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 HMX2 3167 broad.mit.edu 37 10 124908058 124908064 + Frame_Shift_Del DEL AGCCGGA AGCCGGA - TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr10:124908058_124908064delAGCCGGA ENST00000339992.3 + 1 421_427 c.164_170delAGCCGGA c.(163-171)gagccggacfs p.EPD55fs NM_005519.1 NP_005510.1 A2RU54 HMX2_HUMAN H6 family homeobox 2 7 all_neural(114;0.169)|Colorectal(57;0.207)|Glioma(114;0.222) GAGGAGGAGGAGCCGGACGACGGCTGG 0.710000 0 SO:0001589 frameshift_variant ENST00000339992.3 0 1 hg19 CCDS31305.1 TCGA-2J-AAB8-01A-12D-A40W-08 HMX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050841.1 1 0 0 16 135 0 27 0 0 0 27 0 0 0 0 0 0 1 0.491941 18 133 1 27 17 -19.999940 1 1 0 0 1 0 1 1 2.044470 0 0.270000 1.810000 0.268024 0.780000 4.700000e-01 1.000000 1.000000 0.789708 0.780000 0 6.100000e-01 0.980000 ARHGAP5 394 broad.mit.edu 37 14 32586406 32586406 + Frame_Shift_Del DEL T T - TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr14:32586406delT ENST00000345122.3 + 3 4093 c.3778delT c.(3778-3780)tttfs p.F1260fs ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.F1259fs|ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.F1260fs|ARHGAP5_ENST00000433497.1_5'UTR|ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.F1259fs NM_001030055.1 NP_001025226.1 Q13017 RHG05_HUMAN Rho GTPase activating protein 5 55 Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186) LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173) AAGTAATTACTTTGGGATGCC 0.343000 NSCLC(9;77 350 3443 29227 41353) 0 SO:0001589 frameshift_variant ENST00000345122.3 1 0 hg19 CCDS32062.1 TCGA-2J-AAB8-01A-12D-A40W-08 ARHGAP5-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000409735.1 1 0 0 88 484 0 78 1 9.735691e-01 9 25 0 78 2 0 0 0 0 0 0 1 1.000000 104 485 2 76 33 -20.000000 1 1 0 0 1 0 2 2 1.919825 1 0.270000 1.810000 0.270000 0.990000 9.300000e-01 1.000000 1.000000 0.996247 0.990000 1 9.900000e-01 1.000000 SLC4A2 6522 broad.mit.edu 37 7 150772809 150772810 + Frame_Shift_Ins INS - - A rs139739553 byFrequency TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 - A - - Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr7:150772809_150772810insA ENST00000485713.1 + 21 4458_4459 c.3418_3419insA c.(3418-3420)catfs p.H1140fs SLC4A2_ENST00000413384.2_Frame_Shift_Ins_p.H1140fs|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000461735.1_Frame_Shift_Ins_p.H1126fs|SLC4A2_ENST00000392826.2_Frame_Shift_Ins_p.H1131fs|SLC4A2_ENST00000310317.5_Frame_Shift_Ins_p.H1058fs|FASTK_ENST00000489884.1_5'Flank NM_001199692.1 NP_001186621.1 P04920 B3A2_HUMAN solute carrier family 4 (anion exchanger), member 2 33 OV - Ovarian serous cystadenocarcinoma(82;0.0121) TGAGCGGCTGCATCTGCTGCTC 0.599000 0 SO:0001589 frameshift_variant ENST00000485713.1 0 1 hg19 CCDS5917.1 TCGA-2J-AAB8-01A-12D-A40W-08 SLC4A2-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000351039.1 1 0 0 27 399 0 104 0 9.955103e-01 0 126 0 104 2 0 0 0 0 0 0 1 1.000000 29 389 0 101 2 -7.132495 1 1 0 0 1 0 1 1 1.978737 0 0.270000 1.810000 0.233797 0.440000 3.000000e-01 0.620000 0.440000 0.458155 0.440000 0 3.600000e-01 0.540000 OGDHL 55753 broad.mit.edu 37 10 50946068 50946068 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr10:50946068G>A ENST00000374103.4 - 19 2527 c.2442C>T c.(2440-2442)atC>atT p.I814I OGDHL_ENST00000432695.1_Silent_p.I605I|OGDHL_ENST00000419399.1_Silent_p.I757I|OGDHL_ENST00000490844.1_5'UTR NM_018245.2 NP_060715.2 Q9ULD0 OGDHL_HUMAN oxoglutarate dehydrogenase-like 61 AGTTGACCACGATCCAGTTGC 0.622000 0 SO:0001819 synonymous_variant ENST00000374103.4 1 1 hg19 CCDS7234.1 TCGA-2J-AAB8-01A-12D-A40W-08 OGDHL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048007.1 1 0 0 48 1029 0 205 0 0 0 0 205 2 0 0 0 0 0 2 1 1.000000 48 1015 0 198 2 -5.060615 1 1 121412 30 50 1 0 0 0 2.033354 0 0.270000 1.810000 0.262030 0.320000 2.400000e-01 0.420000 0.330000 0.331888 0.320000 0 2.700000e-01 0.380000 HSPA8 3312 broad.mit.edu 37 11 122929855 122929855 + Missense_Mutation SNP A A G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr11:122929855A>G ENST00000532636.1 - 6 1354 c.1235T>C c.(1234-1236)gTc>gCc p.V412A HSPA8_ENST00000534624.1_Missense_Mutation_p.V412A|HSPA8_ENST00000227378.3_Missense_Mutation_p.V412A|HSPA8_ENST00000533540.1_Missense_Mutation_p.V266A|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000453788.2_Missense_Mutation_p.V412A|HSPA8_ENST00000534319.1_Missense_Mutation_p.V176A|HSPA8_ENST00000526110.1_Missense_Mutation_p.V393A|SNORD14E_ENST00000364009.1_RNA|SNORD14C_ENST00000365382.1_RNA P11142 HSP7C_HUMAN heat shock 70kDa protein 8 36 Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) CTTGATGAGGACAGTCATGAC 0.453000 Colon(21;486 594 5900 6733 14272) 0 SO:0001583 missense ENST00000532636.1 0 1 hg19 CCDS8440.1 . . . . . . . . . . A 1.596 -0.527894 0.04112 . . ENSG00000109971 ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000524552 T;T;T;T;T;T;T;T 0.00932 5.53;5.53;5.53;5.53;5.53;5.53;5.53;5.53 4.85 4.85 0.62838 . 0.073163 0.52532 D 0.000068 T 0.00875 0.0029 N 0.26092 0.79 0.80722 D 1 B;B;B 0.06786 0.0;0.001;0.0 B;B;B 0.09377 0.004;0.001;0.004 T 0.46034 -0.9220 10 0.02654 T 1 -23.4681 14.7123 0.69241 1.0:0.0:0.0:0.0 . 412;412;412 Q53GZ6;P11142-2;P11142 .;.;HSP7C_HUMAN A 412;266;412;412;412;176;393;3 ENSP00000437125:V412A;ENSP00000437189:V266A;ENSP00000432083:V412A;ENSP00000404372:V412A;ENSP00000227378:V412A;ENSP00000433316:V176A;ENSP00000433584:V393A;ENSP00000435908:V3A ENSP00000227378:V412A V - 2 0 HSPA8 122435065 0.998000 0.40836 0.932000 0.37286 0.060000 0.15804 3.668000 0.54554 1.935000 0.56089 0.459000 0.35465 GTC TCGA-2J-AAB8-01A-12D-A40W-08 HSPA8-004 PUTATIVE alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000387515.1 0 0 0 4 287 0 45 1 9.968502e-01 31 948 0 45 2 0 0 0 0 0 2 1 0.889421 4 285 0 42 2 -3.100669 1 1 0 0 1 0 1 1 1.962501 0 0.270000 1.810000 0.230526 0.100000 3.000000e-02 0.230000 0.100000 0.118549 0.100000 0 6.000000e-02 0.170000 KCNA4 3739 broad.mit.edu 37 11 30033513 30033513 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr11:30033513C>T ENST00000328224.6 - 2 1946 c.713G>A c.(712-714)gGa>gAa p.G238E KCNA4_ENST00000526518.1_5'Flank NM_002233.3 NP_002224.1 P22459 KCNA4_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 4 78 Dalfampridine(DB06637) CAGGCGGCCTCCTGATTGATA 0.483000 0 SO:0001583 missense ENST00000328224.6 1 1 hg19 CCDS41629.1 . . . . . . . . . . C 22.5 4.291932 0.80914 . . ENSG00000182255 ENST00000328224 T 0.81247 -1.47 4.94 4.94 0.65067 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); 0.000000 0.85682 D 0.000000 D 0.91898 0.7435 M 0.90870 3.155 0.80722 D 1 D 0.76494 0.999 D 0.77004 0.989 D 0.93827 0.7124 10 0.87932 D 0 . 18.1944 0.89817 0.0:1.0:0.0:0.0 . 238 P22459 KCNA4_HUMAN E 238 ENSP00000328511:G238E ENSP00000328511:G238E G - 2 0 KCNA4 29990089 1.000000 0.71417 0.985000 0.45067 0.980000 0.70556 7.787000 0.85759 2.297000 0.77311 0.655000 0.94253 GGA TCGA-2J-AAB8-01A-12D-A40W-08 KCNA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388074.2 1 0 0 52 675 0 150 0 0 0 0 150 2 0 0 0 0 0 2 1 1.000000 52 669 0 148 2 -11.054780 1 1 0 0 1 0 1 1 1.962501 0 0.270000 1.810000 0.230526 0.500000 3.700000e-01 0.640000 0.500000 0.508566 0.500000 0 4.300000e-01 0.570000 RAG1 5896 broad.mit.edu 37 11 36595189 36595189 + Missense_Mutation SNP G G A rs4151026 TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr11:36595189G>A ENST00000299440.5 + 2 447 c.335G>A c.(334-336)cGc>cAc p.R112H NM_000448.2 NP_000439 P15918 RAG1_HUMAN recombination activating gene 1 p.R112L(1) 65 all_lung(20;0.226) all_hematologic(20;0.107) CATCTCTGCCGCATCTGTGGG 0.453000 Familial Hemophagocytic Lymphohistiocytosis Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363) 1 Substitution - Missense(1) SO:0001583 missense Familial Cancer Database FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR ENST00000299440.5 0 1 hg19 CCDS7902.1 . . . . . . . . . . G 32 5.146608 0.94603 . . ENSG00000166349 ENST00000534663;ENST00000299440 T;T 0.74737 -0.87;-0.87 6.14 6.14 0.99180 . 0.000000 0.85682 D 0.000000 D 0.89976 0.6871 M 0.91090 3.175 0.80722 D 1 D 0.76494 0.999 D 0.76575 0.988 D 0.90685 0.4608 10 0.87932 D 0 . 20.8597 0.99761 0.0:0.0:1.0:0.0 . 112 P15918 RAG1_HUMAN H 112 ENSP00000434610:R112H;ENSP00000299440:R112H ENSP00000299440:R112H R + 2 0 RAG1 36551765 1.000000 0.71417 1.000000 0.80357 0.867000 0.49689 8.856000 0.92245 2.937000 0.99478 0.650000 0.86243 CGC TCGA-2J-AAB8-01A-12D-A40W-08 RAG1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389535.1 0 0 0 9 410 0 58 0 0 0 0 58 2 0 0 0 0 0 2 0 0.011318 9 402 1 58 22 -2.382451 0 1 121412 3 40 1 0 1 1 1.962501 0 0.270000 1.810000 0.230526 0.150000 7.000000e-02 0.270000 0.150000 0.165595 0.150000 0 1.000000e-01 0.210000 OR52M1 119772 broad.mit.edu 37 11 4566499 4566499 + Missense_Mutation SNP G G A rs138278883 TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr11:4566499G>A ENST00000360213.1 + 1 79 c.79G>A c.(79-81)Gtc>Atc p.V27I NM_001004137.1 NP_001004137.1 Q8NGK5 O52M1_HUMAN olfactory receptor, family 52, subfamily M, member 1 18 Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577) GTCCCTACACGTCTGGCTCTC 0.542000 0 SO:0001583 missense ENST00000360213.1 0 1 hg19 CCDS31353.1 . . . . . . . . . . G 0.004 -2.289704 0.00248 0.0 1.16E-4 ENSG00000197790 ENST00000360213 T 0.00296 8.24 4.82 -2.26 0.06867 . 0.644741 0.13674 N 0.370680 T 0.00073 0.0002 N 0.11313 0.125 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.28808 -1.0032 10 0.02654 T 1 . 6.5865 0.22624 0.4305:0.4103:0.1592:0.0 . 27 Q8NGK5 O52M1_HUMAN I 27 ENSP00000353343:V27I ENSP00000353343:V27I V + 1 0 OR52M1 4523075 0.000000 0.05858 0.003000 0.11579 0.145000 0.21501 -1.630000 0.02028 -0.158000 0.11040 -0.294000 0.09567 GTC TCGA-2J-AAB8-01A-12D-A40W-08 OR52M1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385847.1 0 0 0 6 258 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 0.965056 6 257 0 65 2 -3.307470 1 1 121412 18 43 1 0 1 1 1.962501 0 0.270000 1.810000 0.230526 0.160000 6.000000e-02 0.320000 0.160000 0.182603 0.160000 0 1.100000e-01 0.250000 GPR133 283383 broad.mit.edu 37 12 131471825 131471825 + Missense_Mutation SNP G G T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:131471825G>T ENST00000261654.5 + 6 1235 c.676G>T c.(676-678)Gat>Tat p.D226Y RP11-76C10.5_ENST00000542980.1_lincRNA|GPR133_ENST00000535015.1_Missense_Mutation_p.D258Y NM_198827.3 NP_942122.2 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 67 all_neural(191;0.0982)|Medulloblastoma(191;0.163) CGGTGCTTTCGATGAGTTCAT 0.542000 0 SO:0001583 missense ENST00000261654.5 1 1 hg19 CCDS9272.1 . . . . . . . . . . G 17.30 3.355239 0.61293 . . ENSG00000111452 ENST00000261654;ENST00000542091;ENST00000535015 D;D;D 0.82803 -1.65;-1.65;-1.65 4.46 4.46 0.54185 Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1); 0.000000 0.85682 D 0.000000 D 0.92688 0.7676 M 0.91818 3.245 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.94367 0.7592 10 0.66056 D 0.02 . 16.1186 0.81325 0.0:0.0:1.0:0.0 . 258;226 B7ZLF7;Q6QNK2 .;GP133_HUMAN Y 226;166;258 ENSP00000261654:D226Y;ENSP00000442501:D166Y;ENSP00000444425:D258Y ENSP00000261654:D226Y D + 1 0 GPR133 130037778 1.000000 0.71417 0.280000 0.24747 0.426000 0.31534 8.703000 0.91344 2.024000 0.59613 0.591000 0.81541 GAT TCGA-2J-AAB8-01A-12D-A40W-08 GPR133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399356.1 0 0 0 9 386 0 90 0 6.961761e-04 0 2 0 90 2 0 0 0 0 0 2 1 0.993714 8 378 0 89 2 -2.683534 1 1 0 0 1 0 1 1 1.830850 1 0.270000 1.810000 0.161305 0.140000 7.000000e-02 0.260000 0.150000 0.160273 0.140000 0 1.000000e-01 0.210000 GSG1 83445 broad.mit.edu 37 12 13240148 13240148 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:13240148C>T ENST00000396302.3 - 5 898 c.700G>A c.(700-702)Gac>Aac p.D234N GSG1_ENST00000432710.2_Silent_p.A205A|GSG1_ENST00000337630.6_Silent_p.A192A|GSG1_ENST00000351606.6_Missense_Mutation_p.D270N|GSG1_ENST00000457134.2_Silent_p.A141A|GSG1_ENST00000396310.2_Silent_p.A161A|GSG1_ENST00000537302.1_Silent_p.A164A|GSG1_ENST00000324458.8_Silent_p.A228A NM_031289.3 NP_112579.2 Q2KHT4 GSG1_HUMAN germ cell associated 1 10 Prostate(47;0.183) AGTTGACAGTCGCTTGGAAGA 0.507000 0 SO:0001583 missense ENST00000396302.3 1 1 hg19 CCDS8659.2 . . . . . . . . . . C 3.860 -0.030023 0.07543 . . ENSG00000111305 ENST00000396302;ENST00000351606;ENST00000405543 T;T 0.38240 1.16;1.15 5.2 -0.697 0.11284 . . . . . T 0.23210 0.0561 . . . 0.80722 D 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.01281 0.0;0.0;0.0 T 0.05550 -1.0878 8 0.36615 T 0.2 . 7.5868 0.27998 0.0:0.1412:0.4491:0.4097 . 270;270;234 Q2KHT4-7;G3XAB9;F1T0A0 .;.;. N 234;270;231 ENSP00000379596:D234N;ENSP00000336857:D270N ENSP00000336857:D270N D - 1 0 GSG1 13131415 0.994000 0.37717 0.994000 0.49952 0.812000 0.45895 0.278000 0.18753 0.004000 0.14682 -0.477000 0.04895 GAC TCGA-2J-AAB8-01A-12D-A40W-08 GSG1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000316545.1 1 0 0 82 432 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 1.000000 80 428 0 118 2 -20.000000 1 1 121412 4 35 1 2 2 4 2.151653 1 0.270000 1.810000 0.305622 0.990000 9.900000e-01 1.000000 1.000000 0.999324 0.990000 1 9.900000e-01 1.000000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2J-AAB8-01A-12D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 18 188 0 73 1 2.647824e-01 4 7 0 73 2 1 1 36 335 0 321 2 1 0.999983 17 185 0 69 2 -7.949440 1 1 0 0 1 2 2 4 2.151653 1 0.270000 1.810000 0.305622 0.720000 4.300000e-01 1.000000 1.000000 0.744243 0.720000 0 5.600000e-01 1.000000 KCNA1 3736 broad.mit.edu 37 12 5021099 5021099 + Silent SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:5021099C>T ENST00000382545.3 + 2 1662 c.555C>T c.(553-555)tgC>tgT p.C185C KCNA1_ENST00000543874.2_Intron NM_000217.2 NP_000208.2 Q09470 KCNA1_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia) 63 Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236) TCATCTTTTGCCTGGAGACGC 0.582000 0 SO:0001819 synonymous_variant ENST00000382545.3 0 1 hg19 CCDS8535.1 TCGA-2J-AAB8-01A-12D-A40W-08 KCNA1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000103343.2 0 0 0 5 348 0 57 0 0 0 0 57 2 0 0 0 0 0 2 1 0.935118 5 342 0 56 2 -3.092612 1 1 0 0 1 1 2 3 2.134376 0 0.270000 1.810000 0.285435 0.120000 4.000000e-02 1.000000 0.110000 0.236770 0.120000 0 7.000000e-02 0.230000 KRT71 112802 broad.mit.edu 37 12 52946543 52946543 + Missense_Mutation SNP C C T rs665522 byFrequency TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:52946543C>T ENST00000267119.5 - 1 388 c.319G>A c.(319-321)Gtc>Atc p.V107I NM_033448.2 NP_258259.1 Q3SY84 K2C71_HUMAN keratin 71 22 CTCTCATTGACGGTAACCTGG 0.617000 0 SO:0001583 missense ENST00000267119.5 1 0 hg19 CCDS8831.1 383 0.17536630036630035 143 0.29065040650406504 60 0.16574585635359115 10 0.017482517482517484 170 0.22427440633245382 C 8.203 0.798579 0.16397 0.300272 0.23686 ENSG00000139648 ENST00000267119 T 0.76839 -1.05 4.82 3.0 0.34707 . 0.000000 0.40728 N 0.001039 T 0.00012 0.0000 L 0.37697 1.125 0.36952 P 0.10709500000000005 B 0.26147 0.143 B 0.21360 0.034 T 0.07501 -1.0769 9 0.23891 T 0.37 . 8.1494 0.31132 0.0:0.6857:0.0:0.3143 rs665522;rs1621577;rs17730179;rs665522 107 Q3SY84 K2C71_HUMAN I 107 ENSP00000267119:V107I ENSP00000267119:V107I V - 1 0 KRT71 51232810 0.001000 0.12720 0.740000 0.30986 0.941000 0.58515 -0.112000 0.10791 0.579000 0.29504 -0.258000 0.10820 GTC TCGA-2J-AAB8-01A-12D-A40W-08 KRT71-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396487.1 0 0 1 62 340 0 59 0 0 0 0 59 2 0 0 0 0 0 2 1 1.000000 61 338 0 58 2 -2.055756 0 1 121410 25482 77 1 1 2 3 2.124965 0 0.270000 1.810000 0.284489 0.990000 9.100000e-01 1.000000 1.000000 0.994994 0.990000 1 9.900000e-01 1.000000 HNRNPA1 3178 broad.mit.edu 37 12 54675182 54675182 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:54675182C>T ENST00000340913.6 + 2 81 c.28C>T c.(28-30)Ccc>Tcc p.P10S CBX5_ENST00000209875.4_5'Flank|HNRNPA1_ENST00000546500.1_Missense_Mutation_p.P10S|RP11-968A15.8_ENST00000553061.1_RNA|RP11-968A15.2_ENST00000547177.1_RNA|HNRNPA1_ENST00000547276.1_Missense_Mutation_p.P10S|HNRNPA1_ENST00000330752.8_Missense_Mutation_p.P10S NM_002136.2|NM_031157.2 NP_002127.1|NP_112420.1 P09651 ROA1_HUMAN heterogeneous nuclear ribonucleoprotein A1 20 TCCTAAAGAGCCCGAACAGCT 0.488000 Colon(83;502 1289 8436 16406 24870) 0 SO:0001583 missense ENST00000340913.6 1 1 hg19 CCDS44909.1 . . . . . . . . . . C 26.1 4.701605 0.88924 . . ENSG00000135486 ENST00000546500;ENST00000547708;ENST00000547617;ENST00000552494;ENST00000340913;ENST00000330752;ENST00000552591;ENST00000551702;ENST00000551133;ENST00000547276;ENST00000548688 D;D;D;D;D;D;D 0.88354 -2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37 4.43 4.43 0.53597 . 0.000000 0.50627 D 0.000115 D 0.89167 0.6638 L 0.33189 0.99 0.54753 D 0.999987 D;D;P;B;D;D 0.58620 0.96;0.98;0.952;0.168;0.98;0.983 P;P;P;B;P;P 0.56278 0.575;0.716;0.575;0.191;0.716;0.795 D 0.90171 0.4235 10 0.59425 D 0.04 . 15.3753 0.74598 0.0:1.0:0.0:0.0 . 10;10;10;10;10;10 F8VRQ1;F8W6I7;F8VSB5;P09651-3;P09651-2;P09651 .;.;.;.;.;ROA1_HUMAN S 10;10;10;10;10;10;10;10;10;10;29 ENSP00000448617:P10S;ENSP00000448229:P10S;ENSP00000341826:P10S;ENSP00000333504:P10S;ENSP00000448117:P10S;ENSP00000447260:P10S;ENSP00000447782:P29S ENSP00000333504:P10S P + 1 0 HNRNPA1 52961449 1.000000 0.71417 1.000000 0.80357 0.940000 0.58332 7.705000 0.84606 2.407000 0.81776 0.491000 0.48974 CCC TCGA-2J-AAB8-01A-12D-A40W-08 HNRNPA1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000405480.1 1 0 1 58 367 0 90 1 1 181 487 0 90 2 0 0 0 0 0 2 1 1.000000 57 362 0 88 2 -19.999980 1 1 0 0 1 1 2 3 2.124965 0 0.270000 1.810000 0.284489 0.990000 8.000000e-01 1.000000 1.000000 0.971104 0.990000 1 9.100000e-01 1.000000 ITGA7 3679 broad.mit.edu 37 12 56086734 56086734 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr12:56086734C>T ENST00000555728.1 - 22 2898 c.2870G>A c.(2869-2871)cGg>cAg p.R957Q ITGA7_ENST00000452168.2_Missense_Mutation_p.R820Q|ITGA7_ENST00000394229.2_Missense_Mutation_p.R913Q|ITGA7_ENST00000553804.1_Missense_Mutation_p.R917Q|ITGA7_ENST00000347027.6_Missense_Mutation_p.R907Q|ITGA7_ENST00000257880.7_Missense_Mutation_p.R957Q|ITGA7_ENST00000257879.6_Missense_Mutation_p.R913Q|ITGA7_ENST00000394230.2_Missense_Mutation_p.R917Q Q13683 ITA7_HUMAN integrin, alpha 7 50 CAGCTCCCGCCGCCTCCTATC 0.597000 0 SO:0001583 missense ENST00000555728.1 1 1 hg19 . . . . . . . . . . C 31 5.096296 0.94197 . . ENSG00000135424 ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728 T;T;T;T;T;T;T;T 0.45668 0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89 5.17 5.17 0.71159 Integrin alpha-2 (1); 0.262756 0.29861 N 0.011019 T 0.57169 0.2035 M 0.72353 2.195 0.34499 D 0.705846 D;P;D;D 0.60160 0.963;0.948;0.969;0.987 P;P;P;P 0.56612 0.745;0.768;0.802;0.776 T 0.69709 -0.5072 10 0.56958 D 0.05 . 14.1032 0.65070 0.0:1.0:0.0:0.0 . 820;957;917;976 Q13683-13;Q13683;Q13683-3;Q4LE35 .;ITA7_HUMAN;.;. Q 917;913;907;820;957;917;913;786;957 ENSP00000452120:R917Q;ENSP00000257879:R913Q;ENSP00000343009:R907Q;ENSP00000393844:R820Q;ENSP00000257880:R957Q;ENSP00000377777:R917Q;ENSP00000377776:R913Q;ENSP00000452387:R957Q ENSP00000257879:R913Q R - 2 0 ITGA7 54373001 0.899000 0.30636 1.000000 0.80357 0.989000 0.77384 1.504000 0.35726 2.706000 0.92434 0.585000 0.79938 CGG TCGA-2J-AAB8-01A-12D-A40W-08 ITGA7-014 KNOWN basic protein_coding protein_coding OTTHUMT00000410138.1 1 0 0 17 190 0 23 0 1.806042e-01 0 9 0 23 2 0 0 0 0 0 2 1 0.999967 17 186 0 22 2 -3.142732 1 1 121412 3 37 1 1 2 3 2.124965 0 0.270000 1.810000 0.284489 0.650000 3.800000e-01 1.000000 0.620000 0.684621 0.650000 0 5.000000e-01 0.900000 LATS2 26524 broad.mit.edu 37 13 21562295 21562295 + Missense_Mutation SNP G G T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr13:21562295G>T ENST00000382592.4 - 4 2029 c.1624C>A c.(1624-1626)Cag>Aag p.Q542K LATS2_ENST00000472754.1_5'Flank|LATS2_ENST00000542899.1_Missense_Mutation_p.Q542K NM_014572.2 NP_055387.2 large tumor suppressor kinase 2 45 all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) CGGAGGCTCTGCTCCATGCCT 0.657000 0 SO:0001583 missense ENST00000382592.4 1 1 hg19 CCDS9294.1 . . . . . . . . . . G 14.63 2.592668 0.46214 . . ENSG00000150457 ENST00000382592;ENST00000542899 T;T 0.58652 0.32;0.32 5.12 5.12 0.69794 . 0.189519 0.37577 N 0.002035 T 0.46288 0.1385 N 0.22421 0.69 0.45979 D 0.998794 P 0.47762 0.9 B 0.40940 0.344 T 0.42172 -0.9467 10 0.30854 T 0.27 . 18.8138 0.92070 0.0:0.0:1.0:0.0 . 542 Q9NRM7 LATS2_HUMAN K 542 ENSP00000372035:Q542K;ENSP00000441817:Q542K ENSP00000372035:Q542K Q - 1 0 LATS2 20460295 1.000000 0.71417 1.000000 0.80357 0.391000 0.30476 4.679000 0.61649 2.691000 0.91804 0.549000 0.68633 CAG TCGA-2J-AAB8-01A-12D-A40W-08 LATS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044102.1 1 0 0 42 303 0 67 0 2.608791e-01 0 8 0 67 2 0 0 0 0 0 2 1 1.000000 42 296 0 64 2 -20.000000 1 1 0 0 1 1 2 3 2.232580 1 0.270000 1.810000 0.325542 0.990000 7.300000e-01 1.000000 1.000000 0.951615 0.990000 1 8.600000e-01 1.000000 LATS2 26524 broad.mit.edu 37 13 21562296 21562296 + Silent SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr13:21562296C>T ENST00000382592.4 - 4 2028 c.1623G>A c.(1621-1623)gaG>gaA p.E541E LATS2_ENST00000472754.1_5'Flank|LATS2_ENST00000542899.1_Silent_p.E541E NM_014572.2 NP_055387.2 large tumor suppressor kinase 2 45 all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244) GGAGGCTCTGCTCCATGCCTG 0.657000 0 SO:0001819 synonymous_variant ENST00000382592.4 1 1 hg19 CCDS9294.1 TCGA-2J-AAB8-01A-12D-A40W-08 LATS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044102.1 1 0 0 44 303 0 65 0 3.265337e-01 0 9 0 65 2 0 0 0 0 0 2 1 1.000000 44 296 0 62 2 -20.000000 1 1 121390 2 35 1 1 2 3 2.232580 1 0.270000 1.810000 0.325542 0.990000 7.700000e-01 1.000000 1.000000 0.966245 0.990000 1 9.000000e-01 1.000000 TJP1 7082 broad.mit.edu 37 15 30020212 30020212 + Nonsense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr15:30020212G>A ENST00000346128.6 - 16 2503 c.2029C>T c.(2029-2031)Cga>Tga p.R677* TJP1_ENST00000356107.6_Nonsense_Mutation_p.R677*|TJP1_ENST00000545208.2_Nonsense_Mutation_p.R677*|RP11-680F8.4_ENST00000560740.1_RNA|TJP1_ENST00000400011.2_Nonsense_Mutation_p.R681* NM_003257.3|NM_175610.2 NP_003248.3|NP_783297.2 Q07157 ZO1_HUMAN tight junction protein 1 68 all_lung(180;7.48e-11)|Breast(32;0.000153) CCAGCGTCTCGTGGTTCACTC 0.393000 Melanoma(77;681 1843 6309 6570) 0 SO:0001587 stop_gained ENST00000346128.6 0 1 hg19 CCDS42007.1 . . . . . . . . . . G 38 7.086799 0.98055 . . ENSG00000104067 ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107 . . . 5.42 3.2 0.36748 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 11.9192 0.52783 0.0:0.0:0.419:0.581 . . . . X 677;681;677;677;677 . . R - 1 2 TJP1 27807504 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 4.681000 0.61663 1.366000 0.46076 0.655000 0.94253 CGA TCGA-2J-AAB8-01A-12D-A40W-08 TJP1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000268237.3 0 0 1 31 255 1 71 1 3.238952e-01 3 15 1 71 3 0 0 0 0 0 2 1 0.997561 31 255 1 71 14 -3.075765 1 1 0 0 1 1 2 3 2.057332 0 0.270000 1.810000 0.271966 0.800000 5.600000e-01 1.000000 1.000000 0.812378 0.800000 0 6.700000e-01 0.960000 ATP8B4 79895 broad.mit.edu 37 15 50223420 50223420 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr15:50223420C>T ENST00000284509.6 - 16 1679 c.1538G>A c.(1537-1539)cGg>cAg p.R513Q ATP8B4_ENST00000559829.1_Missense_Mutation_p.R513Q NM_024837.2 NP_079113.2 Q8TF62 AT8B4_HUMAN ATPase, class I, type 8B, member 4 73 all_lung(180;0.00183) CTCTGGGGTCCGGGATTTAAA 0.398000 0 SO:0001583 missense ENST00000284509.6 1 1 hg19 CCDS32238.1 . . . . . . . . . . C 35 5.454782 0.96223 . . ENSG00000104043 ENST00000284509 T 0.72505 -0.66 5.61 5.61 0.85477 ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1); 0.000000 0.85682 D 0.000000 D 0.87233 0.6126 M 0.90082 3.085 0.58432 D 0.999995 D 0.89917 1.0 D 0.97110 1.0 D 0.89451 0.3730 10 0.87932 D 0 . 17.1302 0.86724 0.0:1.0:0.0:0.0 . 513 Q8TF62 AT8B4_HUMAN Q 513 ENSP00000284509:R513Q ENSP00000284509:R513Q R - 2 0 ATP8B4 48010712 1.000000 0.71417 0.998000 0.56505 0.988000 0.76386 7.532000 0.81985 2.648000 0.89879 0.585000 0.79938 CGG TCGA-2J-AAB8-01A-12D-A40W-08 ATP8B4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000418100.1 1 0 1 41 301 0 69 0 0 0 1 0 69 2 0 0 0 0 0 2 1 1.000000 41 298 0 68 2 -3.075779 1 1 0 0 1 1 2 3 2.061404 0 0.270000 1.810000 0.271966 0.890000 6.500000e-01 1.000000 1.000000 0.883329 0.890000 1 7.600000e-01 1.000000 HCN4 10021 broad.mit.edu 37 15 73616169 73616169 + Nonsense_Mutation SNP G G T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr15:73616169G>T ENST00000261917.3 - 8 3258 c.2265C>A c.(2263-2265)tgC>tgA p.C755* NM_005477.2 NP_005468.1 Q9Y3Q4 HCN4_HUMAN hyperpolarization activated cyclic nucleotide-gated potassium channel 4 55 CGCGGTGCGCGCAGTGGGCCA 0.637000 0 SO:0001587 stop_gained ENST00000261917.3 0 1 hg19 CCDS10248.1 . . . . . . . . . . G 43 10.237229 0.99366 . . ENSG00000138622 ENST00000261917 . . . 3.45 -4.57 0.03421 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.38643 T 0.18 . 5.844 0.18652 0.4255:0.0:0.4383:0.1362 . . . . X 755 . ENSP00000261917:C755X C - 3 2 HCN4 71403222 0.001000 0.12720 0.425000 0.26659 0.252000 0.25951 -1.587000 0.02108 -1.258000 0.02471 0.305000 0.20034 TGC TCGA-2J-AAB8-01A-12D-A40W-08 HCN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268900.2 1 0 1 36 192 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 36 189 0 43 2 -3.345269 1 1 0 0 1 1 2 3 2.061404 0 0.270000 1.810000 0.271966 0.990000 8.500000e-01 1.000000 1.000000 0.987738 0.990000 1 9.900000e-01 1.000000 UMOD 7369 broad.mit.edu 37 16 20355441 20355441 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr16:20355441G>A ENST00000570689.1 - 6 1382 c.1236C>T c.(1234-1236)atC>atT p.I412I UMOD_ENST00000396134.2_Silent_p.I445I|UMOD_ENST00000570331.1_5'Flank|UMOD_ENST00000396142.2_Silent_p.I412I|UMOD_ENST00000396138.4_Silent_p.I461I|UMOD_ENST00000424589.1_Silent_p.I445I|UMOD_ENST00000302509.4_Silent_p.I412I P07911 UROM_HUMAN uromodulin 41 CACGGATGATGATCTCATCTG 0.537000 0 SO:0001819 synonymous_variant ENST00000570689.1 1 1 hg19 CCDS10583.1 TCGA-2J-AAB8-01A-12D-A40W-08 UMOD-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000436862.1 1 0 0 18 256 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 0.999983 17 255 0 54 2 -3.318794 1 1 0 0 1 1 2 3 2.123221 0 0.270000 1.810000 0.283541 0.520000 3.100000e-01 1.000000 0.490000 0.568936 0.520000 0 4.000000e-01 0.710000 SRCAP 10847 broad.mit.edu 37 16 30723277 30723277 + Missense_Mutation SNP C C G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr16:30723277C>G ENST00000262518.4 + 12 1999 c.1614C>G c.(1612-1614)agC>agG p.S538R SNORA30_ENST00000384028.1_RNA|SRCAP_ENST00000344771.4_Missense_Mutation_p.S538R|SRCAP_ENST00000395059.2_Missense_Mutation_p.S538R NM_006662.2 NP_006653.2 Q6ZRS2 SRCAP_HUMAN Snf2-related CREBBP activator protein 136 Colorectal(24;0.198) AATCACAGAGCCAAGCAGATG 0.498000 0 SO:0001583 missense ENST00000262518.4 1 1 hg19 CCDS10689.2 . . . . . . . . . . C 7.096 0.573060 0.13623 . . ENSG00000080603 ENST00000262518;ENST00000395059;ENST00000344771 D;D;D 0.91237 -2.81;-2.79;-2.79 4.74 3.79 0.43588 . 0.097043 0.46442 D 0.000291 D 0.83078 0.5176 L 0.36672 1.1 0.28350 N 0.920921 P;P;P 0.37276 0.589;0.589;0.454 B;B;B 0.33454 0.108;0.164;0.079 T 0.74934 -0.3495 10 0.25751 T 0.34 -10.7481 10.4907 0.44750 0.0:0.9073:0.0:0.0927 . 538;538;538 Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 .;.;SRCAP_HUMAN R 538 ENSP00000262518:S538R;ENSP00000378499:S538R;ENSP00000343042:S538R ENSP00000262518:S538R S + 3 2 SRCAP 30630778 0.997000 0.39634 1.000000 0.80357 0.863000 0.49368 0.795000 0.26972 1.355000 0.45865 0.563000 0.77884 AGC TCGA-2J-AAB8-01A-12D-A40W-08 SRCAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255523.1 1 0 1 33 275 0 42 0 3.015895e-01 1 9 0 42 2 0 0 0 0 0 2 1 1.000000 33 274 0 42 2 -12.847140 1 1 0 0 1 1 2 3 2.093897 0 0.270000 1.810000 0.278763 0.810000 5.700000e-01 1.000000 1.000000 0.823192 0.810000 0 6.800000e-01 0.990000 MARVELD3 91862 broad.mit.edu 37 16 71674725 71674725 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr16:71674725G>A ENST00000299952.4 + 3 1071 c.1028G>A c.(1027-1029)cGc>cAc p.R343H MARVELD3_ENST00000561682.1_Intron|PHLPP2_ENST00000540628.1_3'UTR|MARVELD3_ENST00000565261.1_3'UTR NM_001017967.3|NM_001271329.1 NP_001017967.2|NP_001258258.1 Q96A59 MALD3_HUMAN MARVEL domain containing 3 17 Ovarian(137;0.125) CTCTATGCCCGCAAGGGTCTC 0.587000 0 SO:0001583 missense ENST00000299952.4 0 1 hg19 CCDS32478.1 . . . . . . . . . . G 32 5.120380 0.94385 . . ENSG00000140832 ENST00000299952 D 0.86865 -2.18 5.79 5.79 0.91817 . 0.096682 0.64402 D 0.000001 D 0.93288 0.7861 . . . 0.80722 D 1 D 0.89917 1.0 D 0.69824 0.966 D 0.93287 0.6665 9 0.59425 D 0.04 -23.7209 17.535 0.87827 0.0:0.0:1.0:0.0 . 343 Q96A59-2 . H 343 ENSP00000299952:R343H ENSP00000299952:R343H R + 2 0 MARVELD3 70232226 1.000000 0.71417 1.000000 0.80357 0.966000 0.64601 6.861000 0.75478 2.739000 0.93911 0.655000 0.94253 CGC TCGA-2J-AAB8-01A-12D-A40W-08 MARVELD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268990.1 0 0 0 5 265 0 60 0 5.788246e-02 0 17 0 60 2 0 0 0 0 0 2 1 0.936269 5 262 0 60 2 -2.838471 1 1 121412 1 26 1 1 2 3 2.099584 0 0.270000 1.810000 0.279724 0.150000 5.000000e-02 1.000000 0.140000 0.231663 0.150000 0 9.000000e-02 0.260000 RPA1 6117 broad.mit.edu 37 17 1792037 1792037 + Silent SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:1792037C>T ENST00000254719.5 + 14 1553 c.1443C>T c.(1441-1443)tgC>tgT p.C481C NM_002945.3 NP_002936.1 P27694 RFA1_HUMAN replication protein A1, 70kDa 10 ACCAAGCCTGCCCGACTCAGG 0.483000 Nucleotide excision repair (NER) 0 SO:0001819 synonymous_variant ENST00000254719.5 0 1 hg19 CCDS11014.1 TCGA-2J-AAB8-01A-12D-A40W-08 RPA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207118.2 0 0 0 5 328 0 71 0 2.465291e-01 0 53 0 71 2 0 0 0 0 0 2 1 0.936504 5 325 0 68 2 -3.002491 1 1 0 0 1 0 1 1 1.819173 1 0.270000 1.810000 0.156069 0.100000 3.000000e-02 0.210000 0.100000 0.112894 0.100000 0 6.000000e-02 0.160000 IGFBP4 3487 broad.mit.edu 37 17 38609333 38609333 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:38609333G>A ENST00000269593.4 + 2 721 c.446G>A c.(445-447)cGg>cAg p.R149Q IGFBP4_ENST00000542955.1_Missense_Mutation_p.R49Q NM_001552.2 NP_001543.2 P22692 IBP4_HUMAN insulin-like growth factor binding protein 4 5 Breast(137;0.000496) STAD - Stomach adenocarcinoma(5;5.91e-05) ATTCGAGACCGGAGCACCAGT 0.602000 GBM(160;940 3581 26177) 0 SO:0001583 missense ENST00000269593.4 0 1 hg19 CCDS11367.1 . . . . . . . . . . G 14.76 2.632840 0.47049 . . ENSG00000141753 ENST00000542955;ENST00000269593 T;T 0.26223 1.75;2.1 5.92 4.88 0.63580 Thyroglobulin type-1 (1); 0.660269 0.15633 N 0.252297 T 0.18383 0.0441 N 0.19112 0.55 0.33413 D 0.578843 B 0.24043 0.096 B 0.09377 0.004 T 0.09840 -1.0656 10 0.35671 T 0.21 -4.9399 15.905 0.79419 0.0:0.0:0.8563:0.1437 . 149 P22692 IBP4_HUMAN Q 49;149 ENSP00000437734:R49Q;ENSP00000269593:R149Q ENSP00000269593:R149Q R + 2 0 IGFBP4 35862859 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 2.924000 0.48876 2.818000 0.97014 0.655000 0.94253 CGG TCGA-2J-AAB8-01A-12D-A40W-08 IGFBP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257134.1 0 0 0 4 199 0 29 0 9.978706e-01 0 750 0 29 2 0 0 0 0 0 2 1 0.888876 4 197 0 28 2 -3.587982 1 1 0 0 1 0 1 1 2.046865 0 0.270000 1.810000 0.268024 0.160000 5.000000e-02 0.340000 0.140000 0.177768 0.160000 0 9.000000e-02 0.250000 MAPT 4137 broad.mit.edu 37 17 44060812 44060812 + Silent SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:44060812C>T ENST00000571987.1 + 5 642 c.642C>T c.(640-642)agC>agT p.S214S MAPT_ENST00000431008.3_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000344290.5_Silent_p.S214S|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_Silent_p.S214S|MAPT_ENST00000415613.2_Silent_p.S214S P10636 TAU_HUMAN microtubule-associated protein tau 38 Melanoma(429;0.216) Docetaxel(DB01248)|Paclitaxel(DB01229) GGCCGGGGAGCAAGGAGGAGG 0.687000 0 SO:0001819 synonymous_variant ENST00000571987.1 1 1 hg19 CCDS11501.1 TCGA-2J-AAB8-01A-12D-A40W-08 MAPT-008 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000440133.1 0 0 0 6 77 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 0.959792 6 72 0 23 2 -10.833970 1 1 0 0 1 0 1 1 2.046865 0 0.270000 1.810000 0.268024 0.550000 2.300000e-01 1.000000 1.000000 0.583700 0.550000 0 3.700000e-01 0.790000 PITPNM3 83394 broad.mit.edu 37 17 6428759 6428759 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:6428759G>A ENST00000262483.8 - 3 230 c.143C>T c.(142-144)gCc>gTc p.A48V PITPNM3_ENST00000421306.3_Intron NM_031220.3 NP_112497.2 Q9BZ71 PITM3_HUMAN PITPNM family member 3 36 AATGAGGATGGCATTCTTCCC 0.542000 0 SO:0001583 missense ENST00000262483.8 0 1 hg19 CCDS11076.1 . . . . . . . . . . G 9.783 1.175926 0.21704 . . ENSG00000091622 ENST00000262483 T 0.19806 2.12 4.67 4.67 0.58626 . 0.121347 0.53938 D 0.000043 T 0.32133 0.0819 L 0.34521 1.04 0.41624 D 0.988988 D 0.89917 1.0 D 0.83275 0.996 T 0.02371 -1.1169 10 0.10636 T 0.68 . 15.866 0.79067 0.0:0.0:1.0:0.0 . 48 Q9BZ71 PITM3_HUMAN V 48 ENSP00000262483:A48V ENSP00000262483:A48V A - 2 0 PITPNM3 6369483 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.935000 0.87658 2.538000 0.85594 0.460000 0.39030 GCC TCGA-2J-AAB8-01A-12D-A40W-08 PITPNM3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000219824.2 0 0 0 6 383 0 114 0 1.079356e-03 0 3 0 114 2 0 0 0 0 0 2 1 0.963841 6 378 0 112 2 -2.614401 1 1 0 0 1 0 1 1 1.819173 1 0.270000 1.810000 0.156069 0.100000 4.000000e-02 0.200000 0.100000 0.113112 0.100000 0 6.000000e-02 0.150000 DLG4 1742 broad.mit.edu 37 17 7099798 7099798 + Missense_Mutation SNP G G C TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:7099798G>C ENST00000399506.2 - 10 1371 c.1180C>G c.(1180-1182)Cca>Gca p.P394A DLG4_ENST00000399510.2_Missense_Mutation_p.P437A|DLG4_ENST00000302955.6_Missense_Mutation_p.P391A P78352 DLG4_HUMAN discs, large homolog 4 (Drosophila) 18 Guanidine(DB00536) GTACCTTCTGGTTTATACTGA 0.547000 0 SO:0001583 missense ENST00000399506.2 1 1 hg19 . . . . . . . . . . G 18.12 3.552948 0.65425 . . ENSG00000132535 ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674 T;T;T 0.53857 0.6;0.6;0.6 4.28 4.28 0.50868 PDZ/DHR/GLGF (3); . . . . T 0.69708 0.3141 M 0.72353 2.195 0.80722 D 1 D;D;P;P 0.76494 0.999;0.999;0.77;0.914 D;D;P;P 0.71656 0.953;0.974;0.632;0.698 T 0.74375 -0.3686 9 0.87932 D 0 . 14.277 0.66187 0.0:0.0:1.0:0.0 . 434;394;391;437 B9EGL1;P78352;G5E939;P78352-2 .;DLG4_HUMAN;.;. A 394;391;437;437;334;437 ENSP00000382425:P394A;ENSP00000307471:P391A;ENSP00000382428:P437A ENSP00000293813:P437A P - 1 0 DLG4 7040522 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.219000 0.78000 2.210000 0.71456 0.563000 0.77884 CCA TCGA-2J-AAB8-01A-12D-A40W-08 DLG4-002 KNOWN non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000259419.2 1 0 1 38 195 0 64 0 5.619105e-01 1 10 0 64 2 0 0 0 0 0 2 1 1.000000 37 194 0 63 2 -20.000000 1 1 0 0 1 0 1 1 1.819173 1 0.270000 1.810000 0.156069 0.910000 7.100000e-01 1.000000 0.990000 0.900550 0.910000 1 8.100000e-01 0.980000 ACOX1 51 broad.mit.edu 37 17 73947567 73947567 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:73947567C>T ENST00000301608.4 - 8 1096 c.1036G>A c.(1036-1038)Gca>Aca p.A346T ACOX1_ENST00000537812.1_Missense_Mutation_p.A308T|ACOX1_ENST00000293217.5_Missense_Mutation_p.A346T NM_007292.5 NP_009223.2 Q15067 ACOX1_HUMAN acyl-CoA oxidase 1, palmitoyl 14 Flavin adenine dinucleotide(DB03147) TTCATGTATGCGCCCACAAAC 0.488000 0 SO:0001583 missense ENST00000301608.4 0 1 hg19 CCDS11735.1 . . . . . . . . . . C 8.782 0.928597 0.18131 . . ENSG00000161533 ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781 T;T;T 0.69806 -0.43;-0.43;-0.43 5.72 2.1 0.27182 Acyl-CoA dehydrogenase/oxidase C-terminal (2); 0.481838 0.25035 N 0.033647 T 0.42517 0.1206 N 0.16743 0.435 0.09310 N 1 B;B;B;B 0.23735 0.09;0.09;0.005;0.016 B;B;B;B 0.25987 0.065;0.065;0.007;0.01 T 0.20605 -1.0270 10 0.13853 T 0.58 -0.7919 4.8255 0.13414 0.1402:0.581:0.0:0.2789 . 278;308;346;346 F5H0M0;F5GYQ8;Q15067;Q15067-2 .;.;ACOX1_HUMAN;. T 346;346;308;346;278 ENSP00000301608:A346T;ENSP00000293217:A346T;ENSP00000441257:A308T ENSP00000293217:A346T A - 1 0 ACOX1 71459162 0.180000 0.23148 0.027000 0.17364 0.863000 0.49368 1.554000 0.36266 0.137000 0.18759 0.462000 0.41574 GCA TCGA-2J-AAB8-01A-12D-A40W-08 ACOX1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000439503.1 0 0 0 5 471 0 84 0 2.117014e-02 0 17 0 84 2 0 0 0 0 0 2 1 0.936101 5 466 0 84 2 -1.855854 0 1 121412 3 41 1 0 1 1 1.821458 1 0.270000 1.810000 0.156069 0.060000 2.000000e-02 0.150000 0.070000 0.079508 0.060000 0 4.000000e-02 0.110000 EVPL 2125 broad.mit.edu 37 17 74014618 74014618 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:74014618C>T ENST00000301607.3 - 12 1601 c.1348G>A c.(1348-1350)Gtg>Atg p.V450M EVPL_ENST00000586740.1_Missense_Mutation_p.V450M NM_001988.2 NP_001979.2 Q92817 EVPL_HUMAN envoplakin 54 GGGCCCTGCACGACCCAGGCG 0.662000 0 SO:0001583 missense ENST00000301607.3 0 1 hg19 CCDS11737.1 . . . . . . . . . . C 19.79 3.892323 0.72524 . . ENSG00000167880 ENST00000301607 T 0.72167 -0.63 5.12 5.12 0.69794 . 0.138638 0.48286 D 0.000181 D 0.84415 0.5467 M 0.78637 2.42 0.49213 D 0.999762 D;D 0.89917 1.0;1.0 D;D 0.69142 0.96;0.962 D 0.86389 0.1734 10 0.87932 D 0 -42.0999 18.9474 0.92627 0.0:1.0:0.0:0.0 . 450;450 B7ZLH8;Q92817 .;EVPL_HUMAN M 450 ENSP00000301607:V450M ENSP00000301607:V450M V - 1 0 EVPL 71526213 0.998000 0.40836 0.798000 0.32154 0.603000 0.37013 4.206000 0.58473 2.573000 0.86826 0.561000 0.74099 GTG TCGA-2J-AAB8-01A-12D-A40W-08 EVPL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449483.1 1 0 1 13 69 0 11 1 3.922743e-01 7 1 0 11 2 0 0 0 0 0 2 1 0.999518 13 64 0 11 2 -19.998860 1 1 121316 26 41 1 0 1 1 1.821458 1 0.270000 1.810000 0.156069 0.830000 5.200000e-01 0.990000 0.960000 0.821129 0.830000 0 6.800000e-01 0.950000 TP53 7157 broad.mit.edu 37 17 7578433 7578433 + Nonsense_Mutation SNP G G T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:7578433G>T ENST00000269305.4 - 5 686 c.497C>A c.(496-498)tCa>tAa p.S166* TP53_ENST00000445888.2_Nonsense_Mutation_p.S166*|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Nonsense_Mutation_p.S166*|TP53_ENST00000420246.2_Nonsense_Mutation_p.S166*|TP53_ENST00000359597.4_Nonsense_Mutation_p.S166*|TP53_ENST00000413465.2_Nonsense_Mutation_p.S166* 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.S166*(25)|p.0?(8)|p.S166L(4)|p.Q167fs*14(4)|p.S34*(2)|p.S73*(2)|p.K164fs*3(2)|p.V157_C176del20(1)|p.Y163fs*1(1)|p.P151_V173del23(1)|p.Q165_S166insYKQ(1)|p.Q165_M169delQSQHM(1)|p.Y163fs*14(1)|p.S149fs*72(1)|p.A159_Q167delAMAIYKQSQ(1)|p.S166G(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CATGTGCTGTGACTGCTTGTA 0.632000 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 56 Substitution - Nonsense(29)|Whole gene deletion(8)|Deletion - Frameshift(5)|Substitution - Missense(5)|Deletion - In frame(4)|Insertion - Frameshift(4)|Insertion - In frame(1) 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 15.06 2.721457 0.48728 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 . . . 5.59 4.63 0.57726 . 0.284727 0.34002 N 0.004360 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -10.3004 12.6801 0.56916 0.0803:0.0:0.9197:0.0 . . . . X 166;166;166;166;166;166;155;73;34;73;34 . ENSP00000269305:S166X S - 2 0 TP53 7519158 0.909000 0.30893 0.776000 0.31678 0.112000 0.19704 4.756000 0.62205 1.513000 0.48852 0.655000 0.94253 TCA TCGA-2J-AAB8-01A-12D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 58 225 0 85 0 9.208186e-01 1 18 0 85 2 1 1 205 937 0 1373 2 1 1.000000 57 223 0 82 2 -20.000000 1 1 0 0 1 0 1 1 1.819173 1 0.270000 1.810000 0.156069 0.960000 8.400000e-01 1.000000 0.990000 0.957667 0.960000 1 9.100000e-01 1.000000 DNAH2 146754 broad.mit.edu 37 17 7696378 7696378 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr17:7696378G>A ENST00000572933.1 + 48 8884 c.7424G>A c.(7423-7425)gGc>gAc p.G2475D DNAH2_ENST00000389173.2_Missense_Mutation_p.G2475D Q9P225 DYH2_HUMAN dynein, axonemal, heavy chain 2 p.G2475D(1) 189 all_cancers(10;4.66e-07)|Prostate(122;0.081) CCATTCGGGGGCAAAAGCATG 0.512000 1 Substitution - Missense(1) SO:0001583 missense ENST00000572933.1 0 1 hg19 CCDS32551.1 . . . . . . . . . . G 25.2 4.608500 0.87258 . . ENSG00000183914 ENST00000360606;ENST00000389173 T 0.64260 -0.09 4.39 4.39 0.52855 ATPase, AAA+ type, core (1); 0.127184 0.52532 D 0.000078 D 0.85071 0.5613 H 0.96430 3.82 0.80722 D 1 D 0.63880 0.993 D 0.73708 0.981 D 0.90106 0.4188 10 0.72032 D 0.01 . 15.9412 0.79756 0.0:0.0:1.0:0.0 . 2475 Q9P225 DYH2_HUMAN D 2475 ENSP00000373825:G2475D ENSP00000353818:G2475D G + 2 0 DNAH2 7637103 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.091000 0.94151 2.295000 0.77249 0.632000 0.83419 GGC TCGA-2J-AAB8-01A-12D-A40W-08 DNAH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000440241.1 0 0 0 7 399 1 82 0 0 0 1 1 82 2 0 0 0 0 0 2 0 0.028789 7 397 1 80 17 -2.394499 0 1 121412 1 30 1 0 1 1 1.819173 1 0.270000 1.810000 0.156069 0.110000 4.000000e-02 0.210000 0.110000 0.123959 0.110000 0 7.000000e-02 0.160000 SMAD4 4089 broad.mit.edu 37 18 48584787 48584787 + Nonsense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr18:48584787C>T ENST00000342988.3 + 7 1403 c.865C>T c.(865-867)Cag>Tag p.Q289* SMAD4_ENST00000588745.1_Intron|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.Q289* NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2)|p.Q289*(1) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) CGGCCATCTTCAGCACCACCC 0.463000 39 Whole gene deletion(36)|Unknown(2)|Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000342988.3 0 1 hg19 CCDS11950.1 . . . . . . . . . . C 41 8.836430 0.98972 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 . . . 6.17 6.17 0.99709 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.19147 T 0.46 . 19.6509 0.95805 0.0:1.0:0.0:0.0 . . . . X 289 . ENSP00000341551:Q289X Q + 1 0 SMAD4 46838785 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.603000 0.82811 2.941000 0.99782 0.655000 0.94253 CAG TCGA-2J-AAB8-01A-12D-A40W-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 0 22 371 0 107 0 1.136932e-01 0 10 0 107 2 1 1 41 829 0 1025 2 1 0.999998 22 351 0 103 2 -5.631406 1 1 0 0 1 0 0 0 1.664015 1 0.270000 1.810000 0.096870 0.330000 2.100000e-01 0.470000 0.330000 0.340057 0.330000 0 2.600000e-01 0.410000 ZNF407 55628 broad.mit.edu 37 18 72347372 72347372 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr18:72347372C>T ENST00000299687.5 + 1 4397 c.4397C>T c.(4396-4398)gCc>gTc p.A1466V ZNF407_ENST00000309902.6_Missense_Mutation_p.A1466V|ZNF407_ENST00000582337.1_Missense_Mutation_p.A1466V|ZNF407_ENST00000577538.1_Missense_Mutation_p.A1466V NM_017757.2 NP_060227.2 Q9C0G0 ZN407_HUMAN zinc finger protein 407 67 Esophageal squamous(42;0.131)|Prostate(75;0.173) CTGGCTAGTGCCGGCCACATG 0.498000 0 SO:0001583 missense ENST00000299687.5 0 1 hg19 CCDS45885.1 . . . . . . . . . . C 25.4 4.639450 0.87760 . . ENSG00000215421 ENST00000299687;ENST00000309902 T;T 0.11495 2.77;3.22 5.59 5.59 0.84812 Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.067772 0.56097 D 0.000026 T 0.14056 0.0340 N 0.04880 -0.145 0.39317 D 0.965188 D;D;D 0.67145 0.995;0.995;0.996 D;D;D 0.66602 0.909;0.909;0.945 T 0.18808 -1.0325 10 0.44086 T 0.13 . 12.8789 0.58006 0.0:0.9256:0.0:0.0744 . 1466;1466;1466 Q9C0G0-3;Q9C0G0-2;Q9C0G0 .;.;ZN407_HUMAN V 1466 ENSP00000299687:A1466V;ENSP00000310359:A1466V ENSP00000299687:A1466V A + 2 0 ZNF407 70476360 1.000000 0.71417 0.992000 0.48379 0.910000 0.53928 4.654000 0.61469 0.041000 0.15688 -0.482000 0.04802 GCC TCGA-2J-AAB8-01A-12D-A40W-08 ZNF407-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444903.1 1 0 0 4 78 0 17 0 2.256845e-02 0 4 0 17 2 0 0 0 0 0 2 1 0.889214 4 77 0 17 2 -7.451235 1 1 120846 1 30 1 0 0 0 1.664015 1 0.270000 1.810000 0.096870 0.280000 1.000000e-01 0.530000 0.270000 0.303841 0.280000 0 1.700000e-01 0.420000 EPOR 2057 broad.mit.edu 37 19 11492697 11492697 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr19:11492697G>A ENST00000222139.6 - 3 440 c.336C>T c.(334-336)gcC>gcT p.A112A EPOR_ENST00000592375.2_Silent_p.A112A NM_000121.3 NP_000112.1 P19235 EPOR_HUMAN erythropoietin receptor 5 Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894) TCGACGTGTCGGCTGTAGGCA 0.617000 0 SO:0001819 synonymous_variant ENST00000222139.6 1 1 hg19 CCDS12260.1 TCGA-2J-AAB8-01A-12D-A40W-08 EPOR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458791.1 1 0 1 35 233 0 38 0 0 1 0 0 38 2 0 0 0 0 0 2 1 1.000000 35 232 0 37 2 -15.897840 1 1 0 0 1 1 2 3 2.088449 0 0.270000 1.810000 0.277800 0.990000 7.000000e-01 1.000000 1.000000 0.937271 0.990000 1 8.300000e-01 1.000000 JUNB 3726 broad.mit.edu 37 19 12902601 12902601 + Nonsense_Mutation SNP G G T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr19:12902601G>T ENST00000302754.4 + 1 292 c.16G>T c.(16-18)Gaa>Taa p.E6* NM_002229.2 NP_002220.1 P17275 JUNB_HUMAN jun B proto-oncogene 6 CACTAAAATGGAACAGCCCTT 0.662000 0 SO:0001587 stop_gained ENST00000302754.4 0 1 hg19 CCDS12280.1 . . . . . . . . . . G 39 7.821621 0.98507 . . ENSG00000171223 ENST00000302754 . . . 5.32 5.32 0.75619 . 0.000000 0.85682 U 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 -8.2411 17.7449 0.88418 0.0:0.0:1.0:0.0 . . . . X 6 . ENSP00000303315:E6X E + 1 0 JUNB 12763601 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.685000 0.84117 2.484000 0.83849 0.561000 0.74099 GAA TCGA-2J-AAB8-01A-12D-A40W-08 JUNB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451015.1 0 0 0 5 96 0 25 1 9.984014e-01 42 245 0 25 2 0 0 0 0 0 2 1 0.932357 5 92 0 24 2 -8.488070 1 1 0 0 1 1 2 3 2.088449 0 0.270000 1.810000 0.277800 0.410000 1.500000e-01 1.000000 0.360000 0.461756 0.410000 0 2.600000e-01 0.650000 NWD1 284434 broad.mit.edu 37 19 16910925 16910925 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr19:16910925C>T ENST00000552788.1 + 15 3688 c.3688C>T c.(3688-3690)Ccc>Tcc p.P1230S NWD1_ENST00000379808.3_Missense_Mutation_p.P1230S|NWD1_ENST00000524140.2_Missense_Mutation_p.P1230S|NWD1_ENST00000339803.6_Missense_Mutation_p.P1095S|NWD1_ENST00000523826.1_Missense_Mutation_p.P1024S|CTD-2538G9.6_ENST00000601661.1_RNA|NWD1_ENST00000549814.1_Missense_Mutation_p.P1188S Q149M9 NWD1_HUMAN NACHT and WD repeat domain containing 1 67 CGTCTACTTCCCCAAAATTGG 0.512000 0 SO:0001583 missense ENST00000552788.1 1 1 hg19 . . . . . . . . . . C 20.3 3.959887 0.74016 . . ENSG00000188039 ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803 T;T;T;T;T;T 0.70045 0.55;-0.45;0.55;2.27;1.74;2.27 5.35 5.35 0.76521 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.156902 0.43579 D 0.000556 T 0.68091 0.2963 N 0.12569 0.235 0.37668 D 0.923031 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.996;0.998;0.994 T 0.71836 -0.4472 10 0.33141 T 0.24 -35.9247 16.6115 0.84884 0.0:1.0:0.0:0.0 . 1230;1230;1095 Q149M9;Q149M9-3;C9J2Y8 NWD1_HUMAN;.;. S 1095;1230;1188;1230;1024;1230;1095 ENSP00000428579:P1230S;ENSP00000447548:P1188S;ENSP00000369136:P1230S;ENSP00000428955:P1024S;ENSP00000447224:P1230S;ENSP00000340159:P1095S ENSP00000340159:P1095S P + 1 0 NWD1 16771925 1.000000 0.71417 0.998000 0.56505 0.980000 0.70556 2.938000 0.48987 2.520000 0.84964 0.650000 0.86243 CCC TCGA-2J-AAB8-01A-12D-A40W-08 NWD1-005 NOVEL basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000403569.1 1 0 1 80 428 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 1.000000 80 423 0 102 2 -2.645510 1 1 0 0 1 1 2 3 2.088449 0 0.270000 1.810000 0.277800 0.990000 9.500000e-01 1.000000 1.000000 0.997426 0.990000 1 9.900000e-01 1.000000 EMR1 2015 broad.mit.edu 37 19 6926610 6926610 + Silent SNP T T C TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr19:6926610T>C ENST00000312053.4 + 16 2257 c.2220T>C c.(2218-2220)aaT>aaC p.N740N EMR1_ENST00000381407.5_Silent_p.N599N|EMR1_ENST00000450315.3_Silent_p.N563N|EMR1_ENST00000250572.8_Silent_p.N675N|EMR1_ENST00000381404.4_Silent_p.N688N NM_001974.4 NP_001965.3 Q14246 EMR1_HUMAN egf-like module containing, mucin-like, hormone receptor-like 1 62 all_hematologic(4;0.166) GAATGCATAATCGGTGAGTGA 0.502000 0 SO:0001819 synonymous_variant ENST00000312053.4 0 1 hg19 CCDS12175.1 TCGA-2J-AAB8-01A-12D-A40W-08 EMR1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458485.1 0 0 0 7 376 1 70 0 0 0 1 70 2 0 0 0 0 0 2 0 0.017816 7 370 1 69 18 -7.385072 1 1 0 0 1 1 2 3 2.088449 0 0.270000 1.810000 0.277800 0.140000 6.000000e-02 1.000000 0.130000 0.208924 0.140000 0 9.000000e-02 0.230000 PTCHD2 57540 broad.mit.edu 37 1 11561268 11561268 + Missense_Mutation SNP T T G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:11561268T>G ENST00000294484.6 + 2 357 c.219T>G c.(217-219)tgT>tgG p.C73W PTCHD2_ENST00000389575.3_Missense_Mutation_p.C73W NM_020780.1 NP_065831.1 Q9P2K9 PTHD2_HUMAN patched domain containing 2 76 Ovarian(185;0.249) Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255) ATCCGTGCTGTGCTGGGCTGG 0.627000 0 SO:0001583 missense ENST00000294484.6 1 1 hg19 CCDS41247.1 . . . . . . . . . . T 17.23 3.335812 0.60853 . . ENSG00000204624 ENST00000294484;ENST00000389575 T;T 0.26223 1.75;1.75 5.91 -8.89 0.00785 . 0.141145 0.47455 U 0.000239 T 0.26122 0.0637 N 0.24115 0.695 0.50039 D 0.999844 D 0.63880 0.993 P 0.55923 0.787 T 0.53865 -0.8378 10 0.87932 D 0 -15.4806 20.8583 0.99727 0.0:0.6554:0.0:0.3446 . 73 Q9P2K9 PTHD2_HUMAN W 73 ENSP00000294484:C73W;ENSP00000374226:C73W ENSP00000294484:C73W C + 3 2 PTCHD2 11483855 0.014000 0.17966 0.389000 0.26208 0.982000 0.71751 -1.193000 0.03049 -1.737000 0.01350 -0.250000 0.11733 TGT TCGA-2J-AAB8-01A-12D-A40W-08 PTCHD2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000005770.2 0 0 0 10 293 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 0.996800 10 289 0 47 2 -11.089900 1 1 0 0 1 0 1 1 1.921568 0 0.270000 1.810000 0.203318 0.220000 1.100000e-01 0.390000 0.220000 0.241637 0.220000 0 1.600000e-01 0.310000 PIAS3 10401 broad.mit.edu 37 1 145578668 145578668 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:145578668G>A ENST00000393045.2 + 3 564 c.474G>A c.(472-474)gcG>gcA p.A158A PIAS3_ENST00000369298.1_Silent_p.A123A|PIAS3_ENST00000369299.3_Silent_p.A149A NM_006099.3 NP_006090.2 Q9Y6X2 PIAS3_HUMAN protein inhibitor of activated STAT, 3 28 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) TTGAGGAAGCGCACTTTACCT 0.537000 0 SO:0001819 synonymous_variant ENST00000393045.2 1 1 hg19 CCDS920.2 TCGA-2J-AAB8-01A-12D-A40W-08 PIAS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000038533.4 0 0 0 44 724 0 157 1 5.433264e-01 2 29 0 157 2 0 0 0 0 0 2 1 1.000000 44 717 0 155 2 -6.947408 1 1 121412 30 50 1 2 2 4 2.399819 1 0.270000 1.810000 0.380411 0.520000 3.700000e-01 1.000000 0.500000 0.615345 0.520000 0 4.400000e-01 1.000000 F5 2153 broad.mit.edu 37 1 169529961 169529961 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:169529961G>A ENST00000367797.3 - 4 618 c.417C>T c.(415-417)gaC>gaT p.D139D F5_ENST00000367796.3_Silent_p.D139D|F5_ENST00000546081.1_Silent_p.D2D NM_000130.4 NP_000121 P12259 FA5_HUMAN coagulation factor V (proaccelerin, labile factor) 128 all_hematologic(923;0.208) ART-123(DB05777)|Drotrecogin alfa(DB00055) CCACAGCGTCGTCCATCTTCT 0.517000 0 SO:0001819 synonymous_variant ENST00000367797.3 1 1 hg19 CCDS1281.1 TCGA-2J-AAB8-01A-12D-A40W-08 F5-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000083712.1 0 0 0 16 475 0 63 0 3.672915e-03 0 3 0 63 2 0 0 0 0 0 2 1 0.999928 16 469 0 62 2 -3.313834 1 1 121412 3 37 1 1 3 4 2.399507 1 0.270000 1.810000 0.367363 0.310000 1.700000e-01 1.000000 0.280000 0.461486 0.310000 0 2.300000e-01 1.000000 SELL 6402 broad.mit.edu 37 1 169677858 169677858 + Nonsense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:169677858G>A ENST00000236147.4 - 3 371 c.211C>T c.(211-213)Cga>Tga p.R71* C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR NM_000655.4 NP_000646.2 P14151 LYAM1_HUMAN selectin L 15 all_hematologic(923;0.208) TAATTGTCTCGGCAGAATCTT 0.433000 0 SO:0001587 stop_gained ENST00000236147.4 0 1 hg19 CCDS53427.1 . . . . . . . . . . G 16.80 3.223393 0.58668 . . ENSG00000188404 ENST00000236147 . . . 5.2 2.14 0.27477 . 1.276940 0.05720 N 0.597599 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.16896 T 0.51 -1.1421 13.8848 0.63702 0.0:0.0:0.312:0.688 . . . . X 71 . ENSP00000236147:R71X R - 1 2 SELL 167944482 0.205000 0.23458 0.276000 0.24689 0.016000 0.09150 0.447000 0.21710 0.150000 0.19136 0.585000 0.79938 CGA TCGA-2J-AAB8-01A-12D-A40W-08 SELL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084233.1 1 0 0 7 84 0 18 0 2.297439e-02 0 3 0 18 2 0 0 0 0 0 2 1 0.980502 7 82 0 18 2 -5.150747 1 1 0 0 1 1 3 4 2.399507 1 0.270000 1.810000 0.367363 0.790000 3.300000e-01 1.000000 1.000000 0.772105 0.790000 0 5.100000e-01 1.000000 TNR 7143 broad.mit.edu 37 1 175331865 175331865 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:175331865C>T ENST00000367674.2 - 14 3496 c.2788G>A c.(2788-2790)Gaa>Aaa p.E930K TNR_ENST00000263525.2_Missense_Mutation_p.E930K Q92752 TENR_HUMAN tenascin R p.E930K(2) 177 Renal(580;0.146) AGGCTGATTTCGTATTCGGTA 0.532000 2 Substitution - Missense(2) SO:0001583 missense ENST00000367674.2 1 1 hg19 CCDS1318.1 . . . . . . . . . . C 11.70 1.717377 0.30413 . . ENSG00000116147 ENST00000367674;ENST00000263525;ENST00000367673 T;T 0.58210 0.35;0.35 5.59 5.59 0.84812 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.42017 0.1184 L 0.31420 0.93 0.80722 D 1 P 0.44578 0.838 B 0.40534 0.332 T 0.21042 -1.0257 10 0.15066 T 0.55 . 17.3759 0.87391 0.0:1.0:0.0:0.0 . 930 Q92752 TENR_HUMAN K 930;930;840 ENSP00000356646:E930K;ENSP00000263525:E930K ENSP00000263525:E930K E - 1 0 TNR 173598488 1.000000 0.71417 0.987000 0.45799 0.744000 0.42396 6.819000 0.75262 2.625000 0.88918 0.650000 0.86243 GAA TCGA-2J-AAB8-01A-12D-A40W-08 TNR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084414.4 1 0 1 115 353 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 1.000000 115 345 0 86 2 -5.289538 1 1 121412 3 37 1 1 3 4 2.399507 1 0.270000 1.810000 0.367363 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 OBSCN 84033 broad.mit.edu 37 1 228525760 228525760 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:228525760G>A ENST00000422127.1 + 67 16960 c.16916G>A c.(16915-16917)cGc>cAc p.R5639H OBSCN_ENST00000284548.11_Missense_Mutation_p.R5639H|OBSCN_ENST00000366707.4_Missense_Mutation_p.R3273H|OBSCN_ENST00000570156.2_Missense_Mutation_p.R6596H|OBSCN_ENST00000366709.4_Missense_Mutation_p.R2758H NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) CACCCACTGCGCTGGCTTGTC 0.642000 0 SO:0001583 missense ENST00000422127.1 1 1 hg19 CCDS58065.1 . . . . . . . . . . G 21.5 4.159631 0.78226 . . ENSG00000154358 ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709 T;T;T;T 0.33654 1.4;1.4;1.4;1.4 4.35 2.47 0.30058 Src homology-3 domain (2); 0.296783 0.25143 N 0.032814 T 0.19805 0.0476 N 0.19112 0.55 0.31810 N 0.627308 B;B 0.21381 0.033;0.055 B;B 0.16722 0.007;0.016 T 0.11036 -1.0604 10 0.66056 D 0.02 . 4.4143 0.11448 0.4487:0.0:0.5513:0.0 . 5639;5639 Q5VST9;Q5VST9-3 OBSCN_HUMAN;. H 5639;5639;3273;2758 ENSP00000284548:R5639H;ENSP00000409493:R5639H;ENSP00000355668:R3273H;ENSP00000355670:R2758H ENSP00000284548:R5639H R + 2 0 OBSCN 226592383 1.000000 0.71417 1.000000 0.80357 0.844000 0.47949 5.978000 0.70501 1.202000 0.43218 0.491000 0.48974 CGC TCGA-2J-AAB8-01A-12D-A40W-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 1 0 0 7 125 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 0.972584 5 113 0 28 2 -10.841010 1 1 121124 1 29 1 1 2 3 2.110234 0 0.270000 1.810000 0.281637 0.440000 1.900000e-01 1.000000 0.390000 0.494725 0.440000 0 2.900000e-01 0.680000 OR2M4 26245 broad.mit.edu 37 1 248402643 248402643 + Missense_Mutation SNP C C T rs144805988 TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:248402643C>T ENST00000306687.1 + 1 413 c.413C>T c.(412-414)cCg>cTg p.P138L NM_017504.1 NP_059974.1 Q96R27 OR2M4_HUMAN olfactory receptor, family 2, subfamily M, member 4 p.P138L(1) 50 all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0245) CTCATGAATCCGAAACTCTGT 0.483000 1 Substitution - Missense(1) SO:0001583 missense ENST00000306687.1 1 1 hg19 CCDS31108.1 . . . . . . . . . . c 0.019 -1.462993 0.01062 0.0 2.33E-4 ENSG00000171180 ENST00000306687 T 0.00526 6.8 3.48 -0.649 0.11461 GPCR, rhodopsin-like superfamily (1); 1.195430 0.06309 N 0.702303 T 0.00440 0.0014 L 0.46670 1.46 0.09310 N 1 B 0.06786 0.001 B 0.04013 0.001 T 0.43491 -0.9388 10 0.29301 T 0.29 . 2.7909 0.05388 0.294:0.4613:0.097:0.1477 . 138 Q96R27 OR2M4_HUMAN L 138 ENSP00000306688:P138L ENSP00000306688:P138L P + 2 0 OR2M4 246469266 0.000000 0.05858 0.002000 0.10522 0.039000 0.13416 -0.758000 0.04766 -0.245000 0.09625 -0.414000 0.06135 CCG TCGA-2J-AAB8-01A-12D-A40W-08 OR2M4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097352.1 1 0 1 74 351 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 74 349 0 85 2 -2.734202 1 1 121412 23 45 1 1 2 3 2.110234 0 0.270000 1.810000 0.281637 0.990000 9.900000e-01 1.000000 1.000000 0.999730 0.990000 1 9.900000e-01 1.000000 IL23R 149233 broad.mit.edu 37 1 67724439 67724439 + Silent SNP C C G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:67724439C>G ENST00000347310.5 + 11 1689 c.1518C>G c.(1516-1518)tcC>tcG p.S506S IL23R_ENST00000371002.1_3'UTR|IL23R_ENST00000395227.1_Silent_p.S251S|IL23R_ENST00000473881.1_3'UTR NM_144701.2 NP_653302.2 Q5VWK5 IL23R_HUMAN interleukin 23 receptor 21 AAATTACTTCCTTAACACTTA 0.353000 0 SO:0001819 synonymous_variant ENST00000347310.5 1 1 hg19 CCDS637.1 . . . . . . . . . . C 2.832 -0.242526 0.05906 . . ENSG00000162594 ENST00000425614 . . . 5.71 1.0 0.19881 . . . . . T 0.09158 0.0226 . . . 0.09310 N 1 . . . . . . T 0.36065 -0.9763 4 . . . -36.091 3.472 0.07570 0.1722:0.4723:0.0:0.3555 . . . . R 268 . . P + 2 0 IL23R 67497027 0.000000 0.05858 0.001000 0.08648 0.012000 0.07955 -0.056000 0.11787 -0.077000 0.12752 0.650000 0.86243 CCT TCGA-2J-AAB8-01A-12D-A40W-08 IL23R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025199.2 1 0 0 12 238 0 50 0 0 0 1 0 50 2 0 0 0 0 0 2 1 0.999140 12 236 0 50 2 -2.939154 1 1 0 0 1 0 1 1 1.909717 0 0.270000 1.810000 0.199781 0.320000 1.700000e-01 0.530000 0.320000 0.343033 0.320000 0 2.400000e-01 0.430000 CAMTA1 23261 broad.mit.edu 37 1 7798217 7798217 + Missense_Mutation SNP C C T rs139225365 TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr1:7798217C>T ENST00000303635.7 + 16 4064 c.3857C>T c.(3856-3858)aCa>aTa p.T1286I CAMTA1_ENST00000439411.2_Missense_Mutation_p.T1286I NM_015215.2 NP_056030.1 Q9Y6Y1 CMTA1_HUMAN calmodulin binding transcription activator 1 85 Ovarian(185;0.0634) all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388) GTCCCCGAGACACTCAGCCCC 0.552000 T WWTR1 epitheliod hemangioendothelioma Dom yes 1 1p36.31-p36.23 611501 calmodulin binding transcription activator 1 M 0 SO:0001583 missense ENST00000303635.7 0 1 hg19 CCDS30576.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 13.38|13.38 2.220885|2.220885 0.39201|0.39201 0.0|0.0 2.33E-4|2.33E-4 ENSG00000171735|ENSG00000171735 ENST00000495233|ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646 .|T;T .|0.21191 .|2.03;2.02 5.06|5.06 4.13|4.13 0.48395|0.48395 .|. .|0.382752 .|0.30732 .|N .|0.008991 T|T 0.16854|0.16854 0.0405|0.0405 L|L 0.36672|0.36672 1.1|1.1 0.33546|0.33546 D|D 0.595455|0.595455 .|B;B;B;B .|0.31599 .|0.33;0.112;0.138;0.183 .|B;B;B;B .|0.23716 .|0.048;0.01;0.013;0.016 T|T 0.14783|0.14783 -1.0460|-1.0460 5|10 .|0.34782 .|T .|0.22 -0.2018|-0.2018 15.0419|15.0419 0.71796|0.71796 0.1432:0.8568:0.0:0.0|0.1432:0.8568:0.0:0.0 .|. .|1286;373;242;1286 .|Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1 .|.;.;.;CMTA1_HUMAN Y|I 243|1286;1286;373;242 .|ENSP00000306522:T1286I;ENSP00000402561:T1286I .|ENSP00000306522:T1286I H|T +|+ 1|2 0|0 CAMTA1|CAMTA1 7720804|7720804 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.994000|0.994000 0.84299|0.84299 3.644000|3.644000 0.54381|0.54381 1.213000|1.213000 0.43380|0.43380 0.655000|0.655000 0.94253|0.94253 CAC|ACA TCGA-2J-AAB8-01A-12D-A40W-08 CAMTA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000003588.3 0 0 0 5 201 1 46 0 0 0 1 46 2 0 0 0 0 0 2 0 0.015032 6 194 1 45 15 -7.182630 1 1 0 0 1 0 1 1 1.921568 0 0.270000 1.810000 0.203318 0.170000 6.000000e-02 0.350000 0.160000 0.192083 0.170000 0 1.100000e-01 0.260000 ADRA1D 146 broad.mit.edu 37 20 4202204 4202204 + Missense_Mutation SNP G G A rs147522815 TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr20:4202204G>A ENST00000379453.4 - 2 1801 c.1685C>T c.(1684-1686)gCc>gTc p.A562V NM_000678.3 NP_000669.1 P25100 ADA1D_HUMAN adrenoceptor alpha 1D 14 Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694) GCTGTAGTCGGCCAATTCGTA 0.667000 OREG0025743 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000379453.4 0 1 hg19 CCDS13079.1 . . . . . . . . . . G 14.72 2.618816 0.46736 . . ENSG00000171873 ENST00000379453 T 0.59364 0.27 3.62 -0.0134 0.13984 . . . . . T 0.39279 0.1072 L 0.29908 0.895 0.23089 N 0.99832 B 0.27498 0.18 B 0.22601 0.04 T 0.20174 -1.0283 9 0.32370 T 0.25 . 6.836 0.23937 0.0:0.1711:0.5057:0.3231 . 562 P25100 ADA1D_HUMAN V 562 ENSP00000368766:A562V ENSP00000368766:A562V A - 2 0 ADRA1D 4150204 0.998000 0.40836 0.119000 0.21687 0.634000 0.38068 3.407000 0.52644 0.257000 0.21650 0.305000 0.20034 GCC TCGA-2J-AAB8-01A-12D-A40W-08 ADRA1D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077812.2 0 0 0 5 243 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.934777 5 238 0 46 2 -2.737349 1 1 0 0 1 0 1 1 1.964838 0 0.270000 1.810000 0.238115 0.150000 5.000000e-02 0.310000 0.140000 0.168149 0.150000 0 9.000000e-02 0.230000 CRKL 1399 broad.mit.edu 37 22 21288172 21288172 + Silent SNP C C A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr22:21288172C>A ENST00000354336.3 + 2 926 c.417C>A c.(415-417)gcC>gcA p.A139A NM_005207.3 NP_005198.1 P46109 CRKL_HUMAN v-crk avian sarcoma virus CT10 oncogene homolog-like 14 all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176) GGAATGATGCCGAAGACCTGC 0.502000 Pancreas(85;3 1441 23889 42519 42763) 0 SO:0001819 synonymous_variant ENST00000354336.3 1 1 hg19 CCDS13785.1 TCGA-2J-AAB8-01A-12D-A40W-08 CRKL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320158.1 0 0 0 26 388 1 81 0 1.351651e-01 1 9 1 81 2 0 0 0 0 0 2 1 1.000000 26 387 0 76 2 -2.716709 1 1 0 0 1 0 0 0 1.834852 1 0.270000 1.810000 0.181614 0.410000 2.700000e-01 0.580000 0.410000 0.424189 0.410000 0 3.400000e-01 0.500000 NUP50 10762 broad.mit.edu 37 22 45580351 45580351 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr22:45580351G>A ENST00000347635.4 + 8 1688 c.1222G>A c.(1222-1224)Gtt>Att p.V408I NUP50_ENST00000407019.2_Missense_Mutation_p.V380I|NUP50_ENST00000396096.2_Missense_Mutation_p.V380I|NUP50_ENST00000425733.2_Missense_Mutation_p.V158I NM_007172.3 NP_009103.2 Q9UKX7 NUP50_HUMAN nucleoporin 50kDa 9 Ovarian(80;0.00965)|all_neural(38;0.0244) ATTGCTGAACGTTCTGATTCC 0.393000 0 SO:0001583 missense ENST00000347635.4 1 1 hg19 CCDS14062.1 . . . . . . . . . . G 3.527 -0.096540 0.07010 . . ENSG00000093000 ENST00000347635;ENST00000407019;ENST00000425733;ENST00000396096 T;T;T;T 0.40225 1.04;1.04;1.04;1.04 5.61 3.54 0.40534 Pleckstrin homology-type (1);Ran binding protein 1 (3); 0.172748 0.51477 N 0.000084 T 0.15435 0.0372 N 0.01473 -0.845 0.35957 D 0.834318 B 0.02656 0.0 B 0.12156 0.007 T 0.09907 -1.0653 10 0.20519 T 0.43 -17.1865 8.726 0.34469 0.2845:0.0:0.7155:0.0 . 408 Q9UKX7 NUP50_HUMAN I 408;380;158;380 ENSP00000345895:V408I;ENSP00000385555:V380I;ENSP00000406928:V158I;ENSP00000379403:V380I ENSP00000345895:V408I V + 1 0 NUP50 43959015 1.000000 0.71417 0.040000 0.18447 0.925000 0.55904 3.592000 0.53993 0.849000 0.35215 0.655000 0.94253 GTT TCGA-2J-AAB8-01A-12D-A40W-08 NUP50-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321993.2 1 0 1 21 244 0 63 1 6.502932e-01 5 22 0 63 2 0 0 0 0 0 2 1 0.999997 21 238 0 63 2 -7.875616 1 1 121412 4 39 1 0 0 0 1.831194 1 0.270000 1.810000 0.179130 0.520000 3.300000e-01 0.740000 0.510000 0.533426 0.520000 0 4.200000e-01 0.640000 FASTKD1 79675 broad.mit.edu 37 2 170428438 170428438 + Missense_Mutation SNP G G C TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr2:170428438G>C ENST00000453153.2 - 2 448 c.102C>G c.(100-102)atC>atG p.I34M FASTKD1_ENST00000453929.2_Missense_Mutation_p.I34M NM_024622.3 NP_078898.3 Q53R41 FAKD1_HUMAN FAST kinase domains 1 37 GTTCACAACTGATGGGTCGAA 0.358000 0 SO:0001583 missense ENST00000453153.2 1 1 hg19 CCDS33318.1 . . . . . . . . . . G 8.662 0.900868 0.17686 . . ENSG00000138399 ENST00000453153;ENST00000453929;ENST00000438035;ENST00000445210 T;T 0.17854 2.25;2.25 5.07 0.625 0.17665 . 0.967032 0.08552 N 0.928866 T 0.13756 0.0333 L 0.36672 1.1 0.09310 N 1 P;P;P 0.51240 0.906;0.943;0.906 B;P;B 0.46940 0.332;0.532;0.264 T 0.13388 -1.0511 10 0.34782 T 0.22 -16.7467 0.4362 0.00479 0.2023:0.2566:0.2195:0.3215 . 34;34;34 D3DPC4;Q53R41-2;Q53R41 .;.;FAKD1_HUMAN M 34 ENSP00000400513:I34M;ENSP00000403229:I34M ENSP00000396769:I34M I - 3 3 FASTKD1 170136684 0.020000 0.18652 0.035000 0.18076 0.637000 0.38172 0.239000 0.18023 -0.051000 0.13334 0.591000 0.81541 ATC TCGA-2J-AAB8-01A-12D-A40W-08 FASTKD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000337788.2 1 0 0 25 293 0 73 0 2.551270e-01 1 11 0 73 2 0 0 0 0 0 2 1 1.000000 25 292 0 72 2 -8.179766 1 1 0 0 1 1 2 3 2.115320 0 0.270000 1.810000 0.282591 0.610000 4.000000e-01 1.000000 0.590000 0.648395 0.610000 0 4.900000e-01 0.790000 COL3A1 1281 broad.mit.edu 37 2 189850473 189850473 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr2:189850473G>A ENST00000304636.3 + 4 586 c.416G>A c.(415-417)gGa>gAa p.G139E COL3A1_ENST00000317840.5_Missense_Mutation_p.G139E NM_000090.3 NP_000081 P02461 CO3A1_HUMAN collagen, type III, alpha 1 126 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048) GGCCCCCCTGGAATCTGTGAA 0.448000 0 SO:0001583 missense ENST00000304636.3 1 1 hg19 CCDS2297.1 . . . . . . . . . . G 25.8 4.673160 0.88445 . . ENSG00000168542 ENST00000304636;ENST00000317840 D;D 0.99353 -5.77;-5.77 4.62 4.62 0.57501 . 0.000000 0.40908 D 0.000991 D 0.99327 0.9764 M 0.73598 2.24 0.58432 D 0.999999 D 0.89917 1.0 D 0.97110 1.0 D 0.99087 1.0839 10 0.72032 D 0.01 . 17.6469 0.88151 0.0:0.0:1.0:0.0 . 139 P02461 CO3A1_HUMAN E 139 ENSP00000304408:G139E;ENSP00000315243:G139E ENSP00000304408:G139E G + 2 0 COL3A1 189558718 1.000000 0.71417 1.000000 0.80357 0.940000 0.58332 9.104000 0.94239 2.414000 0.81942 0.313000 0.20887 GGA TCGA-2J-AAB8-01A-12D-A40W-08 COL3A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255899.3 1 0 0 10 151 0 24 0 1 0 2736 0 24 2 0 0 0 0 0 2 1 0.996981 10 149 0 24 2 -13.646850 1 1 0 0 1 1 2 3 2.115320 0 0.270000 1.810000 0.282591 0.500000 2.500000e-01 1.000000 0.460000 0.552598 0.500000 0 3.600000e-01 0.740000 IKZF2 22807 broad.mit.edu 37 2 213914507 213914507 + Missense_Mutation SNP G G C TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr2:213914507G>C ENST00000434687.1 - 6 813 c.504C>G c.(502-504)ttC>ttG p.F168L IKZF2_ENST00000342002.2_Missense_Mutation_p.F174L|IKZF2_ENST00000374327.4_Intron|IKZF2_ENST00000421754.2_Missense_Mutation_p.F142L|IKZF2_ENST00000374319.4_Missense_Mutation_p.F142L|IKZF2_ENST00000413091.3_Missense_Mutation_p.F168L|IKZF2_ENST00000451136.2_Missense_Mutation_p.F142L|IKZF2_ENST00000457361.1_Missense_Mutation_p.F168L Q9UKS7 IKZF2_HUMAN IKAROS family zinc finger 2 (Helios) 23 Esophageal squamous(248;0.0559)|Renal(323;0.218) AAGGACATTTGAACGGCTTCT 0.493000 0 SO:0001583 missense ENST00000434687.1 1 1 hg19 CCDS2395.1 . . . . . . . . . . G 34 5.358031 0.95854 . . ENSG00000030419 ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000413091 T;T;T;T;T;T;T 0.65732 -0.17;-0.17;-0.17;1.98;0.45;1.98;-0.17 6.03 6.03 0.97812 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.64402 D 0.000001 T 0.74329 0.3702 L 0.52823 1.66 0.80722 D 1 D;D;D;D 0.89917 0.99;0.974;1.0;0.994 P;D;D;D 0.79108 0.825;0.969;0.985;0.992 T 0.73984 -0.3810 10 0.54805 T 0.06 -7.0219 13.7134 0.62682 0.0699:0.0:0.9301:0.0 . 142;142;142;168 C9JCG7;C9JTM9;Q9UKS7-2;Q9UKS7 .;.;.;IKZF2_HUMAN L 168;174;168;142;142;142;168 ENSP00000410447:F168L;ENSP00000342876:F174L;ENSP00000412869:F168L;ENSP00000363439:F142L;ENSP00000395203:F142L;ENSP00000399574:F142L;ENSP00000402334:F168L ENSP00000342876:F174L F - 3 2 IKZF2 213622752 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 4.709000 0.61867 2.861000 0.98227 0.655000 0.94253 TTC TCGA-2J-AAB8-01A-12D-A40W-08 IKZF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256593.3 0 0 0 12 261 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 0.999096 12 257 0 50 2 -13.555380 1 1 0 0 1 1 2 3 2.115320 0 0.270000 1.810000 0.282591 0.350000 1.800000e-01 1.000000 0.330000 0.420448 0.350000 0 2.500000e-01 0.510000 ADCY3 109 broad.mit.edu 37 2 25051001 25051001 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr2:25051001G>A ENST00000260600.5 - 13 3053 c.2202C>T c.(2200-2202)ccC>ccT p.P734P RP11-443B20.1_ENST00000606114.1_RNA|ADCY3_ENST00000450524.1_5'UTR|ADCY3_ENST00000405392.1_Intron NM_004036.3 NP_004027.2 O60266 ADCY3_HUMAN adenylate cyclase 3 44 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203) TTGCATTGCTGGGTCCCGTGT 0.602000 OREG0014498 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000260600.5 1 1 hg19 CCDS1715.1 TCGA-2J-AAB8-01A-12D-A40W-08 ADCY3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211574.2 0 0 0 11 168 1 41 0 6.446518e-02 1 21 1 41 4 0 0 0 0 0 2 1 0.998294 11 164 0 41 2 -3.146440 1 1 0 0 1 0 1 1 1.959722 0 0.270000 1.810000 0.226121 0.430000 2.300000e-01 0.710000 0.430000 0.454430 0.430000 0 3.200000e-01 0.570000 RTN4 57142 broad.mit.edu 37 2 55252908 55252908 + Missense_Mutation SNP A A C TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr2:55252908A>C ENST00000337526.6 - 3 2570 c.2327T>G c.(2326-2328)tTt>tGt p.F776C RTN4_ENST00000405240.1_Missense_Mutation_p.F570C|RTN4_ENST00000404909.1_Missense_Mutation_p.F570C|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000354474.6_Missense_Mutation_p.F544C|RTN4_ENST00000394611.2_Missense_Mutation_p.F570C|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.F570C NM_020532.4 NP_065393.1 Q9NQC3 RTN4_HUMAN reticulon 4 36 CATTGACTCAAATGAAGTCTC 0.363000 0 SO:0001583 missense ENST00000337526.6 1 1 hg19 CCDS42684.1 . . . . . . . . . . A 2.415 -0.334465 0.05278 . . ENSG00000115310 ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474 T;T;T;T;T;T 0.17854 2.25;2.25;2.25;2.25;2.25;2.25 5.45 -0.531 0.11894 . 1.868710 0.02414 N 0.081987 T 0.15132 0.0365 L 0.40543 1.245 0.09310 N 1 P 0.36438 0.553 B 0.34824 0.19 T 0.25710 -1.0124 10 0.59425 D 0.04 0.8146 5.228 0.15406 0.3847:0.0:0.4705:0.1449 . 776 Q9NQC3 RTN4_HUMAN C 570;570;776;570;570;544 ENSP00000384471:F570C;ENSP00000349944:F570C;ENSP00000337838:F776C;ENSP00000378109:F570C;ENSP00000385650:F570C;ENSP00000346465:F544C ENSP00000337838:F776C F - 2 0 RTN4 55106412 0.000000 0.05858 0.000000 0.03702 0.359000 0.29487 -0.187000 0.09656 -0.023000 0.13963 -0.242000 0.12053 TTT TCGA-2J-AAB8-01A-12D-A40W-08 RTN4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000251484.1 1 0 1 38 305 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1.000000 37 305 0 80 2 -20.000000 1 1 0 0 1 0 1 1 1.959722 0 0.270000 1.810000 0.226121 0.770000 5.600000e-01 1.000000 1.000000 0.779862 0.770000 0 6.500000e-01 0.890000 ATP2B2 491 broad.mit.edu 37 3 10443850 10443850 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr3:10443850C>T ENST00000352432.4 - 3 649 c.580G>A c.(580-582)Gtg>Atg p.V194M ATP2B2_ENST00000397077.1_Missense_Mutation_p.V194M|ATP2B2_ENST00000383800.4_Missense_Mutation_p.V194M|ATP2B2_ENST00000360273.2_Missense_Mutation_p.V194M|ATP2B2_ENST00000343816.4_Missense_Mutation_p.V194M Q01814 AT2B2_HUMAN ATPase, Ca++ transporting, plasma membrane 2 74 GCCCGGACCACGGTAAATTTC 0.567000 Ovarian(125;1619 1709 15675 19819 38835) 0 SO:0001583 missense ENST00000352432.4 1 1 hg19 CCDS33701.1 . . . . . . . . . . C 31 5.076585 0.94000 . . ENSG00000157087 ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354 D;D;D;D;D;D 0.95001 -3.58;-3.58;-3.58;-3.58;-3.58;-3.58 5.44 5.44 0.79542 ATPase, P-type, ATPase-associated domain (1);ATPase, P-type, cytoplasmic transduction domain A (1); 0.000000 0.85682 D 0.000000 D 0.98585 0.9527 H 0.98525 4.255 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.993;0.997 D 0.99643 1.0989 10 0.87932 D 0 -29.579 19.2768 0.94034 0.0:1.0:0.0:0.0 . 194;206;194 Q01814-7;Q4LE63;Q01814 .;.;AT2B2_HUMAN M 194;194;194;194;194;160;81;194 ENSP00000324172:V194M;ENSP00000373311:V194M;ENSP00000380267:V194M;ENSP00000353414:V194M;ENSP00000344677:V194M;ENSP00000414854:V81M ENSP00000342954:V194M V - 1 0 ATP2B2 10418850 1.000000 0.71417 0.950000 0.38849 0.951000 0.60555 6.066000 0.71185 2.550000 0.86006 0.467000 0.42956 GTG TCGA-2J-AAB8-01A-12D-A40W-08 ATP2B2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000250576.2 1 0 0 51 747 0 173 0 0 0 0 173 2 0 0 0 0 0 2 1 1.000000 51 731 0 168 2 -9.313001 1 1 121412 1 40 1 0 1 1 1.814912 1 0.270000 1.810000 0.157384 0.400000 3.000000e-01 0.520000 0.410000 0.414336 0.400000 0 3.500000e-01 0.470000 WNT7A 7476 broad.mit.edu 37 3 13860914 13860914 + Nonsense_Mutation SNP C C A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr3:13860914C>A ENST00000285018.4 - 4 881 c.577G>T c.(577-579)Gag>Tag p.E193* NM_004625.3 NP_004616.2 O00755 WNT7A_HUMAN wingless-type MMTV integration site family, member 7A 24 ATGTTCTCCTCCAGGATCTGC 0.657000 0 SO:0001587 stop_gained ENST00000285018.4 0 1 hg19 CCDS2616.1 . . . . . . . . . . c 37 6.310859 0.97462 . . ENSG00000154764 ENST00000285018 . . . 4.29 4.29 0.51040 . 0.170785 0.49916 D 0.000132 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 17.1402 0.86750 0.0:1.0:0.0:0.0 . . . . X 193 . ENSP00000285018:E193X E - 1 0 WNT7A 13835915 1.000000 0.71417 1.000000 0.80357 0.805000 0.45488 7.810000 0.86072 2.121000 0.65114 0.558000 0.71614 GAG TCGA-2J-AAB8-01A-12D-A40W-08 WNT7A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252031.2 0 0 0 5 354 0 78 0 1.286831e-02 0 10 0 78 2 0 0 0 0 0 2 0 0.011242 5 350 1 76 16 -2.437979 0 1 0 0 1 0 1 1 1.814912 1 0.270000 1.810000 0.157384 0.090000 3.000000e-02 0.190000 0.090000 0.105073 0.090000 0 5.000000e-02 0.140000 MST1R 4486 broad.mit.edu 37 3 49936064 49936064 + Missense_Mutation SNP A A G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr3:49936064A>G ENST00000296474.3 - 4 1633 c.1606T>C c.(1606-1608)Tgc>Cgc p.C536R MST1R_ENST00000344206.4_Missense_Mutation_p.C536R|CTD-2330K9.2_ENST00000435478.1_RNA NM_002447.2 NP_002438 Q04912 RON_HUMAN macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 37 GCCCTTAGGCAACGCCCACAG 0.612000 0 SO:0001583 missense ENST00000296474.3 1 1 hg19 CCDS2807.1 . . . . . . . . . . A 21.9 4.221236 0.79464 . . ENSG00000164078 ENST00000296474;ENST00000344206 T;T 0.77489 -1.1;-1.1 5.84 5.84 0.93424 . 0.000000 0.85682 D 0.000000 D 0.90563 0.7042 M 0.92026 3.265 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.999;1.0;1.0;0.998 D 0.92564 0.6060 10 0.87932 D 0 -23.5053 16.2118 0.82165 1.0:0.0:0.0:0.0 . 430;536;536;536 Q04912-4;Q04912-6;Q04912-5;Q04912 .;.;.;RON_HUMAN R 536 ENSP00000296474:C536R;ENSP00000341325:C536R ENSP00000296474:C536R C - 1 0 MST1R 49911068 1.000000 0.71417 0.967000 0.41034 0.799000 0.45148 8.290000 0.89925 2.234000 0.73211 0.402000 0.26972 TGC TCGA-2J-AAB8-01A-12D-A40W-08 MST1R-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000345403.1 1 0 1 48 258 0 48 1 8.404697e-01 19 1 0 48 2 0 0 0 0 0 2 1 1.000000 48 254 0 47 2 -20.000000 1 1 0 0 1 0 1 1 1.814912 1 0.270000 1.810000 0.157384 0.910000 7.200000e-01 1.000000 1.000000 0.907571 0.910000 1 8.200000e-01 0.980000 STOX2 56977 broad.mit.edu 37 4 184931519 184931519 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr4:184931519G>A ENST00000308497.4 + 3 2963 c.1528G>A c.(1528-1530)Gaa>Aaa p.E510K STOX2_ENST00000438269.1_Missense_Mutation_p.E510K NM_020225.1 NP_064610.1 Q9P2F5 STOX2_HUMAN storkhead box 2 14 all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283) AGGGACGCCGGAAGACCTTGC 0.547000 0 SO:0001583 missense ENST00000308497.4 1 1 hg19 CCDS47167.1 . . . . . . . . . . G 15.91 2.971202 0.53614 . . ENSG00000173320 ENST00000308497;ENST00000438269 T;T 0.80738 -0.41;-1.41 5.65 5.65 0.86999 . 0.048167 0.85682 D 0.000000 T 0.76011 0.3928 L 0.29908 0.895 0.80722 D 1 B;B 0.32245 0.361;0.083 B;B 0.34652 0.187;0.057 T 0.75717 -0.3220 10 0.72032 D 0.01 -13.8256 19.9142 0.97043 0.0:0.0:1.0:0.0 . 510;510 Q9P2F5-2;Q9P2F5 .;STOX2_HUMAN K 510 ENSP00000311257:E510K;ENSP00000390127:E510K ENSP00000311257:E510K E + 1 0 STOX2 185168513 1.000000 0.71417 0.970000 0.41538 0.426000 0.31534 9.263000 0.95617 2.941000 0.99782 0.655000 0.94253 GAA TCGA-2J-AAB8-01A-12D-A40W-08 STOX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000361433.3 1 0 1 12 58 0 19 0 0 1 0 0 19 2 0 0 0 0 0 2 1 0.999347 12 57 0 19 2 -19.996730 1 1 0 0 1 0 1 1 1.723680 1 0.270000 1.810000 0.161305 0.870000 5.500000e-01 1.000000 1.000000 0.855700 0.870000 1 7.100000e-01 0.990000 STOX2 56977 broad.mit.edu 37 4 184932370 184932370 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr4:184932370G>A ENST00000308497.4 + 3 3814 c.2379G>A c.(2377-2379)gaG>gaA p.E793E STOX2_ENST00000438269.1_Silent_p.E793E NM_020225.1 NP_064610.1 Q9P2F5 STOX2_HUMAN storkhead box 2 14 all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283) CAGAGGAGGAGAAAAATAGAG 0.498000 0 SO:0001819 synonymous_variant ENST00000308497.4 0 1 hg19 CCDS47167.1 TCGA-2J-AAB8-01A-12D-A40W-08 STOX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000361433.3 1 0 0 6 58 0 9 0 0 1 0 0 9 2 0 0 0 0 0 2 1 0.960272 6 54 0 9 2 -11.502260 1 1 0 0 1 0 1 1 1.723680 1 0.270000 1.810000 0.161305 0.590000 2.500000e-01 0.960000 0.560000 0.606028 0.590000 0 4.000000e-01 0.810000 LIN54 132660 broad.mit.edu 37 4 83891489 83891489 + Silent SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr4:83891489C>T ENST00000340417.3 - 4 1319 c.942G>A c.(940-942)tcG>tcA p.S314S LIN54_ENST00000395283.2_Intron|LIN54_ENST00000442461.2_Silent_p.S93S|LIN54_ENST00000505397.1_Silent_p.S314S|LIN54_ENST00000446851.2_Silent_p.S93S|LIN54_ENST00000395282.2_3'UTR|LIN54_ENST00000506560.1_Intron|LIN54_ENST00000510557.1_Silent_p.S93S NM_194282.2 NP_919258.2 Q6MZP7 LIN54_HUMAN lin-54 DREAM MuvB core complex component 14 Hepatocellular(203;0.114) CCTTATTTGGCGATTTCAAAG 0.308000 0 SO:0001819 synonymous_variant ENST00000340417.3 0 1 hg19 CCDS3599.1 TCGA-2J-AAB8-01A-12D-A40W-08 LIN54-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252626.2 0 0 0 5 469 0 75 0 5.487472e-04 0 3 0 75 2 0 0 0 0 0 2 1 0.935737 5 463 0 74 2 -2.196348 0 1 121410 1 32 1 0 0 0 1.945538 0 0.270000 1.810000 0.228330 0.070000 2.000000e-02 0.160000 0.080000 0.087703 0.070000 0 4.000000e-02 0.120000 SPARCL1 8404 broad.mit.edu 37 4 88412840 88412840 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr4:88412840G>A ENST00000282470.6 - 5 1691 c.1221C>T c.(1219-1221)gcC>gcT p.A407A SPARCL1_ENST00000503414.1_Silent_p.A282A|SPARCL1_ENST00000418378.1_Silent_p.A407A NM_004684.4 NP_004675.3 Q14515 SPRL1_HUMAN SPARC-like 1 (hevin) 21 CTGCTTTCTTGGCCTTTAGAA 0.393000 0 SO:0001819 synonymous_variant ENST00000282470.6 1 1 hg19 CCDS3622.1 TCGA-2J-AAB8-01A-12D-A40W-08 SPARCL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253059.2 1 0 1 35 240 0 46 0 1 0 225 0 46 2 0 0 0 0 0 2 1 1.000000 35 240 0 45 2 -3.319203 1 1 0 0 1 0 0 0 1.945538 0 0.270000 1.810000 0.228330 0.880000 6.300000e-01 1.000000 1.000000 0.879089 0.880000 1 7.500000e-01 1.000000 MEGF10 84466 broad.mit.edu 37 5 126771182 126771182 + Splice_Site SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr5:126771182G>A ENST00000274473.6 + 17 2371 c.e17+1 MEGF10_ENST00000503335.2_Splice_Site NM_032446.2 NP_115822.1 Q96KG7 MEG10_HUMAN multiple EGF-like-domains 10 p.?(1) 68 Prostate(80;0.165) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) TGCTCTCAACGTAAGTCTTGT 0.373000 1 Unknown(1) SO:0001630 splice_region_variant ENST00000274473.6 1 1 hg19 CCDS4142.1 . . . . . . . . . . G 28.0 4.881482 0.91740 . . ENSG00000145794 ENST00000503335;ENST00000274473 . . . 5.85 5.85 0.93711 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.1542 0.98100 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . MEGF10 126799081 1.000000 0.71417 1.000000 0.80357 0.951000 0.60555 9.776000 0.99001 2.767000 0.95098 0.563000 0.77884 . TCGA-2J-AAB8-01A-12D-A40W-08 MEGF10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250973.2 1 0 1 20 187 0 59 0 0 0 0 59 2 0 0 0 0 0 2 1 0.999996 20 186 0 56 2 -3.221900 1 1 0 0 1 0 1 1 1.993259 0 0.270000 1.810000 0.235962 0.680000 4.300000e-01 0.980000 1.000000 0.698168 0.680000 0 5.500000e-01 0.840000 PCDHB7 56129 broad.mit.edu 37 5 140554386 140554386 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr5:140554386C>T ENST00000231137.3 + 1 2144 c.1970C>T c.(1969-1971)aCg>aTg p.T657M PCDHB8_ENST00000239444.2_5'Flank NM_018940.2 NP_061763.1 Q9Y5E2 PCDB7_HUMAN protocadherin beta 7 p.T657M(1) 119 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) GCCACCGCCACGCTGCACGTG 0.706000 1 Substitution - Missense(1) SO:0001583 missense ENST00000231137.3 0 1 hg19 CCDS4249.1 . . . . . . . . . . C 14.88 2.667450 0.47677 . . ENSG00000113212 ENST00000231137 T 0.55588 0.51 3.98 3.98 0.46160 Cadherin (4);Cadherin-like (1); . . . . T 0.62792 0.2457 M 0.80332 2.49 0.21967 N 0.999445 D 0.54397 0.966 P 0.49953 0.627 T 0.58244 -0.7670 9 0.66056 D 0.02 . 10.9109 0.47108 0.0:0.9049:0.0:0.0951 . 657 Q9Y5E2 PCDB7_HUMAN M 657 ENSP00000231137:T657M ENSP00000231137:T657M T + 2 0 PCDHB7 140534570 0.004000 0.15560 0.993000 0.49108 0.665000 0.39181 1.710000 0.37920 1.922000 0.55676 0.449000 0.29647 ACG TCGA-2J-AAB8-01A-12D-A40W-08 PCDHB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251803.2 0 0 0 13 654 0 125 0 0 0 1 0 125 2 0 0 0 0 1 2 1 0.998594 10 549 0 141 2 -3.346692 1 1 120648 1 32 1 0 1 1 1.993259 0 0.270000 1.810000 0.235962 0.130000 7.000000e-02 0.230000 0.140000 0.147391 0.130000 0 1.000000e-01 0.180000 THBS4 7060 broad.mit.edu 37 5 79366517 79366517 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr5:79366517G>A ENST00000350881.2 + 12 1694 c.1504G>A c.(1504-1506)Ggc>Agc p.G502S CTD-2201I18.1_ENST00000503007.1_RNA|CTD-2201I18.1_ENST00000514042.1_RNA|THBS4_ENST00000511733.1_Missense_Mutation_p.G411S NM_003248.4 NP_003239.2 P35443 TSP4_HUMAN thrombospondin 4 34 Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261) AGACAGAGATGGCATTGGCGA 0.517000 0 SO:0001583 missense ENST00000350881.2 1 1 hg19 CCDS4049.1 . . . . . . . . . . G 18.90 3.721678 0.68959 . . ENSG00000113296 ENST00000350881;ENST00000511733 D;D 0.98914 -4.89;-5.23 5.17 5.17 0.71159 . 0.049134 0.85682 D 0.000000 D 0.98302 0.9437 M 0.93106 3.38 0.80722 D 1 P 0.46621 0.881 B 0.41619 0.361 D 0.98048 1.0386 10 0.51188 T 0.08 -36.174 12.2251 0.54455 0.0773:0.0:0.9227:0.0 . 502 P35443 TSP4_HUMAN S 502;411 ENSP00000339730:G502S;ENSP00000422298:G411S ENSP00000339730:G502S G + 1 0 THBS4 79402273 1.000000 0.71417 0.999000 0.59377 0.693000 0.40251 6.549000 0.73900 2.703000 0.92315 0.655000 0.94253 GGC TCGA-2J-AAB8-01A-12D-A40W-08 THBS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000226977.1 0 0 0 30 474 0 94 0 9.492904e-01 0 80 0 94 2 0 0 0 0 0 2 1 0.970068 30 468 1 93 18 -6.550211 1 1 0 0 1 0 1 1 1.993259 0 0.270000 1.810000 0.235962 0.420000 2.900000e-01 0.580000 0.420000 0.430816 0.420000 0 3.500000e-01 0.500000 HAPLN1 1404 broad.mit.edu 37 5 82940318 82940318 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr5:82940318G>A ENST00000274341.4 - 4 1489 c.639C>T c.(637-639)ggC>ggT p.G213G NM_001884.3 NP_001875.1 P10915 HPLN1_HUMAN hyaluronan and proteoglycan link protein 1 34 Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142) Hyaluronan(DB08818) ATTGCACAGAGCCATCACTGA 0.587000 0 SO:0001819 synonymous_variant ENST00000274341.4 1 1 hg19 CCDS4061.1 TCGA-2J-AAB8-01A-12D-A40W-08 HAPLN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239256.2 1 0 0 26 309 0 50 0 0 0 1 0 50 2 0 0 0 0 0 2 1 1.000000 26 306 0 46 2 -20.000000 1 1 0 0 1 0 1 1 1.993259 0 0.270000 1.810000 0.235962 0.540000 3.700000e-01 0.760000 0.550000 0.561562 0.540000 0 4.500000e-01 0.660000 GMDS 2762 broad.mit.edu 37 6 2116094 2116094 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr6:2116094C>T ENST00000380815.4 - 4 525 c.256G>A c.(256-258)Gat>Aat p.D86N GMDS_ENST00000530927.1_Missense_Mutation_p.D56N NM_001500.3 NP_001491.1 O60547 GMDS_HUMAN GDP-mannose 4,6-dehydratase GMDS/PDE8B(2) 21 Ovarian(93;0.0733) all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802) TCAGTGAGATCGCCATAGTGC 0.383000 0 SO:0001583 missense ENST00000380815.4 1 1 hg19 CCDS4474.1 . . . . . . . . . . C 34 5.384293 0.95967 . . ENSG00000112699 ENST00000530927;ENST00000380815 D;D 0.95756 -3.8;-3.8 5.64 5.64 0.86602 NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.98520 0.9506 H 0.94582 3.555 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.99289 1.0898 10 0.87932 D 0 -17.6903 19.7154 0.96115 0.0:1.0:0.0:0.0 . 86 O60547 GMDS_HUMAN N 56;86 ENSP00000436726:D56N;ENSP00000370194:D86N ENSP00000370194:D86N D - 1 0 GMDS 2061093 1.000000 0.71417 0.952000 0.39060 0.987000 0.75469 7.487000 0.81328 2.664000 0.90586 0.655000 0.94253 GAT TCGA-2J-AAB8-01A-12D-A40W-08 GMDS-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000043380.3 1 0 1 26 333 0 61 1 9.966404e-01 29 87 0 61 2 0 0 0 0 0 2 1 1.000000 26 330 0 59 2 -3.221858 1 1 0 0 1 0 1 1 1.949924 0 0.270000 1.810000 0.222784 0.500000 3.300000e-01 0.700000 0.500000 0.515317 0.500000 0 4.100000e-01 0.610000 MDN1 23195 broad.mit.edu 37 6 90421896 90421896 + Missense_Mutation SNP C C T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr6:90421896C>T ENST00000369393.3 - 49 7625 c.7510G>A c.(7510-7512)Gaa>Aaa p.E2504K MDN1_ENST00000428876.1_Missense_Mutation_p.E2504K Q9NU22 MDN1_HUMAN MDN1, midasin homolog (yeast) p.E2504K(1) 218 all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246) GTATTCACTTCGACTGCATTG 0.408000 1 Substitution - Missense(1) SO:0001583 missense ENST00000369393.3 0 1 hg19 CCDS5024.1 . . . . . . . . . . C 12.21 1.870955 0.33069 2.27E-4 0.0 ENSG00000112159 ENST00000369393;ENST00000428876 T;T 0.03358 3.96;3.96 5.86 2.99 0.34606 . 0.415320 0.25860 N 0.027823 T 0.00815 0.0027 N 0.19112 0.55 0.26986 N 0.965244 B 0.21688 0.059 B 0.08055 0.003 T 0.47586 -0.9106 10 0.17369 T 0.5 . 11.2019 0.48747 0.0:0.6969:0.238:0.0651 . 2504 Q9NU22 MDN1_HUMAN K 2504 ENSP00000358400:E2504K;ENSP00000413970:E2504K ENSP00000358400:E2504K E - 1 0 MDN1 90478617 0.030000 0.19436 0.017000 0.16124 0.924000 0.55760 0.999000 0.29757 0.757000 0.33036 0.563000 0.77884 GAA TCGA-2J-AAB8-01A-12D-A40W-08 MDN1-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041514.2 0 0 0 9 677 0 159 0 2.313792e-04 0 2 0 159 2 0 0 0 0 0 2 1 0.993981 9 670 0 157 2 -2.268995 0 1 121412 2 44 1 0 0 0 1.885427 1 0.270000 1.810000 0.203318 0.080000 4.000000e-02 0.160000 0.090000 0.098090 0.080000 0 6.000000e-02 0.130000 MUC17 140453 broad.mit.edu 37 7 100692136 100692136 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr7:100692136G>A ENST00000306151.4 + 5 12610 c.12546G>A c.(12544-12546)gaG>gaA p.E4182E NM_001040105.1 NP_001035194.1 Q685J3 MUC17_HUMAN mucin 17, cell surface associated 343 Lung NSC(181;0.136)|all_lung(186;0.182) GGCCACCGGAGACTATCTCTG 0.522000 0 SO:0001819 synonymous_variant ENST00000306151.4 1 1 hg19 CCDS34711.1 TCGA-2J-AAB8-01A-12D-A40W-08 MUC17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347161.1 1 0 0 29 369 0 68 1 7.753961e-01 16 22 0 68 2 0 0 0 0 0 2 1 1.000000 27 360 0 64 2 -8.571638 1 1 121412 1 39 1 0 1 1 1.962996 0 0.270000 1.810000 0.232710 0.510000 3.500000e-01 0.700000 0.510000 0.524188 0.510000 0 4.200000e-01 0.610000 TRPV6 55503 broad.mit.edu 37 7 142572369 142572369 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr7:142572369G>A ENST00000359396.3 - 11 1572 c.1327C>T c.(1327-1329)Cgg>Tgg p.R443W RP11-114L10.2_ENST00000438839.1_RNA NM_018646.3 NP_061116 Q9H1D0 TRPV6_HUMAN transient receptor potential cation channel, subfamily V, member 6 42 Melanoma(164;0.059) CTGATGAGCCGCATCACCATG 0.607000 0 SO:0001583 missense ENST00000359396.3 0 1 hg19 CCDS5874.1 . . . . . . . . . . G 16.96 3.267374 0.59540 . . ENSG00000165125 ENST00000359396;ENST00000311470;ENST00000436401 D;D 0.88975 -2.45;-2.45 4.52 2.68 0.31781 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.93854 0.8034 M 0.89287 3.02 0.80722 D 1 D 0.67145 0.996 P 0.62885 0.908 D 0.93494 0.6838 10 0.56958 D 0.05 -32.9258 11.9495 0.52946 0.0:0.0:0.5445:0.4555 . 443 Q9H1D0 TRPV6_HUMAN W 443;275;66 ENSP00000352358:R443W;ENSP00000411100:R66W ENSP00000310825:R275W R - 1 2 TRPV6 142282491 1.000000 0.71417 1.000000 0.80357 0.832000 0.47134 1.441000 0.35035 0.629000 0.30376 0.561000 0.74099 CGG TCGA-2J-AAB8-01A-12D-A40W-08 TRPV6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347662.1 0 0 0 4 121 0 28 0 1.845472e-03 0 2 0 28 2 0 0 0 0 0 2 1 0.885799 4 118 0 28 2 -3.314468 1 1 121412 4 25 1 0 1 1 1.978737 0 0.270000 1.810000 0.233797 0.240000 8.000000e-02 0.520000 0.220000 0.270622 0.240000 0 1.500000e-01 0.380000 KRBA1 84626 broad.mit.edu 37 7 149431136 149431136 + Nonstop_Mutation SNP A A G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr7:149431136A>G ENST00000485033.2 + 15 2910 c.2910A>G c.(2908-2910)tgA>tgG p.*970W KRBA1_ENST00000479560.1_3'UTR|KRBA1_ENST00000255992.10_Nonstop_Mutation_p.*1030W|KRBA1_ENST00000319551.8_Nonstop_Mutation_p.*970W A5PL33 KRBA1_HUMAN KRAB-A domain containing 1 27 Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) GGGCGCATTGATGGCATTCCT 0.662000 0 SO:0001578 stop_lost ENST00000485033.2 0 1 hg19 . . . . . . . . . . A 1.730 -0.494361 0.04322 . . ENSG00000133619 ENST00000255992;ENST00000319551;ENST00000485033 . . . 4.48 -4.96 0.03038 . . . . . . . . . . . 0.09310 N 1 . . . . . . . . . . . . . . 11.8325 0.52303 0.4242:0.0:0.5758:0.0 . . . . W 1030;970;970 . . X + 3 0 KRBA1 149062069 0.000000 0.05858 0.000000 0.03702 0.011000 0.07611 -0.962000 0.03841 -0.871000 0.04042 0.533000 0.62120 TGA TCGA-2J-AAB8-01A-12D-A40W-08 KRBA1-004 PUTATIVE basic protein_coding protein_coding OTTHUMT00000349841.3 0 0 0 5 76 1 24 0 0 0 1 24 2 0 0 0 0 0 2 0 0.084917 5 75 1 24 11 -9.690517 1 1 0 0 1 0 1 1 1.978737 0 0.270000 1.810000 0.233797 0.450000 1.800000e-01 0.880000 0.410000 0.488501 0.450000 0 2.900000e-01 0.670000 SDK1 221935 broad.mit.edu 37 7 4259748 4259748 + Missense_Mutation SNP C C G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr7:4259748C>G ENST00000404826.2 + 39 5686 c.5547C>G c.(5545-5547)agC>agG p.S1849R SDK1_ENST00000389531.3_Missense_Mutation_p.S1829R NM_152744.3 NP_689957.3 Q7Z5N4 SDK1_HUMAN sidekick cell adhesion molecule 1 153 all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194) CAGGGGTGAGCAAGGTGGTGA 0.572000 0 SO:0001583 missense ENST00000404826.2 1 1 hg19 CCDS34590.1 . . . . . . . . . . C 16.38 3.108140 0.56291 . . ENSG00000146555 ENST00000404826;ENST00000446104;ENST00000389531 T;T 0.58358 0.34;0.34 5.28 5.28 0.74379 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.74253 0.3692 M 0.89904 3.07 0.44352 D 0.997247 D;P;D 0.58620 0.983;0.604;0.962 D;P;D 0.66602 0.945;0.517;0.933 T 0.78981 -0.1989 10 0.87932 D 0 . 10.8802 0.46933 0.0:0.8536:0.0:0.1464 . 1829;336;1849 F8W6X9;F2Z3E9;Q7Z5N4 .;.;SDK1_HUMAN R 1849;97;1829 ENSP00000385899:S1849R;ENSP00000374182:S1829R ENSP00000374182:S1829R S + 3 2 SDK1 4226274 1.000000 0.71417 1.000000 0.80357 0.979000 0.70002 1.082000 0.30803 2.623000 0.88846 0.650000 0.86243 AGC TCGA-2J-AAB8-01A-12D-A40W-08 SDK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323702.1 0 0 0 13 300 0 60 0 6.116147e-03 0 3 0 60 2 0 0 0 0 0 2 1 0.999522 12 297 0 59 2 -14.083400 1 1 121412 1 29 1 2 2 4 2.188676 1 0.270000 1.810000 0.316159 0.360000 1.900000e-01 1.000000 0.330000 0.465774 0.360000 0 2.600000e-01 1.000000 ZFPM2 23414 broad.mit.edu 37 8 106431448 106431448 + Missense_Mutation SNP C C G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr8:106431448C>G ENST00000407775.2 + 2 367 c.117C>G c.(115-117)gaC>gaG p.D39E ZFPM2_ENST00000520492.1_5'UTR NM_012082.3 NP_036214.2 Q8WW38 FOG2_HUMAN zinc finger protein, FOG family member 2 99 OV - Ovarian serous cystadenocarcinoma(57;8.28e-08) CCAAAGGAGACTTTCCATTGG 0.423000 0 SO:0001583 missense ENST00000407775.2 1 1 hg19 CCDS47908.1 . . . . . . . . . . C 13.85 2.361570 0.41801 . . ENSG00000169946 ENST00000407775 T 0.19394 2.15 5.37 5.37 0.77165 . 0.088240 0.42964 D 0.000630 T 0.10809 0.0264 N 0.05124 -0.11 0.80722 D 1 B 0.12630 0.006 B 0.10450 0.005 T 0.20472 -1.0274 10 0.25106 T 0.35 . 12.4488 0.55666 0.0:0.9232:0.0:0.0768 . 39 Q8WW38 FOG2_HUMAN E 39 ENSP00000384179:D39E ENSP00000384179:D39E D + 3 2 ZFPM2 106500624 1.000000 0.71417 1.000000 0.80357 0.959000 0.62525 2.989000 0.49393 2.528000 0.85240 0.591000 0.81541 GAC TCGA-2J-AAB8-01A-12D-A40W-08 ZFPM2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380614.1 1 0 1 42 283 0 49 0 2.319980e-01 0 7 0 49 2 0 0 0 0 0 2 1 1.000000 42 282 0 48 2 -20.000000 1 0 0 0 1 0 1 1 1.971349 0 0.270000 1.810000 0.229429 0.900000 6.600000e-01 1.000000 1.000000 0.892792 0.900000 1 7.700000e-01 1.000000 CSMD3 114788 broad.mit.edu 37 8 113326150 113326150 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr8:113326150G>A ENST00000297405.5 - 49 7925 c.7681C>T c.(7681-7683)Cgg>Tgg p.R2561W CSMD3_ENST00000352409.3_Missense_Mutation_p.R2491W|CSMD3_ENST00000455883.2_Missense_Mutation_p.R2457W|CSMD3_ENST00000343508.3_Missense_Mutation_p.R2521W NM_198123.1 NP_937756.1 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 646 TATCTTATCCGGAAGCCTTTT 0.358000 HNSCC(6;0.00088)|TCGA Ovarian(7;0.080) 0 SO:0001583 missense ENST00000297405.5 1 1 hg19 CCDS6315.1 . . . . . . . . . . G 16.80 3.222747 0.58668 . . ENSG00000164796 ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409 T;T;T;T;T 0.19394 2.15;2.15;2.15;2.15;2.15 5.63 2.35 0.29111 CUB (5); 0.278292 0.30118 N 0.010380 T 0.38931 0.1059 L 0.51422 1.61 0.41494 D 0.988245 D;D;D 0.89917 0.999;0.999;1.0 D;D;D 0.79108 0.944;0.967;0.992 T 0.17745 -1.0359 10 0.45353 T 0.12 . 15.2984 0.73928 0.0:0.0:0.5384:0.4615 . 2457;2561;2521 Q7Z407-3;Q7Z407;Q7Z407-2 .;CSMD3_HUMAN;. W 2521;2561;1831;2457;2491 ENSP00000345799:R2521W;ENSP00000297405:R2561W;ENSP00000341558:R1831W;ENSP00000412263:R2457W;ENSP00000343124:R2491W ENSP00000297405:R2561W R - 1 2 CSMD3 113395326 1.000000 0.71417 1.000000 0.80357 0.793000 0.44817 0.785000 0.26830 0.624000 0.30286 0.579000 0.79373 CGG TCGA-2J-AAB8-01A-12D-A40W-08 CSMD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347141.1 1 0 1 41 259 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 1.000000 39 257 0 54 2 -2.921957 1 1 121408 4 39 1 0 1 1 1.971349 0 0.270000 1.810000 0.229429 0.950000 7.000000e-01 1.000000 1.000000 0.925342 0.950000 1 8.200000e-01 1.000000 GSDMD 79792 broad.mit.edu 37 8 144645015 144645015 + Missense_Mutation SNP A A T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr8:144645015A>T ENST00000526406.1 + 14 2279 c.1396A>T c.(1396-1398)Atg>Ttg p.M466L GSDMD_ENST00000533063.1_Missense_Mutation_p.M514L|GSDMD_ENST00000262580.4_Missense_Mutation_p.M466L NM_001166237.1 NP_001159709.1 P57764 GSDMD_HUMAN gasdermin D 12 CCAGGGCCGCATGTGTGCACT 0.687000 0 SO:0001583 missense ENST00000526406.1 1 1 hg19 CCDS34956.1 . . . . . . . . . . A 0.007 -1.958655 0.00465 . . ENSG00000104518 ENST00000526406;ENST00000533063;ENST00000262580 T;T;T 0.13657 2.65;2.57;2.65 4.9 -3.65 0.04502 . 0.971022 0.08500 N 0.936553 T 0.02380 0.0073 N 0.00436 -1.5 0.09310 N 1 B;B;B 0.06786 0.0;0.0;0.001 B;B;B 0.06405 0.001;0.001;0.002 T 0.44467 -0.9326 10 0.02654 T 1 -4.7448 6.4597 0.21950 0.3686:0.162:0.4693:0.0 . 466;466;514 A8K702;P57764;G3V1A6 .;GSDMD_HUMAN;. L 466;514;466 ENSP00000433209:M466L;ENSP00000433958:M514L;ENSP00000262580:M466L ENSP00000262580:M466L M + 1 0 GSDMD 144716158 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 0.066000 0.14489 -0.378000 0.07918 -0.288000 0.09946 ATG TCGA-2J-AAB8-01A-12D-A40W-08 GSDMD-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382046.3 1 0 1 11 92 0 26 1 9.989103e-01 30 77 0 26 2 0 0 0 0 0 2 1 0.998641 11 92 0 24 2 -17.950580 1 1 0 0 1 0 1 1 1.971349 0 0.270000 1.810000 0.229429 0.750000 4.100000e-01 1.000000 1.000000 0.757447 0.750000 0 5.600000e-01 0.970000 DDHD2 23259 broad.mit.edu 37 8 38107250 38107250 + Missense_Mutation SNP C C G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr8:38107250C>G ENST00000397166.2 + 11 1798 c.1273C>G c.(1273-1275)Cag>Gag p.Q425E DDHD2_ENST00000528888.1_3'UTR|DDHD2_ENST00000517385.1_Missense_Mutation_p.Q44E|DDHD2_ENST00000529845.1_5'Flank|DDHD2_ENST00000520272.2_Missense_Mutation_p.Q425E NM_015214.2 NP_056029.2 O94830 DDHD2_HUMAN DDHD domain containing 2 p.Q425K(1) 28 Colorectal(12;0.000442) all_lung(54;0.0657)|Lung NSC(58;0.175) BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977) CCGAGATCTTCAGGAAATAGG 0.368000 1 Substitution - Missense(1) SO:0001583 missense ENST00000397166.2 0 1 hg19 CCDS34883.1 . . . . . . . . . . C 14.16 2.453824 0.43531 . . ENSG00000085788 ENST00000397166;ENST00000520272;ENST00000440212;ENST00000517385 T;T;T 0.44881 0.91;0.91;0.91 5.5 5.5 0.81552 Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1); 0.113509 0.64402 D 0.000015 T 0.28333 0.0700 L 0.39147 1.195 0.80722 D 1 B;B 0.10296 0.003;0.001 B;B 0.12837 0.008;0.006 T 0.10132 -1.0643 10 0.02654 T 1 -18.2805 9.4121 0.38498 0.2626:0.6029:0.1345:0.0 . 237;425 B4DSR3;O94830 .;DDHD2_HUMAN E 425;425;237;44 ENSP00000380352:Q425E;ENSP00000429932:Q425E;ENSP00000429017:Q44E ENSP00000380352:Q425E Q + 1 0 DDHD2 38226407 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 3.445000 0.52921 2.744000 0.94065 0.655000 0.94253 CAG TCGA-2J-AAB8-01A-12D-A40W-08 DDHD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377251.2 1 0 0 13 125 1 34 1 1.646427e-01 4 17 1 34 4 0 0 0 0 0 2 0 0.492065 13 125 1 33 14 -18.924570 1 1 0 0 1 0 1 1 1.842630 1 0.270000 1.810000 0.157384 0.590000 3.400000e-01 0.900000 0.590000 0.611731 0.590000 0 4.500000e-01 0.760000 ZFHX4 79776 broad.mit.edu 37 8 77763870 77763870 + Missense_Mutation SNP A A T TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr8:77763870A>T ENST00000521891.2 + 10 5161 c.4713A>T c.(4711-4713)aaA>aaT p.K1571N ZFHX4_ENST00000518282.1_Missense_Mutation_p.K1545N|ZFHX4_ENST00000050961.6_Missense_Mutation_p.K1526N|ZFHX4_ENST00000455469.2_Missense_Mutation_p.K1526N NM_024721.4 NP_078997.4 Q86UP3 ZFHX4_HUMAN zinc finger homeobox 4 432 BRCA - Breast invasive adenocarcinoma(89;0.0895) AGCTGAAAAAAGTTTTGCAGG 0.413000 HNSCC(33;0.089) 0 SO:0001583 missense ENST00000521891.2 0 1 hg19 CCDS47878.2 . . . . . . . . . . A 11.15 1.555228 0.27739 . . ENSG00000091656 ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282 T;T;T;T 0.56444 0.46;0.51;0.47;0.47 4.6 0.728 0.18260 Zinc finger, U1-type (1);Zinc finger, C2H2 (1); 0.000000 0.46442 U 0.000298 T 0.63022 0.2476 L 0.57536 1.79 0.58432 D 0.999996 D;D;D 0.76494 0.998;0.999;0.999 D;D;D 0.83275 0.991;0.996;0.996 T 0.60782 -0.7195 10 0.56958 D 0.05 . 8.7254 0.34467 0.4063:0.0:0.5937:0.0 . 1526;1526;1571 Q86UP3;Q86UP3-4;G3V138 ZFHX4_HUMAN;.;. N 1571;1571;1526;1526;1545 ENSP00000430497:K1571N;ENSP00000399605:K1526N;ENSP00000050961:K1526N;ENSP00000430848:K1545N ENSP00000050961:K1526N K + 3 2 ZFHX4 77926425 1.000000 0.71417 1.000000 0.80357 0.980000 0.70556 0.862000 0.27899 0.260000 0.21731 -0.375000 0.07067 AAA TCGA-2J-AAB8-01A-12D-A40W-08 ZFHX4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000379197.2 1 0 0 10 133 0 21 0 0 0 1 0 21 2 0 0 0 0 0 2 1 0.997108 10 132 0 21 2 -14.746630 1 1 0 0 1 0 1 1 1.971349 0 0.270000 1.810000 0.229429 0.490000 2.600000e-01 0.820000 0.480000 0.519694 0.490000 0 3.600000e-01 0.660000 MFHAS1 9258 broad.mit.edu 37 8 8748773 8748773 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr8:8748773G>A ENST00000276282.6 - 1 2382 c.1796C>T c.(1795-1797)tCg>tTg p.S599L NM_004225.2 NP_004216.2 Q9Y4C4 MFHA1_HUMAN malignant fibrous histiocytoma amplified sequence 1 21 Hepatocellular(245;0.217) GTTCTTGTCCGAAACGCCATA 0.642000 Melanoma(103;1201 2045 17515 28966) 0 SO:0001583 missense ENST00000276282.6 0 1 hg19 CCDS34844.1 . . . . . . . . . . G 16.90 3.249044 0.59103 . . ENSG00000147324 ENST00000276282 T 0.37235 1.21 5.28 5.28 0.74379 ROC GTPase (1); 0.172306 0.38837 N 0.001551 T 0.41166 0.1147 L 0.61218 1.895 0.50039 D 0.999841 D 0.62365 0.991 P 0.45558 0.485 T 0.42120 -0.9470 10 0.72032 D 0.01 . 13.7779 0.63066 0.0:0.1534:0.8466:0.0 . 599 Q9Y4C4 MFHA1_HUMAN L 599 ENSP00000276282:S599L ENSP00000276282:S599L S - 2 0 MFHAS1 8786183 1.000000 0.71417 0.386000 0.26170 0.938000 0.57974 4.486000 0.60286 2.736000 0.93811 0.655000 0.94253 TCG TCGA-2J-AAB8-01A-12D-A40W-08 MFHAS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374724.2 0 0 0 5 253 0 45 0 3.564281e-03 0 4 0 45 2 0 0 0 0 0 2 1 0.934211 5 247 0 44 2 -3.254147 1 1 0 0 1 0 1 1 1.868917 1 0.270000 1.810000 0.158695 0.130000 4.000000e-02 0.270000 0.120000 0.145288 0.130000 0 8.000000e-02 0.200000 SEC16A 9919 broad.mit.edu 37 9 139360714 139360714 + Splice_Site SNP A A G TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr9:139360714A>G ENST00000371706.3 - 5 3628 c.e5+1 SEC16A_ENST00000431893.2_Splice_Site|SEC16A_ENST00000290037.6_Splice_Site|SEC16A_ENST00000313050.7_Splice_Site O15027 SC16A_HUMAN SEC16 homolog A (S. cerevisiae) 51 Myeloproliferative disorder(178;0.0511) GCCGCCGCGTACCTGGTGCGA 0.622000 0 SO:0001630 splice_region_variant ENST00000371706.3 0 1 hg19 . . . . . . . . . . A 12.70 2.016902 0.35606 . . ENSG00000148396 ENST00000313050;ENST00000453963;ENST00000371706;ENST00000433860;ENST00000290037;ENST00000431893;ENST00000404925;ENST00000398348 . . . 5.68 5.68 0.88126 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.0933 0.72215 1.0:0.0:0.0:0.0 . . . . . -1 . . . - . . SEC16A 138480535 1.000000 0.71417 0.950000 0.38849 0.057000 0.15508 6.084000 0.71335 2.168000 0.68352 0.528000 0.53228 . TCGA-2J-AAB8-01A-12D-A40W-08 SEC16A-001 KNOWN basic protein_coding protein_coding OTTHUMT00000055077.1 0 0 1 5 41 0 13 1 1.714286e-02 2 0 0 13 2 0 0 0 0 0 2 1 0.933938 5 40 0 13 2 -13.066360 1 1 0 0 1 0 0 0 2.033948 0 0.270000 1.810000 0.262030 0.810000 3.200000e-01 1.000000 1.000000 0.785430 0.810000 0 5.300000e-01 1.000000 SPTLC1 10558 broad.mit.edu 37 9 94794825 94794825 + Silent SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chr9:94794825G>A ENST00000262554.2 - 15 1349 c.1344C>T c.(1342-1344)gtC>gtT p.V448V NM_006415.2 NP_006406.1 O15269 SPTC1_HUMAN serine palmitoyltransferase, long chain base subunit 1 14 L-Serine(DB00133) GTTCCACCGTGACCACAACCC 0.567000 0 SO:0001819 synonymous_variant ENST00000262554.2 1 1 hg19 CCDS6692.1 TCGA-2J-AAB8-01A-12D-A40W-08 SPTLC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055553.1 1 0 1 37 323 0 64 1 9.998319e-01 47 69 0 64 2 0 0 0 0 0 2 1 1.000000 37 319 0 61 2 -20.000000 1 1 0 0 1 0 0 0 2.038432 0 0.270000 1.810000 0.266037 0.750000 5.400000e-01 0.990000 0.750000 0.765779 0.750000 0 6.400000e-01 0.880000 CSF2RA 1438 broad.mit.edu 37 X 1422850 1422850 + Silent SNP T T C TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chrX:1422850T>C ENST00000381524.3 + 11 1167 c.981T>C c.(979-981)atT>atC p.I327I CSF2RA_ENST00000381500.1_Intron|CSF2RA_ENST00000381529.3_Silent_p.I327I|CSF2RA_ENST00000417535.2_Silent_p.I361I|CSF2RA_ENST00000361536.3_Intron|CSF2RA_ENST00000355432.3_Intron|CSF2RA_ENST00000501036.2_Silent_p.I194I|CSF2RA_ENST00000432318.2_Silent_p.I327I|CSF2RA_ENST00000381509.3_Silent_p.I327I|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000498153.1_3'UTR P15509 CSF2R_HUMAN colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) 45 all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122) Sargramostim(DB00020) CTGTGTACATTTATGTGCTCC 0.498000 Esophageal Squamous(131;723 1707 25334 40494 41806) 0 SO:0001819 synonymous_variant ENST00000381524.3 0 1 hg19 CCDS35191.1 . . . . . . . . . . . 7.124 0.578594 0.13686 . . ENSG00000198223 ENST00000381507 . . . 0.806 -0.189 0.13260 . . . . . T 0.55081 0.1898 . . . 0.80722 D 1 . . . . . . T 0.53187 -0.8474 5 0.62326 D 0.03 . 3.1091 0.06352 0.0:0.6445:0.0:0.3555 . . . . S 283 . ENSP00000370918:F283S F + 2 0 CSF2RA 1382850 0.000000 0.05858 0.005000 0.12908 0.103000 0.19146 -0.764000 0.04735 -0.087000 0.12528 0.084000 0.15446 TTT TCGA-2J-AAB8-01A-12D-A40W-08 CSF2RA-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000035013.2 0 0 0 7 1268 1 284 0 6.470946e-04 0 6 1 284 2 0 0 0 0 0 2 0 0.003256 7 1242 2 278 22 -20.000000 1 1 0 0 1 0 1 1 0.270000 1.810000 0.270000 0.010000 0 0.040000 0.020000 0.023168 0.010000 0 0 0.030000 PHEX 5251 broad.mit.edu 37 X 22117217 22117217 + Missense_Mutation SNP G G A TCGA-2J-AAB8-01A-12D-A40W-08 TCGA-2J-AAB8-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx f17f4584-79ab-476e-860d-9b99d4d45141 617be344-0a3d-4f77-bc31-6950e06229b6 g.chrX:22117217G>A ENST00000379374.4 + 9 1592 c.1027G>A c.(1027-1029)Gtc>Atc p.V343I PHEX_ENST00000418858.3_Missense_Mutation_p.V46I|PHEX_ENST00000537599.1_Missense_Mutation_p.V343I|PHEX_ENST00000475778.1_3'UTR|PHEX_ENST00000535894.1_Missense_Mutation_p.V246I NM_000444.4 NP_000435.3 P78562 PHEX_HUMAN phosphate regulating endopeptidase homolog, X-linked 42 GGTGGTCCGCGTCCCGCAGTA 0.443000 0 SO:0001583 missense ENST00000379374.4 1 1 hg19 CCDS14204.1 . . . . . . . . . . G 27.1 4.801058 0.90538 . . ENSG00000102174 ENST00000379374;ENST00000537599;ENST00000535894;ENST00000418858 T;T;T;T 0.73789 -0.78;-0.78;-0.78;-0.78 5.46 5.46 0.80206 Peptidase M13 (1); 0.109879 0.64402 D 0.000008 T 0.71592 0.3358 L 0.39147 1.195 0.45995 D 0.998802 D;D 0.56746 0.977;0.964 B;P 0.44860 0.332;0.462 T 0.75836 -0.3177 10 0.62326 D 0.03 . 18.3838 0.90459 0.0:0.0:1.0:0.0 . 343;343 F5GXU4;P78562 .;PHEX_HUMAN I 343;343;246;46 ENSP00000368682:V343I;ENSP00000440362:V343I;ENSP00000439418:V246I;ENSP00000443531:V46I ENSP00000368682:V343I V + 1 0 PHEX 22027138 1.000000 0.71417 0.843000 0.33291 0.944000 0.59088 7.562000 0.82300 2.282000 0.76494 0.529000 0.55759 GTC TCGA-2J-AAB8-01A-12D-A40W-08 PHEX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056035.1 1 0 1 42 289 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 41 285 0 48 2 -18.129090 1 1 121412 2 41 1 0 1 1 0.270000 1.810000 0.270000 0.460000 3.400000e-01 0.600000 0.470000 0.474361 0.460000 0 4.000000e-01 0.540000