10 0.31617 T 0.26 . 9.1177 0.36769 0.2002:0.0:0.7998:0.0 . 2072 Q8NB66 UN13C_HUMAN N 2072;2072;2070 ENSP00000260323:D2072N;ENSP00000438156:D2072N;ENSP00000442569:D2070N ENSP00000260323:D2072N D + 1 0 UNC13C 52703299 1 0.714170 9.970000e-01 0.539660 0.333000 0.286660 4.974000 0.637710 1.196000 0.431290 0.563000 7.788400e-01 GAC TCGA-IB-A5SO-01A-11D-A32N-08 UNC13C-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000419028.3 1 0 0 11 89 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.998651 11 89 0 36 2 0 0 0 0 36 2 -17.842960 1 1 0 0 1 1 2 3 2.072761 0 0.230000 1.870000 0.239619 0.990000 0.540000 1.000000 1.000000 0.904033 0.990000 1 0.740000 1.000000 CCNB2 9133 broad.mit.edu 37 15 59409031 59409031 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr15:59409031G>A ENST00000288207.2 + 6 931 c.740G>A c.(739-741)cGa>cAa p.R247Q CCNB2_ENST00000559622.1_Missense_Mutation_p.R166Q NM_004701.3 NP_004692.1 O95067 CCNB2_HUMAN cyclin B2 9 TCCCAAATCCGAGAAATGGAA 0.413000 0 SO:0001583 missense ENST00000288207.2 0 1 hg19 CCDS10170.1 . . . . . . . . . . G 16.810000 3.225727 0.586680 . . ENSG00000157456 ENST00000288207 T 0.10960 2.82 5.28 4.35 0.52113 Cyclin, N-terminal (1);Cyclin-like (3); 0.118236 0.53938 D 0.000046 T 0.16727 0.0402 M 0.70842 2.15 0.525010 D 0.999952 P;P 0.43826 0.812;0.818 B;B 0.40782 0.163;0.34 T 0.02617 -1.1133 10 0.72032 D 0.01 . 14.4633 0.67467 0.0:0.0:0.8518:0.1482 . 247;247 Q53HG9;O95067 .;CCNB2_HUMAN Q 247 ENSP00000288207:R247Q ENSP00000288207:R247Q R + 2 0 CCNB2 57196323 1 0.714170 1 0.803570 0.997000 0.918780 4.381000 0.595870 1.318000 0.451700 0.650000 8.624300e-01 CGA TCGA-IB-A5SO-01A-11D-A32N-08 CCNB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256016.1 0 0 0 7 482 0 110 0 2.790772e-01 0 64 0 110 2 0 0 0 0 0 2 1 0.980325 8 478 0 109 2 0 0 0 0 110 2 -2.196000 0 1 0 0 1 1 2 3 2.072761 0 0.230000 1.870000 0.239619 0.130000 0.050000 1.000000 0.130000 0.218748 0.130000 0 0.090000 0.220000 EFTUD1 79631 broad.mit.edu 37 15 82530841 82530841 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr15:82530841G>A ENST00000268206.7 - 7 706 c.538C>T c.(538-540)Ctt>Ttt p.L180F EFTUD1_ENST00000359445.3_Missense_Mutation_p.L129F NM_024580.5 NP_078856.4 Q7Z2Z2 ETUD1_HUMAN elongation factor Tu GTP binding domain containing 1 32 GAAGTAAAAAGAGTCCCTGTG 0.453000 0 SO:0001583 missense ENST00000268206.7 0 1 hg19 CCDS42071.1 . . . . . . . . . . G 13.720000 2.320203 0.410960 . . ENSG00000140598 ENST00000268206;ENST00000359445 T;T 0.77229 -1.08;-1.08 4.49 4.49 0.54785 Protein synthesis factor, GTP-binding (1); 0.000000 0.47093 U 0.000251 T 0.81706 0.4879 L 0.38692 1.165 0.584320 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.83275 0.995;0.996 T 0.76184 -0.3052 10 0.13470 T 0.59 -0.0792 17.7897 0.88548 0.0:0.0:1.0:0.0 . 129;180 Q7Z2Z2-2;Q7Z2Z2 .;ETUD1_HUMAN F 180;129 ENSP00000268206:L180F;ENSP00000352418:L129F ENSP00000268206:L180F L - 1 0 EFTUD1 80317896 1 0.714170 1 0.803570 0.966000 0.646010 4.644000 0.613970 2.501000 0.843560 0.405000 2.747000e-01 CTT TCGA-IB-A5SO-01A-11D-A32N-08 EFTUD1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000419252.1 0 0 0 8 93 0 24 1 2.189100e-01 3 7 0 24 2 0 0 0 0 0 2 1 0.973788 8 70 0 24 2 0 0 0 0 24 2 -13.375620 1 1 0 0 1 1 2 3 2.072761 0 0.230000 1.870000 0.239619 0.740000 0.350000 1.000000 1.000000 0.748493 0.740000 0 0.520000 1.000000 MAPK8IP3 23162 broad.mit.edu 37 16 1814146 1814146 + Silent SNP C C A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr16:1814146C>A ENST00000250894.4 + 18 2210 c.2053C>A c.(2053-2055)Cgg>Agg p.R685R MAPK8IP3_ENST00000356010.5_Silent_p.R679R NM_015133.3 NP_055948.2 Q9UPT6 JIP3_HUMAN mitogen-activated protein kinase 8 interacting protein 3 42 GGAGGACACGCGGATGAAGAA 0.672000 0 SO:0001819 synonymous_variant ENST00000250894.4 0 1 hg19 CCDS10442.2 TCGA-IB-A5SO-01A-11D-A32N-08 MAPK8IP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250508.2 0 0 0 6 239 0 43 0 7.651603e-01 0 110 0 43 2 0 0 0 0 0 2 1 0.964167 6 236 0 42 2 0 0 0 0 43 2 -3.549492 1 1 0 0 1 0 1 1 2.030129 0 0.230000 1.870000 0.228225 0.220000 0.090000 0.430000 0.210000 0.242490 0.220000 0 0.140000 0.330000 PPL 5493 broad.mit.edu 37 16 4935121 4935121 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr16:4935121G>A ENST00000345988.2 - 22 3624 c.3535C>T c.(3535-3537)Cgg>Tgg p.R1179W PPL_ENST00000590782.2_Missense_Mutation_p.R1177W NM_002705.4 NP_002696 O60437 PEPL_HUMAN periplakin 62 GGGTCTGGCCGCACGATCTCC 0.627000 0 SO:0001583 missense ENST00000345988.2 0 1 hg19 CCDS10526.1 . . . . . . . . . . G 21.900000 4.222315 0.794640 . . ENSG00000118898 ENST00000345988 T 0.56941 0.43 5.65 5.65 0.86999 . 0.000000 0.85682 D 0.000000 T 0.74520 0.3727 M 0.73598 2.24 0.807220 D 1.000000 D 0.89917 1.0 D 0.91635 0.999 T 0.76473 -0.2946 10 0.87932 D 0 . 19.7311 0.96182 0.0:0.0:1.0:0.0 . 1179 O60437 PEPL_HUMAN W 1179 ENSP00000340510:R1179W ENSP00000340510:R1179W R - 1 2 PPL 4875122 1 0.714170 1 0.803570 0.771000 0.436740 5.493000 0.668990 2.677000 0.911610 0.561000 7.409900e-01 CGG TCGA-IB-A5SO-01A-11D-A32N-08 PPL-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251715.1 0 0 0 6 474 0 130 0 6.154226e-01 0 154 0 130 2 0 0 0 0 0 2 1 0.964034 6 469 0 129 2 0 0 0 0 130 2 -2.417411 0 1 0 0 1 0 1 1 2.030129 0 0.230000 1.870000 0.228225 0.110000 0.040000 0.220000 0.110000 0.125109 0.110000 0 0.070000 0.170000 NUTF2 10204 broad.mit.edu 37 16 67904796 67904796 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr16:67904796G>A ENST00000219169.4 + 5 647 c.364G>A c.(364-366)Gcc>Acc p.A122T NUTF2_ENST00000568396.2_Missense_Mutation_p.A122T|NUTF2_ENST00000569436.2_Missense_Mutation_p.A122T|EDC4_ENST00000358933.5_5'Flank NM_005796.1 NP_005787.1 P61970 NTF2_HUMAN nuclear transport factor 2 4 Ovarian(137;0.0563) GTTCAGGCTCGCCCTGCACAA 0.517000 0 SO:0001583 missense ENST00000219169.4 1 1 hg19 CCDS10848.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 20.700000 4.031459 0.755040 . . ENSG00000102898 ENST00000219169 . . . 5.35 5.35 0.76521 . 0.053987 0.64402 D 0.000001 T 0.61751 0.2372 M 0.82323 2.585 0.807220 D 1.000000 B 0.33583 0.418 B 0.18561 0.022 T 0.63712 -0.6575 9 0.14252 T 0.57 -33.3308 18.6568 0.91456 0.0:0.0:1.0:0.0 . 122 P61970 NTF2_HUMAN T 122 . ENSP00000219169:A122T A + 1 0 NUTF2 66462297 1 0.714170 1 0.803570 0.996000 0.888480 6.263000 0.725210 2.500000 0.843290 0.655000 9.425300e-01 GCC TCGA-IB-A5SO-01A-11D-A32N-08 NUTF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268871.1 1 0 1 13 241 0 64 1 9.999987e-01 79 449 0 64 2 0 0 0 0 0 2 1 0.999549 12 240 0 64 2 0 0 0 0 64 2 -4.479433 1 1 0 0 1 0 1 1 2.030129 0 0.230000 1.870000 0.228225 0.450000 0.250000 0.710000 0.430000 0.468146 0.450000 0 0.340000 0.580000 FOXC2 2303 broad.mit.edu 37 16 86601494 86601494 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr16:86601494G>A ENST00000320354.4 + 1 638 c.553G>A c.(553-555)Gag>Aag p.E185K RP11-463O9.5_ENST00000563280.1_RNA NM_005251.2 NP_005242.1 Q99958 FOXC2_HUMAN forkhead box C2 (MFH-1, mesenchyme forkhead 1) 15 CCACCTCAAGGAGCCGCCCCC 0.682000 Late-onset Hereditary Lymphedema 0 SO:0001583 missense Familial Cancer Database Hereditary Lymphedema type II, Meige Lymphedema ENST00000320354.4 0 1 hg19 CCDS10958.1 . . . . . . . . . . g 15.190000 2.758706 0.494680 . . ENSG00000176692 ENST00000320354 D 0.95001 -3.58 4.23 4.23 0.50019 . 1.447760 0.04727 U 0.420400 D 0.91935 0.7446 L 0.39898 1.24 0.480870 D 0.999582 B 0.11235 0.004 B 0.09377 0.004 T 0.70608 -0.4825 10 0.11182 T 0.66 . 15.2735 0.73723 0.0:0.0:1.0:0.0 . 185 Q99958 FOXC2_HUMAN K 185 ENSP00000326371:E185K ENSP00000326371:E185K E + 1 0 FOXC2 85158995 1 0.714170 1 0.803570 0.772000 0.437240 5.154000 0.648940 1.917000 0.555160 0.553000 6.901800e-01 GAG TCGA-IB-A5SO-01A-11D-A32N-08 FOXC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269104.2 0 0 0 5 232 0 52 0 1.005082e-02 0 6 0 52 2 0 0 0 0 0 2 1 0.936095 5 229 0 52 2 0 0 0 0 52 2 -6.701517 1 1 119448 1 27 1 0 1 1 2.030129 0 0.230000 1.870000 0.228225 0.190000 0.070000 0.400000 0.180000 0.214705 0.190000 0 0.120000 0.300000 MAPT 4137 broad.mit.edu 37 17 44060672 44060672 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr17:44060672C>T ENST00000571987.1 + 5 502 c.502C>T c.(502-504)Cgc>Tgc p.R168C MAPT_ENST00000431008.3_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.R168C|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.R168C|MAPT_ENST00000415613.2_Missense_Mutation_p.R168C P10636 TAU_HUMAN microtubule-associated protein tau 38 Melanoma(429;0.216) Docetaxel(DB01248)|Paclitaxel(DB01229) AGAGGCCACACGCCAACCTTC 0.692000 0 SO:0001583 missense ENST00000571987.1 0 1 hg19 CCDS11501.1 . . . . . . . . . . C 13.270000 2.188535 0.386090 . . ENSG00000186868 ENST00000344290;ENST00000262410;ENST00000415613 T;T;T 0.10382 2.88;2.88;2.88 4.03 -2.5 0.06384 . 2.448770 0.01389 N 0.013192 T 0.05777 0.0151 N 0.08118 0 0.093100 N 1.000000 B;B 0.11235 0.004;0.001 B;B 0.06405 0.002;0.0 T 0.37934 -0.9684 10 0.52906 T 0.07 4.9526 4.149 0.10228 0.0:0.3518:0.3326:0.3156 . 168;168 P10636-9;P10636 .;TAU_HUMAN C 168 ENSP00000340820:R168C;ENSP00000262410:R168C;ENSP00000410838:R168C ENSP00000262410:R168C R + 1 0 MAPT 41416509 0 0.058580 0 0.037020 0.427000 0.315640 -2.823000 0.007480 -0.148000 0.112340 0.561000 7.409900e-01 CGC TCGA-IB-A5SO-01A-11D-A32N-08 MAPT-008 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000440133.1 1 0 0 5 59 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 0.932078 5 56 0 16 2 0 0 0 0 16 2 -11.928930 1 1 121062 3 26 1 1 2 3 2.061943 0 0.230000 1.870000 0.237888 0.740000 0.290000 1.000000 1.000000 0.739722 0.740000 0 0.470000 1.000000 POLR2A 5430 broad.mit.edu 37 17 7405016 7405016 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr17:7405016G>A ENST00000322644.6 + 14 2716 c.2317G>A c.(2317-2319)Gga>Aga p.G773R NM_000937.4 NP_000928 P24928 RPB1_HUMAN polymerase (RNA) II (DNA directed) polypeptide A, 220kDa 50 Prostate(122;0.173) GGTCGTGTCCGGAGCTAAAGG 0.483000 0 SO:0001583 missense ENST00000322644.6 0 1 hg19 CCDS32548.1 . . . . . . . . . . G 28.800000 4.947770 0.925930 . . ENSG00000181222 ENST00000535204;ENST00000322644 D 0.97378 -4.36 5.82 5.82 0.92795 RNA polymerase Rpb1, domain 4 (1); 0.000000 0.85682 D 0.000000 D 0.99275 0.9747 H 0.99249 4.485 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 D 0.98602 1.0659 10 0.87932 D 0 -6.8597 18.8608 0.92271 0.0:0.0:1.0:0.0 . 773 P24928 RPB1_HUMAN R 729;773 ENSP00000314949:G773R ENSP00000314949:G773R G + 1 0 SLC35G6 7345740 1 0.714170 9.040000e-01 0.355700 0.986000 0.746190 9.627000 0.984120 2.761000 0.948540 0.655000 9.425300e-01 GGA TCGA-IB-A5SO-01A-11D-A32N-08 POLR2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437967.1 0 0 0 4 198 0 47 0 6.193507e-01 0 95 0 47 2 0 0 0 0 0 2 1 0.888876 4 196 0 46 2 0 0 0 0 47 2 -3.080377 1 1 0 0 1 0 1 1 1.883826 1 0.230000 1.870000 0.162588 0.170000 0.050000 0.370000 0.160000 0.190999 0.170000 0 0.100000 0.270000 PRPSAP1 5635 broad.mit.edu 37 17 74309083 74309083 + Silent SNP G G A rs148092431 TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr17:74309083G>A ENST00000446526.3 - 9 1312 c.867C>T c.(865-867)gaC>gaT p.D289D PRPSAP1_ENST00000588364.1_5'UTR|PRPSAP1_ENST00000324684.4_Silent_p.D186D NM_002766.2 NP_002757.2 Q14558 KPRA_HUMAN phosphoribosyl pyrophosphate synthetase-associated protein 1 17 TCTCCACATCGTCAATAATGT 0.512000 0 SO:0001819 synonymous_variant ENST00000446526.3 1 1 hg19 CCDS11743.2 TCGA-IB-A5SO-01A-11D-A32N-08 PRPSAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342480.2 1 0 0 38 348 0 99 1 9.999305e-01 31 102 0 99 2 0 0 0 0 0 2 1 1.000000 37 344 0 97 2 0 0 0 0 99 2 -12.917470 1 1 121412 26 47 1 1 2 3 2.061943 0 0.230000 1.870000 0.237888 0.870000 0.630000 1.000000 1.000000 0.871956 0.870000 1 0.740000 1.000000 TP53 7157 broad.mit.edu 37 17 7578263 7578263 + Nonsense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr17:7578263G>A ENST00000269305.4 - 6 775 c.586C>T c.(586-588)Cga>Tga p.R196* TP53_ENST00000445888.2_Nonsense_Mutation_p.R196*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.R196*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R196*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R196*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R196* 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.R196*(167)|p.R64*(14)|p.R103*(14)|p.0?(8)|p.R196fs*51(7)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.R196R(2)|p.I195fs*50(1)|p.R64fs*>27(1)|p.R103fs*51(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.I195fs*12(1)|p.P59_E66>Q(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CCTTCCACTCGGATAAGATGC 0.552000 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 232 Substitution - Nonsense(195)|Deletion - Frameshift(11)|Whole gene deletion(8)|Deletion - In frame(5)|Complex - deletion inframe(5)|Unknown(5)|Substitution - coding silent(2)|Complex - frameshift(1) GRCh37 CM941329 TP53 M SO:0001587 stop_gained 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 0 1 hg19 CCDS11118.1 . . . . . . . . . . G 14.020000 2.409843 0.427150 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 . . . 5.41 4.44 0.53790 . 0.000000 0.85682 D 0.000000 . . . . . . 0.807220 A 1.000000 . . . . . . . . . . 0.02654 T 1 -19.9531 12.3046 0.54895 0.0827:0.0:0.9173:0.0 . . . . X 196;196;196;196;196;196;185;103;64;103;64 . ENSP00000269305:R196X R - 1 2 TP53 7518988 1 0.714170 9.970000e-01 0.539660 0.023000 0.107830 2.166000 0.424060 1.427000 0.472760 -0.140000 1.422600e-01 CGA TCGA-IB-A5SO-01A-11D-A32N-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 15 173 0 47 1 9.642332e-01 5 62 0 47 2 1 1 138 1197 0 959 2 1 0.999889 15 172 0 46 2 0 0 0 0 47 2 -2.806926 1 1 121412 1 40 1 0 1 1 1.883826 1 0.230000 1.870000 0.162588 0.630000 0.370000 0.960000 0.630000 0.653231 0.630000 0 0.490000 0.800000 DNAH17 8632 broad.mit.edu 37 17 76455199 76455199 + Missense_Mutation SNP C C T rs139080560 byFrequency TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr17:76455199C>T ENST00000585328.1 - 61 9854 c.9730G>A c.(9730-9732)Gtc>Atc p.V3244I DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Missense_Mutation_p.V3235I NM_173628.3 NP_775899.3 Q9UFH2 DYH17_HUMAN dynein, axonemal, heavy chain 17 116 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) TAGAAGCGGACGATGTTGATG 0.637000 0 SO:0001583 missense ENST00000585328.1 1 1 hg19 5 0.0022893772893772895 5 0.01016260162601626 0 0.0 0 0.0 0 0.0 C 14.200000 2.464303 0.437360 0.011802 0.0 ENSG00000187775 ENST00000300671;ENST00000389840 T 0.79141 -1.24 5.35 5.35 0.76521 . 0.000000 0.56097 D 0.000022 T 0.58452 0.2123 L 0.35487 1.065 0.337270 D 0.617749 P 0.35481 0.504 B 0.29716 0.106 T 0.67601 -0.5629 10 0.09590 T 0.72 . 18.6873 0.91570 0.0:1.0:0.0:0.0 . 3244 E7EUM8 . I 3244;3235 ENSP00000374490:V3235I ENSP00000300671:V3244I V - 1 0 DNAH17 73966794 9.980000e-01 0.408360 9.910000e-01 0.477400 0.991000 0.796840 3.678000 0.546270 2.491000 0.840630 0.655000 9.425300e-01 GTC TCGA-IB-A5SO-01A-11D-A32N-08 DNAH17-001 PUTATIVE not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000318962.2 0 0 0 78 857 1 257 0 0 0 1 1 257 2 0 0 0 0 0 2 1 1.000000 78 847 1 252 14 0 0 0 1 257 2 -17.904050 1 0 121406 130 58 1 1 2 3 2.061943 0 0.230000 1.870000 0.237888 0.730000 0.580000 1.000000 0.730000 0.757204 0.730000 0 0.650000 0.850000 FCGBP 8857 broad.mit.edu 37 19 40433869 40433869 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr19:40433869G>A ENST00000221347.6 - 2 407 c.400C>T c.(400-402)Cgg>Tgg p.R134W NM_003890.2 NP_003881.2 Q9Y6R7 FCGBP_HUMAN Fc fragment of IgG binding protein 165 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) TGGATGGGCCGCAGCAGTGTC 0.597000 0 SO:0001583 missense ENST00000221347.6 0 1 hg19 CCDS12546.1 . . . . . . . . . . G 6.404000 0.442631 0.121640 . . ENSG00000090920 ENST00000221347 T 0.18338 2.22 4.13 -8.27 0.01017 . 0.899723 0.09194 N 0.835531 T 0.04137 0.0115 N 0.00926 -1.1 0.093100 N 1.000000 B 0.12630 0.006 B 0.04013 0.001 T 0.45991 -0.9223 10 0.37606 T 0.19 . 8.3971 0.32564 0.6469:0.0:0.1439:0.2092 . 134 Q9Y6R7 FCGBP_HUMAN W 134 ENSP00000221347:R134W ENSP00000221347:R134W R - 1 2 FCGBP 45125709 0 0.058580 0 0.037020 0.294000 0.273930 -0.060000 0.117120 -1.660000 0.014860 0.655000 9.425300e-01 CGG TCGA-IB-A5SO-01A-11D-A32N-08 FCGBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462507.1 0 0 0 4 191 0 60 0 0 0 1 0 60 2 0 0 0 0 0 2 1 0.888803 4 189 0 59 2 0 0 0 0 60 2 -3.486999 1 1 121412 12 40 1 1 2 3 2.086413 0 0.230000 1.870000 0.242201 0.210000 0.060000 1.000000 0.180000 0.307651 0.210000 0 0.120000 0.400000 PSG7 5676 broad.mit.edu 37 19 43441294 43441294 + RNA SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr19:43441294C>T ENST00000406070.2 - 0 31 PSG7_ENST00000471557.1_RNA|PSG7_ENST00000446844.3_RNA NM_002783.2 NP_002774.2 Q13046 PSG7_HUMAN pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene) Prostate(69;0.00682) TTCCTGAGCACGGCTGTCAGC 0.617000 0 ENST00000406070.2 0 1 hg19 TCGA-IB-A5SO-01A-11D-A32N-08 PSG7-001 KNOWN basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000321431.2 0 0 0 25 181 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 25 179 0 55 2 0 0 0 0 55 2 -6.057421 1 1 0 0 1 1 2 3 2.086413 0 0.230000 1.870000 0.242201 0.990000 0.730000 1.000000 1.000000 0.963390 0.990000 1 0.890000 1.000000 TMEM143 55260 broad.mit.edu 37 19 48837419 48837419 + Missense_Mutation SNP C C G TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr19:48837419C>G ENST00000293261.3 - 7 1327 c.1011G>C c.(1009-1011)gaG>gaC p.E337D TMEM143_ENST00000541566.1_Missense_Mutation_p.E227D|TMEM143_ENST00000436660.2_Missense_Mutation_p.E272D|TMEM143_ENST00000377431.2_Missense_Mutation_p.E237D|TMEM143_ENST00000435956.3_Missense_Mutation_p.E302D NM_018273.2 NP_060743.2 Q96AN5 TM143_HUMAN transmembrane protein 143 14 all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113) TGTGCGCCAGCTCCAACGCCT 0.701000 OREG0025605 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000293261.3 0 1 hg19 CCDS12716.1 . . . . . . . . . . C 11.210000 1.571313 0.280030 . . ENSG00000161558 ENST00000293261;ENST00000377431;ENST00000435956;ENST00000436660;ENST00000541566 T;T;T 0.50548 0.74;0.76;0.75 4.02 1.82 0.25136 . 0.104192 0.39274 N 0.001413 T 0.33294 0.0858 L 0.47716 1.5 0.276860 N 0.946273 B;B;B;B 0.15930 0.015;0.0;0.004;0.001 B;B;B;B 0.17979 0.02;0.002;0.015;0.004 T 0.17745 -1.0359 10 0.18710 T 0.47 -14.1542 5.1988 0.15252 0.0:0.6356:0.1716:0.1929 . 272;237;302;337 B4DPF8;Q96AN5-2;B4DMT0;Q96AN5 .;.;.;TM143_HUMAN D 337;237;302;272;227 ENSP00000293261:E337D;ENSP00000397038:E302D;ENSP00000444275:E227D ENSP00000293261:E337D E - 3 2 TMEM143 53529231 1 0.714170 1 0.803570 0.273000 0.266830 0.755000 0.264050 0.299000 0.226610 0.313000 2.088700e-01 GAG TCGA-IB-A5SO-01A-11D-A32N-08 TMEM143-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465622.1 1 0 1 8 61 0 17 1 6.245019e-01 5 12 0 17 2 0 0 0 0 0 2 1 0.990252 8 60 0 17 2 0 0 0 0 17 2 -14.738920 1 1 0 0 1 1 2 3 2.086413 0 0.230000 1.870000 0.242201 0.990000 0.510000 1.000000 1.000000 0.914492 0.990000 1 0.760000 1.000000 PSMB4 5692 broad.mit.edu 37 1 151372521 151372521 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr1:151372521G>A ENST00000290541.6 + 2 259 c.205G>A c.(205-207)Gca>Aca p.A69T NM_002796.2 NP_002787.2 P28070 PSB4_HUMAN proteasome (prosome, macropain) subunit, beta type, 4 14 Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) GGTGATTGCCGCAGACATGCT 0.582000 0 SO:0001583 missense ENST00000290541.6 0 1 hg19 CCDS996.1 . . . . . . . . . . G 37.000000 6.114497 0.972960 . . ENSG00000159377 ENST00000290541 T 0.41758 0.99 5.34 5.34 0.76211 Proteasome, beta-type subunit, conserved site (1); 0.000000 0.85682 D 0.000000 T 0.56630 0.1998 M 0.66378 2.025 0.807220 D 1.000000 D;D 0.89917 1.0;0.999 D;P 0.70487 0.969;0.846 T 0.59899 -0.7367 10 0.66056 D 0.02 -10.9451 17.6208 0.88080 0.0:0.0:1.0:0.0 . 69;69 B4DFL3;P28070 .;PSB4_HUMAN T 69 ENSP00000290541:A69T ENSP00000290541:A69T A + 1 0 PSMB4 149639145 1 0.714170 8.810000e-01 0.345550 0.995000 0.863560 9.355000 0.970870 2.502000 0.843850 0.561000 7.409900e-01 GCA TCGA-IB-A5SO-01A-11D-A32N-08 PSMB4-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034885.1 0 0 0 5 527 0 120 0 9.928319e-01 0 1049 0 120 2 0 0 0 0 0 2 1 0.936566 5 523 0 120 2 0 0 0 0 120 2 -2.160619 0 1 0 0 1 0 0 0 1.976688 0 0.230000 1.870000 0.206267 0.080000 0.020000 0.170000 0.080000 0.094100 0.080000 0 0.050000 0.130000 CSMD2 114784 broad.mit.edu 37 1 34011733 34011733 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr1:34011733G>A ENST00000373381.4 - 57 9180 c.9004C>T c.(9004-9006)Cgc>Tgc p.R3002C NM_001281956.1|NM_052896.3 NP_001268885.1|NP_443128.2 Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) CAGCTGAAGCGCATCACAGTG 0.612000 0 SO:0001583 missense ENST00000373381.4 1 1 hg19 . . . . . . . . . . G 19.580000 3.854909 0.717190 . . ENSG00000121904 ENST00000373381 T 0.66815 -0.23 4.97 4.97 0.65823 Complement control module (2);Sushi/SCR/CCP (3); 0.213233 0.38217 N 0.001762 D 0.84005 0.5377 M 0.93678 3.445 0.807220 D 1.000000 D;D 0.76494 0.994;0.999 P;D 0.70487 0.832;0.969 D 0.85887 0.1426 10 0.48119 T 0.1 . 10.9638 0.47399 0.0:0.0:0.7096:0.2904 . 2858;3002 Q7Z408;E7EUA6 CSMD2_HUMAN;. C 3002 ENSP00000362479:R3002C ENSP00000241312:R2858C R - 1 0 CSMD2 33784320 1 0.714170 9.950000e-01 0.509660 0.865000 0.495280 3.711000 0.548680 2.591000 0.875370 0.650000 8.624300e-01 CGC TCGA-IB-A5SO-01A-11D-A32N-08 CSMD2-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 0 21 192 0 64 1 1.210693e-01 2 4 0 64 2 0 0 0 0 0 2 1 0.999998 21 189 0 64 2 0 0 0 0 64 2 -3.318813 1 1 0 0 1 0 0 0 1.989740 0 0.230000 1.870000 0.211873 0.830000 0.540000 1.000000 1.000000 0.833104 0.830000 0 0.670000 1.000000 SSBP3 23648 broad.mit.edu 37 1 54708959 54708959 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr1:54708959C>T ENST00000371320.3 - 10 1075 c.665G>A c.(664-666)gGc>gAc p.G222D SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000357475.4_Missense_Mutation_p.G202D|SSBP3_ENST00000371319.3_Missense_Mutation_p.G195D|SSBP3_ENST00000417664.2_Missense_Mutation_p.G112D NM_145716.2 NP_663768.1 Q9BWW4 SSBP3_HUMAN single stranded DNA binding protein 3 11 TGGTCTCATGCCGCTGCCGTA 0.562000 0 SO:0001583 missense ENST00000371320.3 0 1 hg19 CCDS591.1 . . . . . . . . . . c 25.800000 4.676502 0.884450 . . ENSG00000157216 ENST00000417664;ENST00000371320;ENST00000371319;ENST00000357475;ENST00000444533;ENST00000525990 . . . 3.94 3.94 0.45596 . 0.000000 0.85682 U 0.000000 T 0.78717 0.4327 M 0.75085 2.285 0.807220 D 1.000000 D;P;P 0.89917 1.0;0.951;0.866 D;P;P 0.97110 1.0;0.743;0.686 T 0.81534 -0.0889 9 0.59425 D 0.04 -1.6526 17.3039 0.87189 0.0:1.0:0.0:0.0 . 195;202;222 Q9BWW4-2;Q9BWW4-3;Q9BWW4 .;.;SSBP3_HUMAN D 112;222;195;202;53;85 . ENSP00000350067:G202D G - 2 0 SSBP3 54481547 1 0.714170 1 0.803570 0.995000 0.863560 6.969000 0.760920 2.493000 0.841230 0.479000 4.491300e-01 GGC TCGA-IB-A5SO-01A-11D-A32N-08 SSBP3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000022721.1 0 0 0 7 930 0 315 0 5.130608e-01 0 211 0 315 2 0 0 0 0 0 2 1 0.979464 7 915 0 311 2 0 0 0 0 315 2 -1.721604 0 1 0 0 1 0 0 0 1.989740 0 0.230000 1.870000 0.211873 0.060000 0.020000 0.130000 0.070000 0.072092 0.060000 0 0.040000 0.100000 WLS 79971 broad.mit.edu 37 1 68615942 68615942 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr1:68615942C>T ENST00000262348.4 - 6 1154 c.901G>A c.(901-903)Gac>Aac p.D301N GNG12-AS1_ENST00000413628.1_RNA|WLS_ENST00000370976.3_Missense_Mutation_p.D210N|WLS_ENST00000354777.2_Missense_Mutation_p.D299N|WLS_ENST00000491811.1_5'UTR|GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000540432.1_Missense_Mutation_p.D301N NM_024911.6 NP_079187.3 Q5T9L3 WLS_HUMAN wntless Wnt ligand secretion mediator 20 TGTCGGATGTCACCAAACAGC 0.512000 0 SO:0001583 missense ENST00000262348.4 1 1 hg19 CCDS642.1 . . . . . . . . . . C 34.000000 5.309247 0.956290 . . ENSG00000116729 ENST00000540432;ENST00000354777;ENST00000262348;ENST00000370976 T;T;T;T 0.47528 0.84;0.84;0.84;0.84 4.85 4.85 0.62838 . 0.000000 0.85682 D 0.000000 T 0.64627 0.2615 M 0.76838 2.35 0.807220 D 1.000000 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;1.0;1.0;1.0 T 0.68032 -0.5516 10 0.51188 T 0.08 -33.6655 18.0034 0.89203 0.0:1.0:0.0:0.0 . 301;210;301;299 F5H4K0;Q5JRS7;Q5T9L3;Q5T9L3-2 .;.;WLS_HUMAN;. N 301;299;301;210 ENSP00000446112:D301N;ENSP00000346829:D299N;ENSP00000262348:D301N;ENSP00000360015:D210N ENSP00000262348:D301N D - 1 0 WLS 68388530 1 0.714170 9.530000e-01 0.391690 0.943000 0.588930 7.298000 0.788150 2.248000 0.741660 0.563000 7.788400e-01 GAC TCGA-IB-A5SO-01A-11D-A32N-08 WLS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025368.1 1 0 1 47 383 0 107 1 1 31 188 0 107 2 0 0 0 0 0 2 1 1.000000 47 376 0 104 2 0 0 0 0 107 2 -16.639770 1 1 0 0 1 0 0 0 1.989740 0 0.230000 1.870000 0.211873 0.920000 0.690000 1.000000 1.000000 0.910024 0.920000 1 0.800000 1.000000 TGM6 343641 broad.mit.edu 37 20 2397961 2397961 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr20:2397961C>T ENST00000202625.2 + 10 1481 c.1420C>T c.(1420-1422)Cgc>Tgc p.R474C TGM6_ENST00000381423.1_Missense_Mutation_p.R474C NM_198994.2 NP_945345.2 O95932 TGM3L_HUMAN transglutaminase 6 52 L-Glutamine(DB00130) AATCTGGATCCGCAGGGCTGG 0.622000 0 SO:0001583 missense ENST00000202625.2 0 1 hg19 CCDS13025.1 . . . . . . . . . . C 14.460000 2.542366 0.452800 . . ENSG00000166948 ENST00000202625;ENST00000381423 T;T 0.80909 -1.27;-1.43 4.54 4.54 0.55810 . 0.768164 0.11873 N 0.521286 D 0.82527 0.5056 L 0.47716 1.5 0.318040 N 0.628010 D;D 0.69078 0.997;0.991 P;B 0.53861 0.736;0.332 T 0.82133 -0.0608 10 0.56958 D 0.05 -9.2741 12.6614 0.56815 0.0:1.0:0.0:0.0 . 474;474 O95932-2;O95932 .;TGM3L_HUMAN C 474 ENSP00000202625:R474C;ENSP00000370831:R474C ENSP00000202625:R474C R + 1 0 TGM6 2345961 1.870000e-01 0.232380 1.230000e-01 0.217940 0.315000 0.280870 4.094000 0.577210 2.368000 0.804030 0.563000 7.788400e-01 CGC TCGA-IB-A5SO-01A-11D-A32N-08 TGM6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077581.2 1 0 0 6 82 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.965514 6 81 0 23 2 0 0 0 0 23 2 -10.554140 1 1 121412 3 27 1 0 0 0 1.986965 0 0.230000 1.870000 0.211873 0.600000 0.250000 1.000000 1.000000 0.623929 0.600000 0 0.400000 0.850000 GNAS 2778 broad.mit.edu 37 20 57484421 57484421 + Missense_Mutation SNP G G A rs121913495 TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr20:57484421G>A ENST00000371085.3 + 8 1026 c.602G>A c.(601-603)cGt>cAt p.R201H GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186H|GNAS_ENST00000371102.4_Missense_Mutation_p.R830H|GNAS_ENST00000354359.7_Missense_Mutation_p.R202H|GNAS_ENST00000371095.3_Missense_Mutation_p.R187H|GNAS_ENST00000306090.10_Missense_Mutation_p.R187H|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844H NM_000516.4 NP_000507.1 P63092 GNAS2_HUMAN GNAS complex locus p.R201H(81)|p.R844H(4)|p.R201L(2)|p.R844L(1) 441 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CTTCGCTGCCGTGTCCTGACT 0.423000 Mis pituitary adenoma McCune-Albright syndrome; pseudohypoparathyroidism, type IA TSP Lung(22;0.16) Colon(117;935 1597 6045 8307 46442) Dom yes 20 20q13.2 2778 guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1 yes E 88 Substitution - Missense(88) SO:0001583 missense ENST00000371085.3 1 1 hg19 CCDS13472.1 . . . . . . . . . . G 35.000000 5.430570 0.961500 . . ENSG00000087460 ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090 D;D;D;D;D;D;D 0.99458 -5.93;-5.93;-5.93;-5.93;-5.93;-2.96;-5.93 5.53 5.53 0.82687 G protein alpha subunit, helical insertion (2); 0.000000 0.85682 D 0.000000 D 0.99799 0.9914 H 0.98965 4.385 0.807220 D 1.000000 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.997;0.994;0.983;1.0 D 0.96812 0.9597 10 0.87932 D 0 . 19.4606 0.94915 0.0:0.0:1.0:0.0 . 201;202;186;844 P63092;A6NI00;P63092-3;Q5JWF2 GNAS2_HUMAN;.;.;GNAS1_HUMAN H 844;830;187;201;202;186;187 ENSP00000360141:R844H;ENSP00000360143:R830H;ENSP00000360136:R187H;ENSP00000360126:R201H;ENSP00000346328:R202H;ENSP00000265620:R186H;ENSP00000304472:R187H ENSP00000265620:R186H R + 2 0 GNAS 56917816 1 0.714170 9.630000e-01 0.404240 0.936000 0.576290 9.291000 0.960700 2.596000 0.877370 0.563000 7.788400e-01 CGT TCGA-IB-A5SO-01A-11D-A32N-08 GNAS-015 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000080431.2 0 0 0 5 210 0 47 1 1 88 4606 0 47 2 1 9.209650e-01 14 633 1 387 8 1 0.937507 5 209 0 47 2 0 0 0 0 47 2 -2.856930 1 1 121412 10 32 1 0 0 0 1.986965 0 0.230000 1.870000 0.211873 0.210000 0.070000 0.420000 0.200000 0.230858 0.210000 0 0.130000 0.320000 OPRL1 4987 broad.mit.edu 37 20 62729805 62729805 + Silent SNP C C A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr20:62729805C>A ENST00000349451.3 + 6 1178 c.766C>A c.(766-768)Cgg>Agg p.R256R OPRL1_ENST00000355631.4_Silent_p.R256R|OPRL1_ENST00000336866.2_Silent_p.R256R NM_001200019.1 NP_001186948.1 P41146 OPRX_HUMAN opiate receptor-like 1 19 all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08) AGAGAAGGACCGGAACCTGCG 0.657000 0 SO:0001819 synonymous_variant ENST00000349451.3 1 1 hg19 CCDS13556.1 TCGA-IB-A5SO-01A-11D-A32N-08 OPRL1-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080295.1 0 0 0 9 387 0 100 0 9.588831e-03 0 6 0 100 2 0 0 0 0 0 2 1 0.993412 9 374 0 92 2 0 0 0 0 100 2 -2.942797 1 1 0 0 1 0 0 0 1.986965 0 0.230000 1.870000 0.211873 0.190000 0.090000 0.350000 0.190000 0.211459 0.190000 0 0.140000 0.270000 HLCS 3141 broad.mit.edu 37 21 38269180 38269180 + Silent SNP T T C TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr21:38269180T>C ENST00000399120.1 - 7 2661 c.1431A>G c.(1429-1431)acA>acG p.T477T HLCS_ENST00000482273.1_5'UTR|HLCS_ENST00000336648.4_Silent_p.T477T NM_001242784.1 NP_001229713.1 P50747 BPL1_HUMAN holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase) 24 Myeloproliferative disorder(46;0.0422) Biotin(DB00121) GACGCATCGTTGTGGGGGTCA 0.493000 0 SO:0001819 synonymous_variant ENST00000399120.1 1 1 hg19 CCDS13647.1 TCGA-IB-A5SO-01A-11D-A32N-08 HLCS-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000194687.2 1 0 0 16 190 0 41 1 7.552221e-01 8 26 0 41 2 0 0 0 0 0 2 1 0.999942 16 189 0 41 2 0 0 0 0 41 2 -19.986980 1 1 0 0 1 1 2 3 2.057065 0 0.230000 1.870000 0.237019 0.700000 0.410000 1.000000 1.000000 0.721233 0.700000 0 0.540000 0.920000 POFUT2 23275 broad.mit.edu 37 21 46705777 46705777 + Silent SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr21:46705777G>A ENST00000349485.5 - 2 224 c.198C>T c.(196-198)atC>atT p.I66I BX322557.10_ENST00000454115.2_RNA|POFUT2_ENST00000471540.1_5'Flank|POFUT2_ENST00000331343.7_Silent_p.I66I NM_133635.4 NP_598368.2 Q9Y2G5 OFUT2_HUMAN protein O-fucosyltransferase 2 20 GGAGAGAGGCGATTCGGATAT 0.572000 0 SO:0001819 synonymous_variant ENST00000349485.5 0 1 hg19 CCDS13719.1 TCGA-IB-A5SO-01A-11D-A32N-08 POFUT2-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192573.2 0 0 0 5 515 0 114 0 1.805907e-01 0 66 0 114 2 0 0 0 0 0 2 1 0.933907 5 503 0 113 2 0 0 0 0 114 2 -2.865559 1 1 121412 6 40 1 1 2 3 2.057065 0 0.230000 1.870000 0.237019 0.090000 0.020000 1.000000 0.080000 0.158133 0.090000 0 0.050000 0.150000 RFTN2 130132 broad.mit.edu 37 2 198498522 198498522 + Missense_Mutation SNP T T C TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr2:198498522T>C ENST00000295049.4 - 4 1174 c.638A>G c.(637-639)gAa>gGa p.E213G NM_144629.2 NP_653230.2 Q52LD8 RFTN2_HUMAN raftlin family member 2 30 ATGAAGTTCTTCCTCAATTCC 0.408000 0 SO:0001583 missense ENST00000295049.4 1 1 hg19 CCDS2323.1 . . . . . . . . . . T 17.430000 3.387682 0.619560 . . ENSG00000162944 ENST00000295049 T 0.33865 1.39 5.27 2.9 0.33743 . 2.309500 0.01453 N 0.015562 T 0.39462 0.1079 L 0.57536 1.79 0.346980 D 0.726430 B 0.17268 0.021 B 0.15484 0.013 T 0.33548 -0.9864 10 0.48119 T 0.1 -12.8873 8.1485 0.31126 0.0:0.1588:0.0:0.8412 . 213 Q52LD8 RFTN2_HUMAN G 213 ENSP00000295049:E213G ENSP00000295049:E213G E - 2 0 RFTN2 198206767 1 0.714170 4.310000e-01 0.267350 0.956000 0.617450 2.615000 0.463680 0.945000 0.376050 0.533000 6.212000e-01 GAA TCGA-IB-A5SO-01A-11D-A32N-08 RFTN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256106.2 1 0 0 27 316 0 119 0 2.536066e-01 1 11 0 119 2 0 0 0 0 0 2 1 1.000000 26 313 0 119 2 0 0 0 0 119 2 -8.915772 1 1 121410 1 32 1 0 0 0 1.986160 0 0.230000 1.870000 0.210013 0.660000 0.450000 0.920000 0.660000 0.679870 0.660000 0 0.550000 0.800000 CLK1 1195 broad.mit.edu 37 2 201724929 201724929 + Silent SNP G G T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr2:201724929G>T ENST00000321356.4 - 4 535 c.400C>A c.(400-402)Cga>Aga p.R134R CLK1_ENST00000409769.2_5'Flank|CLK1_ENST00000434813.2_Silent_p.R176R|CLK1_ENST00000492793.1_5'Flank|Y_RNA_ENST00000516950.1_RNA NM_004071.3 NP_004062.2 P49759 CLK1_HUMAN CDC-like kinase 1 33 CTTTTCCTTCGGTGACTCTTC 0.463000 0 SO:0001819 synonymous_variant ENST00000321356.4 0 1 hg19 CCDS2331.1 TCGA-IB-A5SO-01A-11D-A32N-08 CLK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256192.2 0 0 0 5 331 0 87 1 9.518986e-01 8 360 0 87 2 0 0 0 0 0 2 1 0.937010 5 329 0 87 2 0 0 0 0 87 2 -2.072577 0 1 0 0 1 0 0 0 1.986160 0 0.230000 1.870000 0.210013 0.130000 0.040000 0.270000 0.130000 0.148776 0.130000 0 0.080000 0.200000 ABCA12 26154 broad.mit.edu 37 2 215807679 215807679 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr2:215807679C>T ENST00000272895.7 - 50 7625 c.7406G>A c.(7405-7407)tGt>tAt p.C2469Y AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.C2151Y NM_173076.2 NP_775099.2 Q86UK0 ABCAC_HUMAN ATP-binding cassette, sub-family A (ABC1), member 12 139 Renal(323;0.127) AGATCCAATACATTGAAACTT 0.393000 Ovarian(66;664 1488 5121 34295) 0 SO:0001583 missense ENST00000272895.7 0 1 hg19 CCDS33372.1 . . . . . . . . . . C 26.200000 4.711011 0.891120 . . ENSG00000144452 ENST00000272895;ENST00000389661 D;D 0.97870 -4.58;-4.58 5.65 5.65 0.86999 ABC transporter-like (1); 0.000000 0.85682 D 0.000000 D 0.98406 0.9470 L 0.58969 1.84 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.97110 0.998;1.0 D 0.99529 1.0960 10 0.87932 D 0 . 19.6795 0.95957 0.0:1.0:0.0:0.0 . 2469;2151 Q86UK0;Q86UK0-2 ABCAC_HUMAN;. Y 2469;2151 ENSP00000272895:C2469Y;ENSP00000374312:C2151Y ENSP00000272895:C2469Y C - 2 0 ABCA12 215515924 1 0.714170 9.870000e-01 0.457990 0.971000 0.663760 7.521000 0.818320 2.821000 0.970950 0.650000 8.624300e-01 TGT TCGA-IB-A5SO-01A-11D-A32N-08 ABCA12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000337111.1 0 0 0 4 156 0 39 0 4.084699e-02 0 10 0 39 2 0 0 0 0 0 2 1 0.888400 4 154 0 39 2 0 0 0 0 39 2 -6.383204 1 1 121390 1 26 1 0 0 0 1.986160 0 0.230000 1.870000 0.210013 0.230000 0.070000 0.490000 0.210000 0.255481 0.230000 0 0.140000 0.360000 DNMT3A 1788 broad.mit.edu 37 2 25505560 25505560 + Silent SNP T T C TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr2:25505560T>C ENST00000264709.3 - 4 535 c.198A>G c.(196-198)ccA>ccG p.P66P DNMT3A_ENST00000406659.3_Silent_p.P66P|DNMT3A_ENST00000321117.5_Silent_p.P66P NM_175629.2 NP_783328.1 Q9Y6K1 DNM3A_HUMAN DNA (cytosine-5-)-methyltransferase 3 alpha 1021 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CAGGGTCCTTTGGCGTGTCAC 0.542000 Mis, F, N, S AML Rec yes 2 2p23 1788 DNA (cytosine-5-)-methyltransferase 3 alpha L 0 SO:0001819 synonymous_variant ENST00000264709.3 1 1 hg19 CCDS33157.1 TCGA-IB-A5SO-01A-11D-A32N-08 DNMT3A-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000211587.1 1 0 0 14 289 0 85 0 2.046271e-01 0 17 0 85 2 0 0 0 0 0 2 1 0.999761 14 287 0 85 2 0 0 0 0 85 2 -15.864010 1 1 0 0 1 0 0 0 1.986160 0 0.230000 1.870000 0.210013 0.390000 0.220000 0.620000 0.390000 0.411677 0.390000 0 0.300000 0.510000 GPR128 84873 broad.mit.edu 37 3 100365497 100365497 + Nonsense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr3:100365497C>T ENST00000273352.3 + 10 1463 c.1195C>T c.(1195-1197)Caa>Taa p.Q399* SNORA31_ENST00000517180.1_RNA|GPR128_ENST00000475887.1_Nonsense_Mutation_p.Q104* NM_032787.2 NP_116176.2 Q96K78 GP128_HUMAN G protein-coupled receptor 128 56 ATATGGCTGTCAAAAAGACAA 0.398000 Pancreas(87;185 1975 7223 18722) 0 SO:0001587 stop_gained ENST00000273352.3 0 1 hg19 CCDS2938.1 . . . . . . . . . . C 32.000000 5.120168 0.943850 . . ENSG00000144820 ENST00000273352;ENST00000475887 . . . 5.32 -5.99 0.02213 . 1.572660 0.03413 N 0.205109 . . . . . . 0.807220 A 1.000000 . . . . . . . . . . 0.02654 T 1 . 0.2344 0.00184 0.3615:0.1523:0.1933:0.293 . . . . X 399;104 . ENSP00000273352:Q399X Q + 1 0 GPR128 101848187 0 0.058580 3.000000e-03 0.115790 0.199000 0.239340 -1.251000 0.028820 -0.824000 0.042950 -0.176000 1.317100e-01 CAA TCGA-IB-A5SO-01A-11D-A32N-08 GPR128-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353236.1 1 0 0 25 223 0 59 0 2.386741e-01 1 8 0 59 2 0 0 0 0 0 2 1 1.000000 23 221 0 59 2 0 0 0 0 59 2 -3.318801 1 1 0 0 1 1 2 3 2.038053 0 0.230000 1.870000 0.233526 0.880000 0.590000 1.000000 1.000000 0.871718 0.880000 1 0.720000 1.000000 SLC6A1 6529 broad.mit.edu 37 3 11067472 11067472 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr3:11067472C>T ENST00000287766.4 + 9 1284 c.863C>T c.(862-864)gCg>gTg p.A288V SLC6A1_ENST00000536032.1_Missense_Mutation_p.A110V NM_003042.3 NP_003033.3 P30531 SC6A1_HUMAN solute carrier family 6 (neurotransmitter transporter), member 1 26 Ovarian(110;0.0392) Clobazam(DB00349)|Tiagabine(DB00906) TGGCTGGATGCGGCAACCCAG 0.517000 0 SO:0001583 missense ENST00000287766.4 0 1 hg19 CCDS2603.1 . . . . . . . . . . C 29.700000 5.030610 0.935750 . . ENSG00000157103 ENST00000287766;ENST00000536032 D;D 0.91124 -2.79;-2.79 4.98 4.98 0.66077 . 0.000000 0.64402 D 0.000004 D 0.97461 0.9169 H 0.98682 4.3 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 D 0.99016 1.0816 10 0.87932 D 0 . 18.4501 0.90700 0.0:1.0:0.0:0.0 . 288 P30531 SC6A1_HUMAN V 288;110 ENSP00000287766:A288V;ENSP00000445171:A110V ENSP00000287766:A288V A + 2 0 SLC6A1 11042472 1 0.714170 9.840000e-01 0.447390 0.797000 0.450370 7.449000 0.806430 2.595000 0.876830 0.561000 7.409900e-01 GCG TCGA-IB-A5SO-01A-11D-A32N-08 SLC6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102767.2 0 0 0 5 472 1 132 0 3.629301e-03 0 7 1 132 2 0 0 0 0 0 2 0 0.028615 5 467 1 132 14 0 0 0 1 132 2 -1.941839 0 1 0 0 1 0 1 1 1.887303 1 0.230000 1.870000 0.168826 0.080000 0.030000 0.180000 0.080000 0.099865 0.080000 0 0.050000 0.140000 TGFBR2 7048 broad.mit.edu 37 3 30715708 30715708 + Nonsense_Mutation SNP G G T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr3:30715708G>T ENST00000295754.5 + 5 1748 c.1366G>T c.(1366-1368)Gaa>Taa p.E456* TGFBR2_ENST00000359013.4_Nonsense_Mutation_p.E481* NM_003242.5 NP_003233.4 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II (70/80kDa) 53 GGTGCTCTGGGAAATGACATC 0.458000 0 SO:0001587 stop_gained ENST00000295754.5 0 1 hg19 CCDS2648.1 . . . . . . . . . . G 43.000000 9.989757 0.993120 . . ENSG00000163513 ENST00000295754;ENST00000359013;ENST00000439925 . . . 5.75 5.75 0.90469 . 0.000000 0.85682 D 0.000000 . . . . . . 0.807220 A 1.000000 . . . . . . . . . . 0.87932 D 0 . 19.9662 0.97271 0.0:0.0:1.0:0.0 . . . . X 456;481;286 . ENSP00000295754:E456X E + 1 0 TGFBR2 30690712 1 0.714170 1 0.803570 0.990000 0.784780 9.869000 0.998100 2.701000 0.922440 0.650000 8.624300e-01 GAA TCGA-IB-A5SO-01A-11D-A32N-08 TGFBR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252994.2 0 0 0 22 246 1 68 0 9.451447e-01 9 282 1 68 15 1 1 95 825 0 689 2 1 0.931598 22 242 1 68 14 0 0 0 1 68 2 -8.033695 1 1 0 0 1 0 1 1 1.887303 1 0.230000 1.870000 0.168826 0.650000 0.420000 0.930000 0.650000 0.672867 0.650000 0 0.530000 0.800000 CELSR3 1951 broad.mit.edu 37 3 48677390 48677390 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr3:48677390G>A ENST00000164024.4 - 34 9908 c.9628C>T c.(9628-9630)Cgg>Tgg p.R3210W CELSR3_ENST00000544264.1_Missense_Mutation_p.R3215W NM_001407.2 NP_001398.2 Q9NYQ7 CELR3_HUMAN cadherin, EGF LAG seven-pass G-type receptor 3 83 GAGGGGTGCCGGCTAGGCACC 0.657000 0 SO:0001583 missense ENST00000164024.4 1 1 hg19 CCDS2775.1 . . . . . . . . . . G 20.200000 3.946434 0.736720 . . ENSG00000008300 ENST00000164024;ENST00000544264 T;T 0.73047 -0.71;-0.71 4.92 1.72 0.24424 . . . . . T 0.68952 0.3057 L 0.34521 1.04 0.320230 N 0.600519 D;D;D 0.71674 0.99;0.995;0.998 P;P;P 0.53490 0.727;0.661;0.661 T 0.74377 -0.3685 9 0.72032 D 0.01 . 12.4996 0.55948 0.0:0.0:0.4274:0.5726 . 3215;3210;3308 Q9NYQ7-2;Q9NYQ7;Q5Y190 .;CELR3_HUMAN;. W 3210;3215 ENSP00000164024:R3210W;ENSP00000445694:R3215W ENSP00000164024:R3210W R - 1 2 CELSR3 48652394 9.990000e-01 0.422020 9.960000e-01 0.522420 0.912000 0.541700 2.199000 0.427150 1.035000 0.399720 0.561000 7.409900e-01 CGG TCGA-IB-A5SO-01A-11D-A32N-08 CELSR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257523.1 1 0 1 32 255 0 87 1 2.310148e-01 3 5 0 87 2 1 1 76 676 0 418 2 1 1.000000 32 251 0 87 2 0 0 0 0 87 2 -2.920871 1 1 120994 2 32 1 0 1 1 1.887303 1 0.230000 1.870000 0.168826 0.890000 0.630000 1.000000 1.000000 0.879673 0.890000 1 0.750000 1.000000 RBM6 10180 broad.mit.edu 37 3 50085685 50085685 + Missense_Mutation SNP T T G TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr3:50085685T>G ENST00000266022.4 + 7 1824 c.1565T>G c.(1564-1566)cTa>cGa p.L522R RBM6_ENST00000442092.1_5'UTR|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000422955.1_5'UTR|RBM6_ENST00000443081.1_Missense_Mutation_p.L390R NM_005777.2 NP_005768.1 P78332 RBM6_HUMAN RNA binding motif protein 6 33 CAGGGAACTCTAATGATCCAG 0.433000 0 SO:0001583 missense ENST00000266022.4 1 1 hg19 CCDS2809.1 . . . . . . . . . . T 18.370000 3.608302 0.665580 . . ENSG00000004534 ENST00000266022;ENST00000443081 T;T 0.10192 2.9;2.9 5.62 5.62 0.85841 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2); 0.208568 0.30859 N 0.008727 T 0.29423 0.0733 M 0.71206 2.165 0.807220 D 1.000000 D;D 0.55800 0.973;0.973 D;P 0.64144 0.922;0.898 T 0.00998 -1.1486 9 . . . -3.54 13.227 0.59921 0.0:0.0:0.0:1.0 . 390;522 E9PGM9;P78332 .;RBM6_HUMAN R 522;390 ENSP00000266022:L522R;ENSP00000396466:L390R . L + 2 0 RBM6 50060689 1 0.714170 1 0.803570 0.982000 0.717510 4.266000 0.588710 2.141000 0.664460 0.528000 5.322800e-01 CTA TCGA-IB-A5SO-01A-11D-A32N-08 RBM6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345528.4 1 0 1 15 107 0 30 1 9.999134e-01 27 96 0 30 2 0 0 0 0 0 2 1 0.999902 15 106 0 30 2 0 0 0 0 30 2 -9.156553 1 1 0 0 1 0 1 1 1.887303 1 0.230000 1.870000 0.168826 0.950000 0.580000 1.000000 1.000000 0.901392 0.950000 1 0.750000 1.000000 PPP3CA 5530 broad.mit.edu 37 4 101947138 101947138 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr4:101947138G>A ENST00000394854.3 - 14 2133 c.1450C>T c.(1450-1452)Ccg>Tcg p.P484S PPP3CA_ENST00000507176.1_Missense_Mutation_p.P386S|PPP3CA_ENST00000323055.6_Missense_Mutation_p.P432S|PPP3CA_ENST00000523694.2_Missense_Mutation_p.P417S|PPP3CA_ENST00000512215.1_Missense_Mutation_p.P252S|PPP3CA_ENST00000394853.4_Missense_Mutation_p.P474S NM_000944.4 NP_000935.1 Q08209 PP2BA_HUMAN protein phosphatase 3, catalytic subunit, alpha isozyme 20 CTGCGAGGCGGCATCCTCTCA 0.468000 0 SO:0001583 missense ENST00000394854.3 0 1 hg19 CCDS34037.1 . . . . . . . . . . G 19.900000 3.913627 0.729830 . . ENSG00000138814 ENST00000512215;ENST00000394854;ENST00000323055;ENST00000394853;ENST00000507176;ENST00000523694 T;T;T;T;T;T 0.05319 3.46;3.46;3.46;3.46;3.46;3.46 5.79 5.79 0.91817 . 0.000000 0.85682 D 0.000000 T 0.35248 0.0925 M 0.89904 3.07 0.807220 D 1.000000 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;1.0;0.998;1.0;1.0 T 0.28650 -1.0037 10 0.87932 D 0 -9.9218 20.0473 0.97613 0.0:0.0:1.0:0.0 . 484;252;432;474;386;417 Q08209;A8W6Z8;A8W6Z7;Q08209-2;E7ETC2;A1A441 PP2BA_HUMAN;.;.;.;.;. S 252;484;432;474;386;417 ENSP00000422781:P252S;ENSP00000378323:P484S;ENSP00000320580:P432S;ENSP00000378322:P474S;ENSP00000422990:P386S;ENSP00000429350:P417S ENSP00000320580:P432S P - 1 0 PPP3CA 102166161 1 0.714170 1 0.803570 0.995000 0.863560 9.502000 0.979810 2.722000 0.931590 0.655000 9.425300e-01 CCG TCGA-IB-A5SO-01A-11D-A32N-08 PPP3CA-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000258379.2 0 0 0 5 477 0 115 0 5.228945e-01 0 150 0 115 2 0 0 0 0 0 2 1 0.934340 6 466 0 114 2 0 0 0 0 115 2 -1.796728 0 1 0 0 1 0 0 0 1.992893 0 0.230000 1.870000 0.213724 0.090000 0.030000 0.190000 0.090000 0.104761 0.090000 0 0.050000 0.140000 ANK2 287 broad.mit.edu 37 4 114179218 114179218 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr4:114179218C>T ENST00000357077.4 + 12 1254 c.1201C>T c.(1201-1203)Cca>Tca p.P401S ANK2_ENST00000264366.6_Missense_Mutation_p.P401S|ANK2_ENST00000394537.3_Missense_Mutation_p.P401S|ANK2_ENST00000506722.1_Missense_Mutation_p.P380S NM_001148.4 NP_001139.3 Q01484 ANK2_HUMAN ankyrin 2, neuronal 248 Ovarian(17;0.0448)|Hepatocellular(203;0.218) TGGTTTTACTCCACTGCACAT 0.398000 0 SO:0001583 missense ENST00000357077.4 0 1 hg19 CCDS3702.1 . . . . . . . . . . C 29.000000 4.969555 0.928550 . . ENSG00000145362 ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056 T;T;T;T;T;T;T 0.78003 -1.14;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28 5.95 5.95 0.96441 Ankyrin repeat-containing domain (3); 0.000000 0.53938 D 0.000051 D 0.88768 0.6526 M 0.75884 2.315 0.807220 D 1.000000 D;P;P;P;D 0.89917 1.0;0.63;0.911;0.635;0.998 D;P;P;B;D 0.87578 0.998;0.495;0.755;0.396;0.997 D 0.88615 0.3159 10 0.72032 D 0.01 . 20.3748 0.98911 0.0:1.0:0.0:0.0 . 401;401;401;380;380 Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9 ANK2_HUMAN;.;.;.;. S 380;380;380;416;401;401;401;380 ENSP00000423799:P380S;ENSP00000421011:P380S;ENSP00000421067:P380S;ENSP00000424722:P416S;ENSP00000378044:P401S;ENSP00000349588:P401S;ENSP00000264366:P401S ENSP00000264366:P401S P + 1 0 ANK2 114398667 1 0.714170 1 0.803570 0.998000 0.957120 7.776000 0.855600 2.817000 0.969820 0.563000 7.788400e-01 CCA TCGA-IB-A5SO-01A-11D-A32N-08 ANK2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000256422.2 0 0 0 7 188 0 42 0 1.034847e-02 0 4 0 42 2 0 0 0 0 0 2 1 0.980837 7 187 0 42 2 0 0 0 0 42 2 -2.846626 1 1 0 0 1 0 0 0 1.992893 0 0.230000 1.870000 0.213724 0.320000 0.140000 0.580000 0.300000 0.339321 0.320000 0 0.210000 0.450000 NAF1 92345 broad.mit.edu 37 4 164050411 164050411 + Nonsense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr4:164050411G>A ENST00000274054.2 - 8 1316 c.1123C>T c.(1123-1125)Cga>Tga p.R375* NAF1_ENST00000422287.2_Intron|NAF1_ENST00000509434.1_Intron NM_138386.2 NP_612395.2 Q96HR8 NAF1_HUMAN nuclear assembly factor 1 ribonucleoprotein 21 all_hematologic(180;0.166) Prostate(90;0.109) GAAAATCCTCGTGTGAATTCT 0.448000 0 SO:0001587 stop_gained ENST00000274054.2 0 1 hg19 CCDS3803.1 . . . . . . . . . . G 15.350000 2.808836 0.504210 . . ENSG00000145414 ENST00000274054 . . . 4.71 -1.19 0.09585 . 0.519016 0.17234 N 0.181810 . . . . . . 0.807220 D 1.000000 . . . . . . . . . . 0.05721 T 0.95 -2.034 3.5873 0.07975 0.0796:0.3444:0.2622:0.3139 . . . . X 375 . ENSP00000274054:R375X R - 1 2 NAF1 164269861 5.000000e-03 0.159910 1.000000e-03 0.086480 0.006000 0.054640 0.134000 0.159320 -0.399000 0.076680 -0.218000 1.254300e-01 CGA TCGA-IB-A5SO-01A-11D-A32N-08 NAF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000364684.2 0 0 0 8 248 0 76 0 2.313585e-01 1 25 0 76 2 0 0 0 0 0 2 1 0.989174 8 245 0 75 2 0 0 0 0 76 2 -3.657908 1 1 0 0 1 0 0 0 1.992893 0 0.230000 1.870000 0.213724 0.270000 0.120000 0.490000 0.260000 0.292805 0.270000 0 0.190000 0.380000 CCDC110 256309 broad.mit.edu 37 4 186379493 186379493 + Missense_Mutation SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr4:186379493C>T ENST00000307588.3 - 6 2323 c.2248G>A c.(2248-2250)Gta>Ata p.V750I CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.V713I|CCDC110_ENST00000510617.1_Missense_Mutation_p.V750I NM_152775.3 NP_689988.1 Q8TBZ0 CC110_HUMAN coiled-coil domain containing 110 p.V750I(1) 30 all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749) ATGCTTCTTACGTAATTTTCT 0.284000 1 Substitution - Missense(1) SO:0001583 missense ENST00000307588.3 0 1 hg19 CCDS3843.1 . . . . . . . . . . C 11.850000 1.763163 0.312280 . . ENSG00000168491 ENST00000393540;ENST00000307588;ENST00000510617 T;T;T 0.28895 1.59;1.59;1.59 5.54 3.55 0.40652 . 0.441395 0.19156 N 0.121335 T 0.30386 0.0763 M 0.63428 1.95 0.093100 N 1.000000 D;D;D 0.60575 0.988;0.988;0.988 P;P;P 0.50934 0.654;0.654;0.654 T 0.18871 -1.0323 10 0.14252 T 0.57 -6.4794 1.659 0.02787 0.2086:0.4783:0.1387:0.1745 . 750;713;750 B4DZA2;Q8TBZ0-2;Q8TBZ0 .;.;CC110_HUMAN I 713;750;750 ENSP00000377172:V713I;ENSP00000306776:V750I;ENSP00000427246:V750I ENSP00000306776:V750I V - 1 0 CCDC110 186616487 2.500000e-02 0.190820 9.310000e-01 0.372120 0.983000 0.724000 0.893000 0.283360 1.471000 0.481210 0.650000 8.624300e-01 GTA TCGA-IB-A5SO-01A-11D-A32N-08 CCDC110-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000360519.2 1 0 0 4 72 0 17 0 0 0 0 17 2 0 0 0 0 0 2 1 0.892229 4 72 0 17 2 0 0 0 0 17 2 -3.928482 1 1 121348 6 33 1 0 0 0 1.992893 0 0.230000 1.870000 0.213724 0.480000 0.160000 0.980000 1.000000 0.515705 0.480000 0 0.290000 0.730000 SORCS2 57537 broad.mit.edu 37 4 7716916 7716916 + Silent SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr4:7716916C>T ENST00000507866.2 + 17 2239 c.2130C>T c.(2128-2130)taC>taT p.Y710Y SORCS2_ENST00000329016.9_Silent_p.Y538Y NM_020777.2 NP_065828.2 Q96PQ0 SORC2_HUMAN sortilin-related VPS10 domain containing receptor 2 42 CCAGCGACTACGGATTTGAGC 0.597000 0 SO:0001819 synonymous_variant ENST00000507866.2 1 1 hg19 CCDS47008.1 TCGA-IB-A5SO-01A-11D-A32N-08 SORCS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358685.4 1 0 0 44 457 0 129 0 1.902927e-01 0 9 0 129 2 0 0 0 0 0 2 1 1.000000 42 449 0 129 2 0 0 0 0 129 2 -12.488550 1 1 120932 10 44 1 0 0 0 1.992893 0 0.230000 1.870000 0.213724 0.740000 0.550000 0.960000 0.740000 0.755469 0.740000 0 0.640000 0.860000 FAM71B 153745 broad.mit.edu 37 5 156590199 156590199 + Silent SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr5:156590199C>T ENST00000302938.4 - 2 1172 c.1077G>A c.(1075-1077)tcG>tcA p.S359S NM_130899.2 NP_570969.2 Q8TC56 FA71B_HUMAN family with sequence similarity 71, member B p.S359S(1) 68 Renal(175;0.00212) Medulloblastoma(196;0.0523)|all_neural(177;0.21) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) CCCCCGCCATCGAGGTGGAAG 0.572000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000302938.4 1 1 hg19 CCDS4335.1 TCGA-IB-A5SO-01A-11D-A32N-08 FAM71B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252570.2 1 0 1 21 185 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.999998 21 183 0 60 2 0 0 0 0 61 2 -9.351058 1 1 121410 2 35 1 0 0 0 1.987370 0 0.230000 1.870000 0.211873 0.860000 0.560000 1.000000 1.000000 0.853580 0.860000 1 0.700000 1.000000 UGT3A1 133688 broad.mit.edu 37 5 35954469 35954469 + Silent SNP C C T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr5:35954469C>T ENST00000274278.3 - 7 1764 c.1407G>A c.(1405-1407)acG>acA p.T469T UGT3A1_ENST00000513233.1_5'Flank NM_152404.3 NP_689617.3 Q6NUS8 UD3A1_HUMAN UDP glycosyltransferase 3 family, polypeptide A1 46 all_lung(31;0.000197) Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) GCTTGAGGTGCGTCGCTCCCC 0.602000 0 SO:0001819 synonymous_variant ENST00000274278.3 1 1 hg19 CCDS3913.1 TCGA-IB-A5SO-01A-11D-A32N-08 UGT3A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253770.2 1 0 0 5 155 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 0.936468 5 153 0 49 2 0 0 0 0 49 2 -3.673073 1 1 0 0 1 0 0 0 1.987370 0 0.230000 1.870000 0.211873 0.280000 0.100000 0.560000 0.260000 0.307381 0.280000 0 0.180000 0.420000 GRIK2 2898 broad.mit.edu 37 6 102337618 102337618 + Missense_Mutation SNP G G A rs141189363 byFrequency TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr6:102337618G>A ENST00000421544.1 + 11 2118 c.1628G>A c.(1627-1629)cGc>cAc p.R543H GRIK2_ENST00000369138.1_Missense_Mutation_p.R543H|GRIK2_ENST00000413795.1_Missense_Mutation_p.R543H|GRIK2_ENST00000318991.6_Missense_Mutation_p.R543H|GRIK2_ENST00000369137.3_Missense_Mutation_p.R543H|GRIK2_ENST00000369134.4_Missense_Mutation_p.R494H NM_021956.4 NP_068775.1 Q13002 GRIK2_HUMAN glutamate receptor, ionotropic, kainate 2 83 all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599) ATTTTGTACCGCAAGCCCAAT 0.468000 0 SO:0001583 missense ENST00000421544.1 0 1 hg19 CCDS5048.1 . . . . . . . . . . G 23.100000 4.374924 0.825730 6.81E-4 2.33E-4 ENSG00000164418 ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000436862 T;T;T;T;T;T;T 0.54071 2.55;2.55;2.55;0.59;2.55;2.55;2.55 5.6 5.6 0.85130 Ionotropic glutamate receptor (1); 0.104915 0.64402 D 0.000002 T 0.45617 0.1351 M 0.69463 2.115 0.807220 D 1.000000 P;P;P 0.40875 0.731;0.611;0.731 B;B;B 0.37888 0.26;0.133;0.26 T 0.56025 -0.8047 10 0.66056 D 0.02 . 19.6182 0.95643 0.0:0.0:1.0:0.0 . 543;543;543 Q13002-5;Q13002;Q13002-2 .;GRIK2_HUMAN;. H 543;543;543;543;543;543;494;142 ENSP00000397026:R543H;ENSP00000405596:R543H;ENSP00000358134:R543H;ENSP00000358133:R543H;ENSP00000313276:R543H;ENSP00000358130:R494H;ENSP00000407140:R142H ENSP00000313276:R543H R + 2 0 GRIK2 102444311 1 0.714170 1 0.803570 0.999000 0.989320 9.869000 0.998100 2.626000 0.889560 0.650000 8.624300e-01 CGC TCGA-IB-A5SO-01A-11D-A32N-08 GRIK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043718.1 0 0 0 7 492 0 153 0 0 0 1 0 153 2 0 0 0 0 0 2 1 0.979601 6 485 0 153 2 0 0 0 0 153 2 -1.775606 0 1 121412 16 47 1 0 0 0 1.985308 0 0.230000 1.870000 0.210013 0.120000 0.050000 0.230000 0.120000 0.134322 0.120000 0 0.080000 0.180000 PTPRK 5796 broad.mit.edu 37 6 128306921 128306921 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr6:128306921G>A ENST00000368215.3 - 22 3192 c.3193C>T c.(3193-3195)Cgg>Tgg p.R1065W PTPRK_ENST00000368227.3_Missense_Mutation_p.R1083W|PTPRK_ENST00000368226.4_Missense_Mutation_p.R1066W|PTPRK_ENST00000532331.1_Missense_Mutation_p.R1088W|PTPRK_ENST00000368213.5_Missense_Mutation_p.R1072W|PTPRK_ENST00000368207.3_Missense_Mutation_p.R1098W|PTPRK_ENST00000368210.3_Missense_Mutation_p.R1084W Q15262 PTPRK_HUMAN protein tyrosine phosphatase, receptor type, K PTPRK/RSPO3(10) 72 TTGACTCGCCGGATAAAGGAA 0.498000 0 SO:0001583 missense ENST00000368215.3 0 1 hg19 . . . . . . . . . . G 24.900000 4.580797 0.867480 . . ENSG00000152894 ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207 D;D;D;D;D;D;D 0.84800 -1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9 5.82 5.82 0.92795 Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1); 0.000000 0.85682 D 0.000000 D 0.94716 0.8295 H 0.94925 3.6 0.807220 D 1.000000 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;1.0;0.991;0.985 D 0.95321 0.8420 10 0.87932 D 0 . 20.0864 0.97801 0.0:0.0:1.0:0.0 . 1088;1072;1065;1066 B7ZMG0;Q15262-3;Q15262;Q15262-2 .;.;PTPRK_HUMAN;. W 1066;1083;1088;1072;1084;1065;1098 ENSP00000357209:R1066W;ENSP00000357210:R1083W;ENSP00000432973:R1088W;ENSP00000357196:R1072W;ENSP00000357193:R1084W;ENSP00000357198:R1065W;ENSP00000357190:R1098W ENSP00000357190:R1098W R - 1 2 PTPRK 128348614 1 0.714170 1 0.803570 0.932000 0.569680 5.548000 0.672550 2.753000 0.944830 0.650000 8.624300e-01 CGG TCGA-IB-A5SO-01A-11D-A32N-08 PTPRK-005 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000042163.1 0 0 0 4 162 0 37 0 8.941209e-01 0 168 0 37 2 0 0 0 0 0 2 1 0.888481 4 160 0 36 2 0 0 0 0 37 2 -2.481789 0 1 121412 1 28 1 0 0 0 1.985308 0 0.230000 1.870000 0.210013 0.220000 0.070000 0.470000 0.200000 0.246569 0.220000 0 0.130000 0.350000 MOXD1 26002 broad.mit.edu 37 6 132649632 132649632 + Silent SNP G G A rs145443994 TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr6:132649632G>A ENST00000367963.3 - 5 883 c.765C>T c.(763-765)caC>caT p.H255H MOXD1_ENST00000336749.3_Silent_p.H187H NM_015529.2 NP_056344.2 Q6UVY6 MOXD1_HUMAN monooxygenase, DBH-like 1 37 Breast(56;0.0495) GATAGCACTCGTGGCCGGACT 0.517000 0 SO:0001819 synonymous_variant ENST00000367963.3 1 1 hg19 CCDS5152.2 TCGA-IB-A5SO-01A-11D-A32N-08 MOXD1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000125837.1 1 0 0 10 234 0 64 0 9.965837e-01 0 237 0 64 2 0 0 0 0 0 2 1 0.996927 10 232 0 61 2 0 0 0 0 64 2 -4.232748 1 1 121412 5 40 1 0 0 0 1.985308 0 0.230000 1.870000 0.210013 0.350000 0.180000 0.590000 0.340000 0.373173 0.350000 0 0.250000 0.480000 SASH1 23328 broad.mit.edu 37 6 148853965 148853965 + Missense_Mutation SNP A A G TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr6:148853965A>G ENST00000367467.3 + 14 2072 c.1597A>G c.(1597-1599)Acc>Gcc p.T533A NM_015278.3 NP_056093.3 O94885 SASH1_HUMAN SAM and SH3 domain containing 1 52 Ovarian(120;0.0169) TGATTCCTCAACCAGCAACCG 0.557000 0 SO:0001583 missense ENST00000367467.3 1 1 hg19 CCDS5212.1 . . . . . . . . . . A 6.118000 0.389937 0.115810 . . ENSG00000111961 ENST00000367467;ENST00000535767 T 0.42131 0.98 5.27 2.89 0.33648 . 0.166954 0.56097 N 0.000035 T 0.07683 0.0193 N 0.11427 0.14 0.290130 N 0.886778 B;B 0.21309 0.054;0.004 B;B 0.20955 0.032;0.017 T 0.38735 -0.9647 10 0.17369 T 0.5 -14.7724 9.7654 0.40557 0.7217:0.0:0.2783:0.0 . 514;533 Q6P4R9;O94885 .;SASH1_HUMAN A 533;294 ENSP00000356437:T533A ENSP00000356437:T533A T + 1 0 SASH1 148895658 9.760000e-01 0.341440 8.930000e-01 0.350520 0.867000 0.496890 1.935000 0.401730 0.039000 0.156320 -1.139000 1.908000e-02 ACC TCGA-IB-A5SO-01A-11D-A32N-08 SASH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042619.1 0 0 0 9 307 0 70 0 1.333870e-01 1 19 0 70 2 0 0 0 0 0 2 1 0.994142 9 304 0 69 2 0 0 0 0 70 2 -9.822795 1 1 121412 1 30 1 0 0 0 1.985308 0 0.230000 1.870000 0.210013 0.240000 0.120000 0.430000 0.240000 0.263367 0.240000 0 0.170000 0.340000 SYNE1 23345 broad.mit.edu 37 6 152457816 152457816 + Silent SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr6:152457816G>A ENST00000367255.5 - 141 26197 c.25596C>T c.(25594-25596)gaC>gaT p.D8532D SYNE1_ENST00000341594.5_Silent_p.D8144D|SYNE1_ENST00000265368.4_Silent_p.D8532D|SYNE1_ENST00000354674.4_Silent_p.D710D|SYNE1_ENST00000539504.1_Silent_p.D687D|SYNE1_ENST00000448038.1_Silent_p.D8484D|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000356820.4_Silent_p.D3056D|SYNE1_ENST00000423061.1_Silent_p.D8484D NM_182961.3 NP_892006.3 Q8NF91 SYNE1_HUMAN spectrin repeat containing, nuclear envelope 1 524 Ovarian(120;0.0955) BRCA - Breast invasive adenocarcinoma(37;0.243) AGCACACTCGGTCCCAGCGCC 0.612000 HNSCC(10;0.0054) 0 SO:0001819 synonymous_variant ENST00000367255.5 0 1 hg19 CCDS5236.2 TCGA-IB-A5SO-01A-11D-A32N-08 SYNE1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000334755.2 0 0 0 5 287 0 90 0 5.078251e-01 0 88 0 90 2 0 0 0 0 0 2 1 0.924948 5 266 0 81 2 0 0 0 0 90 2 -3.316814 1 1 0 0 1 0 0 0 1.985308 0 0.230000 1.870000 0.210013 0.150000 0.050000 0.310000 0.140000 0.170752 0.150000 0 0.090000 0.230000 COG5 10466 broad.mit.edu 37 7 107002815 107002815 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr7:107002815G>A ENST00000347053.3 - 9 1029 c.979C>T c.(979-981)Cgt>Tgt p.R327C COG5_ENST00000393603.2_Missense_Mutation_p.R327C|COG5_ENST00000297135.3_Missense_Mutation_p.R327C NM_181733.2 NP_859422.2 Q9UP83 COG5_HUMAN component of oligomeric golgi complex 5 40 AATGAGGCACGCAAAGCTGCA 0.398000 0 SO:0001583 missense ENST00000347053.3 0 1 hg19 CCDS5743.1 . . . . . . . . . . G 18.710000 3.682211 0.680420 . . ENSG00000164597 ENST00000347053;ENST00000297135;ENST00000393603 T;T;T 0.32988 1.43;1.43;1.43 5.69 4.81 0.61882 . 0.000000 0.85682 D 0.000000 T 0.57242 0.2040 M 0.87547 2.89 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.91635 0.995;0.999 T 0.62923 -0.6751 10 0.87932 D 0 -12.3955 8.6738 0.34167 0.0696:0.0:0.6723:0.258 . 327;327 Q9UP83;Q9UP83-2 COG5_HUMAN;. C 327 ENSP00000334703:R327C;ENSP00000297135:R327C;ENSP00000377228:R327C ENSP00000297135:R327C R - 1 0 COG5 106790051 1 0.714170 9.900000e-01 0.471750 0.616000 0.374500 5.822000 0.692650 1.540000 0.493010 0.655000 9.425300e-01 CGT TCGA-IB-A5SO-01A-11D-A32N-08 COG5-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000060216.4 0 0 0 4 166 0 39 0 2.897549e-01 0 37 0 39 2 0 0 0 0 0 2 1 0.891327 4 166 0 39 2 0 0 0 0 39 2 -2.800004 1 1 0 0 1 0 1 1 1.898206 1 0.230000 1.870000 0.167792 0.200000 0.060000 0.440000 0.190000 0.227102 0.200000 0 0.120000 0.320000 CPA5 93979 broad.mit.edu 37 7 130008354 130008354 + Silent SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr7:130008354G>A ENST00000485477.1 + 12 2356 c.1227G>A c.(1225-1227)ccG>ccA p.P409P CPA5_ENST00000461828.1_Silent_p.P409P|CPA5_ENST00000355388.3_Silent_p.P409P|CPA5_ENST00000474905.1_Silent_p.P409P|CPA5_ENST00000466363.2_Silent_p.P409P|CPA5_ENST00000431780.2_Missense_Mutation_p.R381Q|CPA5_ENST00000393213.3_Silent_p.P409P Q8WXQ8 CBPA5_HUMAN carboxypeptidase A5 23 Melanoma(18;0.0435) TCCTGCTGCCGGCCACACAGA 0.612000 0 SO:0001819 synonymous_variant ENST00000485477.1 0 1 hg19 CCDS5819.1 . . . . . . . . . . G 0.705000 -0.789176 0.028840 . . ENSG00000158525 ENST00000431780;ENST00000479492 T 0.12774 2.65 5.85 -11.7 0.00046 . . . . . T 0.05777 0.0151 . . . 0.807220 D 1.000000 B 0.06786 0.001 B 0.04013 0.001 T 0.31420 -0.9944 7 . . . . 8.197 0.31402 0.6118:0.1479:0.1748:0.0655 . 381 G3V0G8 . Q 381;58 ENSP00000393045:R381Q . R + 2 0 CPA5 129795590 0 0.058580 4.600000e-02 0.188390 0.006000 0.054640 -3.373000 0.004930 -3.150000 0.002310 -4.470000 5.000000e-05 CGG TCGA-IB-A5SO-01A-11D-A32N-08 CPA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349712.1 0 0 0 6 421 0 136 0 4.306536e-03 0 6 0 136 2 0 0 0 0 0 2 1 0.963398 6 414 0 133 2 0 0 0 0 136 2 -2.603785 1 1 121412 2 37 1 0 1 1 1.898206 1 0.230000 1.870000 0.167792 0.110000 0.040000 0.230000 0.110000 0.129761 0.110000 0 0.070000 0.180000 STK31 56164 broad.mit.edu 37 7 23792437 23792437 + Missense_Mutation SNP A A G TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr7:23792437A>G ENST00000355870.3 + 9 1238 c.1119A>G c.(1117-1119)atA>atG p.I373M STK31_ENST00000354639.3_Missense_Mutation_p.I350M|STK31_ENST00000428484.1_Missense_Mutation_p.I350M|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000433467.2_Missense_Mutation_p.I373M NM_031414.4 NP_113602.2 Q9BXU1 STK31_HUMAN serine/threonine kinase 31 67 AGATGGAAATACTGAAAGAAA 0.333000 0 SO:0001583 missense ENST00000355870.3 1 1 hg19 CCDS5386.1 . . . . . . . . . . A 1.604000 -0.525678 0.041410 . . ENSG00000196335 ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484 T;T;T;T 0.14144 2.53;2.53;2.53;2.53 4.94 -4.71 0.03279 . 0.667143 0.15196 N 0.275271 T 0.05731 0.0150 N 0.20685 0.6 0.093100 N 1.000000 B;B 0.10296 0.003;0.003 B;B 0.09377 0.004;0.004 T 0.36841 -0.9731 10 0.19147 T 0.46 1.7106 5.3799 0.16186 0.3532:0.2924:0.3544:0.0 . 373;373 B4DZ06;Q9BXU1 .;STK31_HUMAN M 373;373;350;350 ENSP00000348132:I373M;ENSP00000411852:I373M;ENSP00000346660:I350M;ENSP00000406146:I350M ENSP00000346660:I350M I + 3 3 STK31 23758962 0 0.058580 2.000000e-03 0.105220 0.209000 0.243380 -1.076000 0.034200 -0.604000 0.057600 -0.376000 6.991000e-02 ATA TCGA-IB-A5SO-01A-11D-A32N-08 STK31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214036.2 1 0 1 16 154 0 29 0 2.860507e-02 0 3 0 29 2 0 0 0 0 0 2 1 0.999945 16 153 0 28 2 0 0 0 0 29 2 -19.999460 1 1 0 0 1 1 2 3 2.067945 0 0.230000 1.870000 0.238754 0.850000 0.500000 1.000000 1.000000 0.839022 0.850000 1 0.660000 1.000000 AUTS2 26053 broad.mit.edu 37 7 69583117 69583117 + Splice_Site SNP G G C TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr7:69583117G>C ENST00000342771.4 + 3 843 c.e3-1 AUTS2_ENST00000403018.2_Splice_Site|AUTS2_ENST00000406775.2_Splice_Site NM_015570.2 NP_056385.1 Q8WXX7 AUTS2_HUMAN autism susceptibility candidate 2 50 all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093) TTTGCCTTTAGCTCAAGCCAG 0.498000 0 SO:0001630 splice_region_variant ENST00000342771.4 0 1 hg19 CCDS5539.1 . . . . . . . . . . G 24.300000 4.512937 0.853890 . . ENSG00000158321 ENST00000406775;ENST00000342771;ENST00000403018 . . . 5.34 5.34 0.76211 . . . . . . . . . . . 0.807220 D 1.000000 . . . . . . . . . . . . . . 19.2224 0.93803 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . AUTS2 69221053 1 0.714170 1 0.803570 0.991000 0.796840 8.302000 0.899530 2.765000 0.950210 0.655000 9.425300e-01 . TCGA-IB-A5SO-01A-11D-A32N-08 AUTS2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251971.2 0 0 0 4 220 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 0.874074 4 205 0 49 2 0 0 0 0 49 2 -5.493321 1 0 0 0 1 1 2 3 2.067945 0 0.230000 1.870000 0.238754 0.180000 0.050000 1.000000 0.150000 0.257217 0.180000 0 0.100000 0.320000 MIOS 54468 broad.mit.edu 37 7 7625382 7625382 + Missense_Mutation SNP G G C TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr7:7625382G>C ENST00000340080.4 + 7 2185 c.1764G>C c.(1762-1764)ttG>ttC p.L588F MIOS_ENST00000405785.1_Missense_Mutation_p.L588F NM_019005.3 NP_061878.3 Q9NXC5 MIO_HUMAN missing oocyte, meiosis regulator, homolog (Drosophila) 32 ACCCGTATTTGTGTGTCATGT 0.383000 0 SO:0001583 missense ENST00000340080.4 0 1 hg19 CCDS43554.1 . . . . . . . . . . G 14.140000 2.445831 0.434290 . . ENSG00000164654 ENST00000340080;ENST00000405785 T;T 0.58210 0.35;0.35 5.46 -5.98 0.02220 . 0.000000 0.85682 D 0.000000 T 0.52370 0.1730 L 0.55834 1.745 0.496870 D 0.999814 D 0.54964 0.969 P 0.61592 0.891 T 0.59284 -0.7483 10 0.66056 D 0.02 -7.714 4.7574 0.13092 0.2284:0.4582:0.2193:0.0941 . 588 Q9NXC5 MIO_HUMAN F 588 ENSP00000339881:L588F;ENSP00000384088:L588F ENSP00000339881:L588F L + 3 2 MIOS 7591907 3.930000e-01 0.252370 1.130000e-01 0.215220 0.612000 0.373160 -0.341000 0.078110 -1.651000 0.015040 -0.229000 1.229400e-01 TTG TCGA-IB-A5SO-01A-11D-A32N-08 MIOS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000326218.1 0 0 0 6 403 0 85 1 2.242233e-01 4 48 0 85 2 0 0 0 0 0 2 1 0.964440 6 400 0 85 2 0 0 0 0 85 2 -3.090841 1 1 0 0 1 1 2 3 2.067945 0 0.230000 1.870000 0.238754 0.140000 0.050000 1.000000 0.130000 0.217516 0.140000 0 0.090000 0.230000 VPS13B 157680 broad.mit.edu 37 8 100833605 100833605 + Silent SNP A A T TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr8:100833605A>T ENST00000358544.2 + 50 9264 c.9153A>T c.(9151-9153)acA>acT p.T3051T VPS13B_ENST00000357162.2_Silent_p.T3026T|VPS13B_ENST00000395996.1_3'UTR NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) ATAACCTGACATCTCCAAAGT 0.398000 Colon(161;2205 2542 7338 31318) 0 SO:0001819 synonymous_variant ENST00000358544.2 0 1 hg19 CCDS6280.1 TCGA-IB-A5SO-01A-11D-A32N-08 VPS13B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000277138.1 0 0 0 5 356 0 72 1 2.768465e-02 3 12 0 72 2 0 0 0 0 0 2 1 0.937503 5 355 0 72 2 0 0 0 0 72 2 -5.769193 1 1 0 0 1 1 2 3 2.088967 0 0.230000 1.870000 0.243057 0.140000 0.040000 1.000000 0.120000 0.246512 0.140000 0 0.080000 0.260000 RP1 6101 broad.mit.edu 37 8 55539165 55539165 + Missense_Mutation SNP C C G TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr8:55539165C>G ENST00000220676.1 + 4 2871 c.2723C>G c.(2722-2724)gCt>gGt p.A908G NM_006269.1 NP_006260.1 P56715 RP1_HUMAN retinitis pigmentosa 1 (autosomal dominant) 169 all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123) OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285) GAGGCTATTGCTCATCATTCA 0.328000 Colon(91;1014 1389 7634 14542 40420) 0 SO:0001583 missense ENST00000220676.1 1 1 hg19 CCDS6160.1 . . . . . . . . . . C 12.110000 1.838250 0.325130 . . ENSG00000104237 ENST00000220676 T 0.47869 0.83 5.65 4.76 0.60689 . 0.812455 0.10842 N 0.628097 T 0.35189 0.0923 L 0.29908 0.895 0.093100 N 0.999998 P 0.39282 0.666 B 0.33339 0.162 T 0.20273 -1.0280 10 0.72032 D 0.01 . 10.4038 0.44246 0.0:0.7852:0.137:0.0778 . 908 P56715 RP1_HUMAN G 908 ENSP00000220676:A908G ENSP00000220676:A908G A + 2 0 RP1 55701718 9.360000e-01 0.317500 3.990000e-01 0.263330 0.958000 0.622580 1.179000 0.319930 1.357000 0.459040 0.655000 9.425300e-01 GCT TCGA-IB-A5SO-01A-11D-A32N-08 RP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378532.2 1 0 0 14 143 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 0.999790 13 143 0 41 2 0 0 0 0 41 2 -19.549700 1 1 0 0 1 1 2 3 2.088967 0 0.230000 1.870000 0.243057 0.830000 0.470000 1.000000 1.000000 0.819491 0.830000 0 0.620000 1.000000 TGFBR1 7046 broad.mit.edu 37 9 101900330 101900330 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr9:101900330G>A ENST00000374994.4 + 4 881 c.764G>A c.(763-765)cGt>cAt p.R255H TGFBR1_ENST00000552516.1_Missense_Mutation_p.R259H|TGFBR1_ENST00000374990.2_Missense_Mutation_p.R178H|TGFBR1_ENST00000550253.1_Missense_Mutation_p.R186H NM_004612.2 NP_004603.1 P36897 TGFR1_HUMAN transforming growth factor, beta receptor 1 p.R255L(1) 27 Acute lymphoblastic leukemia(62;0.0559) GTAATGTTACGTCATGAAAAC 0.378000 1 Substitution - Missense(1) SO:0001583 missense ENST00000374994.4 0 1 hg19 CCDS6738.1 . . . . . . . . . . G 24.200000 4.510468 0.853890 . . ENSG00000106799 ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000549021;ENST00000550253 D;D;D;D;D 0.93953 -3.32;-3.32;-3.32;-3.32;-3.32 5.36 5.36 0.76844 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 D 0.95993 0.8695 L 0.61218 1.895 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 D 0.95388 0.8479 9 . . . . 17.8646 0.88792 0.0:0.0:1.0:0.0 . 178;255 P36897-3;P36897 .;TGFR1_HUMAN H 255;255;178;259;109;186 ENSP00000364133:R255H;ENSP00000364129:R178H;ENSP00000447297:R259H;ENSP00000449028:R109H;ENSP00000450052:R186H . R + 2 0 TGFBR1 100940151 1 0.714170 1 0.803570 0.434000 0.317750 9.810000 0.992210 2.530000 0.853050 0.655000 9.425300e-01 CGT TCGA-IB-A5SO-01A-11D-A32N-08 TGFBR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053390.3 0 0 0 6 300 0 61 0 6.602985e-01 0 108 0 61 2 0 2.338840e-01 6 657 6 384 20 1 0.965382 6 300 0 61 2 0 0 0 0 61 2 -3.054871 1 1 0 0 1 1 2 3 2.076687 0 0.230000 1.870000 0.240481 0.190000 0.070000 1.000000 0.170000 0.275784 0.190000 0 0.120000 0.320000 ACTL7B 10880 broad.mit.edu 37 9 111617095 111617095 + Silent SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr9:111617095G>A ENST00000374667.3 - 1 2144 c.1116C>T c.(1114-1116)gcC>gcT p.A372A NM_006686.3 NP_006677.1 Q9Y614 ACL7B_HUMAN actin-like 7B 20 TCTCAGGAGCGGCAGCCACTG 0.647000 0 SO:0001819 synonymous_variant ENST00000374667.3 0 1 hg19 CCDS6771.1 TCGA-IB-A5SO-01A-11D-A32N-08 ACTL7B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053571.1 0 0 0 4 250 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 0.876181 4 235 0 74 2 0 0 0 0 75 2 -3.923896 1 1 121220 1 31 1 1 2 3 2.076687 0 0.230000 1.870000 0.240481 0.160000 0.050000 1.000000 0.130000 0.250266 0.160000 0 0.090000 0.290000 FBXW5 54461 broad.mit.edu 37 9 139835466 139835466 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr9:139835466G>A ENST00000325285.3 - 9 1694 c.1615C>T c.(1615-1617)Cgc>Tgc p.R539C FBXW5_ENST00000483559.1_5'UTR NM_018998.3 NP_061871.1 Q969U6 FBXW5_HUMAN F-box and WD repeat domain containing 5 p.R539C(1) 12 all_cancers(76;0.11) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.19) CGTGGGGAGCGCCAGGCTTTG 0.672000 1 Substitution - Missense(1) SO:0001583 missense ENST00000325285.3 0 1 hg19 CCDS7014.1 . . . . . . . . . . G 25.800000 4.674100 0.884450 0.0 1.18E-4 ENSG00000159069 ENST00000325285 T 0.67345 -0.26 4.61 4.61 0.57282 WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);WD40-repeat-containing domain (1); 0.063203 0.64402 D 0.000004 T 0.80808 0.4694 M 0.71296 2.17 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.981 D 0.83522 0.0086 10 0.72032 D 0.01 -0.5139 16.0315 0.80582 0.0:0.0:1.0:0.0 . 404;539 Q59ET5;Q969U6 .;FBXW5_HUMAN C 539 ENSP00000313034:R539C ENSP00000313034:R539C R - 1 0 FBXW5 138955287 1 0.714170 1 0.803570 0.917000 0.548040 7.184000 0.777050 2.126000 0.654370 0.561000 7.409900e-01 CGC TCGA-IB-A5SO-01A-11D-A32N-08 FBXW5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055227.1 0 0 1 3 15 0 10 1 9.999967e-01 103 490 0 10 2 0 0 0 0 1 2 1 0.813268 3 15 0 10 2 0 0 0 0 10 2 -9.064747 1 1 0 0 1 1 2 3 2.074935 0 0.230000 1.870000 0.240481 0.990000 0.450000 1.000000 1.000000 0.934444 0.990000 1 0.840000 1.000000 ABCA2 20 broad.mit.edu 37 9 139908435 139908435 + Silent SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr9:139908435G>A ENST00000371605.3 - 27 4440 c.4293C>T c.(4291-4293)ggC>ggT p.G1431G ABCA2_ENST00000265662.5_Silent_p.G1432G|ABCA2_ENST00000341511.6_Silent_p.G1432G Q9BZC7 ABCA2_HUMAN ATP-binding cassette, sub-family A (ABC1), member 2 41 all_cancers(76;0.16) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.123) TCAGCCACCCGCCGTCCAGCT 0.657000 0 SO:0001819 synonymous_variant ENST00000371605.3 1 1 hg19 TCGA-IB-A5SO-01A-11D-A32N-08 ABCA2-202 KNOWN basic protein_coding protein_coding 0 0 0 9 216 0 37 0 6.703683e-01 1 54 0 37 2 0 0 0 0 0 2 1 0.993896 9 211 0 36 2 0 0 0 0 37 2 -10.803910 1 1 120222 11 40 1 1 2 3 2.074935 0 0.230000 1.870000 0.240481 0.380000 0.180000 1.000000 0.350000 0.442569 0.380000 0 0.260000 0.570000 OSTF1 26578 broad.mit.edu 37 9 77752511 77752511 + Missense_Mutation SNP G G A TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chr9:77752511G>A ENST00000346234.6 + 8 616 c.466G>A c.(466-468)Gtc>Atc p.V156I NM_012383.4 NP_036515.4 Q92882 OSTF1_HUMAN osteoclast stimulating factor 1 2 TGCAGATATCGTCCAGTTGCT 0.398000 0 SO:0001583 missense ENST00000346234.6 1 1 hg19 CCDS6651.1 . . . . . . . . . . G 28.000000 4.878070 0.916640 . . ENSG00000134996 ENST00000346234 T 0.71698 -0.59 5.51 5.51 0.81932 Ankyrin repeat-containing domain (4); 0.000000 0.85682 D 0.000000 T 0.77294 0.4109 L 0.31752 0.955 0.807220 D 1.000000 D;D 0.89917 1.0;0.959 D;P 0.78314 0.991;0.893 T 0.77313 -0.2634 10 0.45353 T 0.12 -17.9865 18.188 0.89798 0.0:0.0:1.0:0.0 . 156;156 A8K646;Q92882 .;OSTF1_HUMAN I 156 ENSP00000340836:V156I ENSP00000340836:V156I V + 1 0 OSTF1 76942331 1 0.714170 1 0.803570 0.978000 0.694770 8.757000 0.916570 2.585000 0.873010 0.563000 7.788400e-01 GTC TCGA-IB-A5SO-01A-11D-A32N-08 OSTF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052704.1 1 0 1 21 199 0 44 1 1 67 282 0 44 2 0 0 0 0 0 2 1 0.999998 19 197 0 44 2 0 0 0 0 44 2 -8.913195 1 1 121410 3 31 1 1 2 3 2.076687 0 0.230000 1.870000 0.240481 0.860000 0.550000 1.000000 1.000000 0.853697 0.860000 1 0.690000 1.000000 SPANXD 64648 broad.mit.edu 37 X 140785682 140785682 + Missense_Mutation SNP G G C TCGA-IB-A5SO-01A-11D-A32N-08 TCGA-IB-A5SO-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx f21270ad-5de6-4066-9e11-f25ed1d27377 72019813-f98e-42f7-a8ca-798553f65d04 g.chrX:140785682G>C ENST00000370515.3 - 2 567 c.234C>G c.(232-234)aaC>aaG p.N78K NM_032417.2|NM_145665.1 NP_115793.1|NP_663698.1 Q9BXN6 SPNXD_HUMAN SPANX family, member D 9 Acute lymphoblastic leukemia(192;7.65e-05) TTTGGAGGGGGTTGATTCTGT 0.448000 0 SO:0001583 missense ENST00000370515.3 1 1 hg19 CCDS14675.1 . . . . . . . . . . N 8.302000 0.820191 0.166780 . . ENSG00000196406 ENST00000370515 T 0.09445 2.98 . . . . . . . . T 0.25457 0.0619 . . . 0.093100 N 1.000000 D 0.69078 0.997 D 0.81914 0.995 T 0.06789 -1.0807 6 0.72032 D 0.01 . . . . . 78 Q9BXN6 SPNXD_HUMAN K 78 ENSP00000359546:N78K ENSP00000359546:N78K N - 3 2 SPANXD 140613348 5.500000e-02 0.206270 4.800000e-02 0.189610 0.048000 0.145420 0.075000 0.146860 0.068000 0.165740 0.068000 1.538800e-01 AAC TCGA-IB-A5SO-01A-11D-A32N-08 SPANXD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058598.1 0 0 0 50 452 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 46 393 0 159 2 0 0 0 0 147 2 -16.283330 1 1 0 0 1 0 1 1 0.230000 1.870000 0.230000 0.420000 0.320000 0.550000 0.430000 0.437029 0.420000 0 0.370000 0.490000