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 BRCA2 675 broad.mit.edu 37 13 32937480 32937480 + Frame_Shift_Del DEL A A - rs80359059 TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 A - A A Valid Somatic Phase_I WXS targeted Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr13:32937480delA ENST00000380152.3 + 18 8374 c.8141delA c.(8140-8142)caafs p.Q2714fs BRCA2_ENST00000544455.1_Frame_Shift_Del_p.Q2714fs P51587 BRCA2_HUMAN breast cancer 2, early onset 183 Lung SC(185;0.0262) GCAGATACCCAAAAAGTGGCC 0.398000 D, Mis, N, F, S breast, ovarian, pancreatic breast, ovarian, pancreatic, leukemia (FANCB, FANCD1) Homologous recombination Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia TCGA Ovarian(8;0.087) Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332) yes Rec yes Hereditary breast/ovarian cancer 13 13q12 675 familial breast/ovarian cancer gene 2 L, E 0 SO:0001589 frameshift_variant Familial Cancer Database incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups) ENST00000380152.3 1 0 hg19 CCDS9344.1 TCGA-FB-AAPU-01A-31D-A40W-08 BRCA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046000.2 1 0 0 113 457 0 157 0 1.802622e-01 0 4 0 157 2 1 1 199 640 1 978 5 1 1.000000 127 454 11 156 56 -2.970215 1 1 0 0 1 0 1 1 1.989277 0 0.700000 2 0.698946 0.560000 4.700000e-01 0.660000 0.560000 0.567008 0.560000 0 5.100000e-01 6.100000e-01 TNRC6C 57690 broad.mit.edu 37 17 76047129 76047153 + Frame_Shift_Del DEL CCCCCAACAGAACTGGGCTAGCAAA CCCCCAACAGAACTGGGCTAGCAAA - rs114241857 by1000genomes TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:76047129_76047153delCCCCCAACAGAACTGGGCTAGCAAA ENST00000588061.1 + 5 2713_2737 c.1986_2010delCCCCCAACAGAACTGGGCTAGCAAA c.(1984-2010)ggcccccaacagaactgggctagcaaafs p.GPQQNWASK662fs TNRC6C_ENST00000335749.4_Frame_Shift_Del_p.GPQQNWASK662fs|TNRC6C_ENST00000301624.4_Frame_Shift_Del_p.GPQQNWASK662fs|TNRC6C_ENST00000544502.1_Frame_Shift_Del_p.GPQQNWASK662fs|TNRC6C_ENST00000588847.1_Frame_Shift_Del_p.GPQQNWASK662fs|TNRC6C_ENST00000541771.1_Frame_Shift_Del_p.GPQQNWASK662fs Q9HCJ0 TNR6C_HUMAN trinucleotide repeat containing 6C 40 BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973) TAAAACCTGGCCCCCAACAGAACTGGGCTAGCAAACCCCAAGACA 0.538000 0 SO:0001589 frameshift_variant ENST00000588061.1 0 1 hg19 CCDS45798.1 TCGA-FB-AAPU-01A-31D-A40W-08 TNRC6C-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000395947.1 1 0 0 9 70 0 20 0 3.524145e-01 0 10 0 20 2 0 0 0 0 1 0.999242 27 86 0 20 2 -15.673500 1 1 0 0 1 1 2 3 2.677864 1 0.700000 2 0.777778 0.450000 2.200000e-01 0.750000 0.450000 0.474433 0.450000 0 3.300000e-01 6.100000e-01 PRSS1 5644 broad.mit.edu 37 7 142459745 142459747 + In_Frame_Del DEL CAT CAT - TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 CAT - CAT CAT Valid Somatic Phase_I WXS targeted Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr7:142459745_142459747delCAT ENST00000311737.7 + 3 327_329 c.321_323delCAT c.(319-324)gacatc>gac p.I108del PRSS1_ENST00000486171.1_In_Frame_Del_p.I122del NM_002769.4 NP_002760.1 P07477 TRY1_HUMAN protease, serine, 1 (trypsin 1) 38 Melanoma(164;0.047) all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165) all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189) Aprotinin(DB06692) TGAACAATGACATCATGTTAATC 0.547000 0 SO:0001651 inframe_deletion ENST00000311737.7 1 1 hg19 CCDS5872.1 TCGA-FB-AAPU-01A-31D-A40W-08 PRSS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352538.2 1 0 0 241 728 0 140 1 8.703207e-01 2 11 0 140 2 1 1 710 1974 2 2111 9 1 1.000000 271 660 4 126 49 -20.000000 1 0 0 0 1 1 2 3 2.507732 1 0.700000 2 0.760383 0.900000 7.900000e-01 1.000000 0.890000 0.912016 0.900000 1 8.400000e-01 1 ABCA1 19 broad.mit.edu 37 9 107591266 107591282 + Frame_Shift_Del DEL CCAGAGGATGCTGTTGT CCAGAGGATGCTGTTGT - rs144845639 byFrequency TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:107591266_107591282delCCAGAGGATGCTGTTGT ENST00000374736.3 - 15 2424_2440 c.2030_2046delACAACAGCATCCTCTGG c.(2029-2046)gacaacagcatcctctggfs p.DNSILW677fs ABCA1_ENST00000494467.1_5'UTR NM_005502.3 NP_005493.2 O95477 ABCA1_HUMAN ATP-binding cassette, sub-family A (ABC1), member 1 115 Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599) ACCAGCTAAACCAGAGGATGCTGTTGTCCAGGCCCAT 0.539000 0 SO:0001589 frameshift_variant ENST00000374736.3 0 1 hg19 CCDS6762.1 TCGA-FB-AAPU-01A-31D-A40W-08 ABCA1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053491.1 1 0 0 21 179 0 42 0 1.233966e-02 0 2 0 42 2 0 0 0 0 1 0.659346 60 217 2 44 27 -20.000000 1 1 0 0 1 1 2 3 2.013462 0 0.700000 2 0.701046 0.300000 1.900000e-01 0.450000 0.300000 0.311601 0.300000 0 2.400000e-01 3.700000e-01 BIRC2 329 broad.mit.edu 37 11 102221640 102221640 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr11:102221640G>C ENST00000227758.2 + 3 2360 c.961G>C c.(961-963)Gat>Cat p.D321H BIRC2_ENST00000532672.1_Missense_Mutation_p.D300H|BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.D272H NM_001166.4|NM_001256163.1 NP_001157.1|NP_001243092.1 Q13490 BIRC2_HUMAN baculoviral IAP repeat containing 2 26 all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093) Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151) ATCTGGAGATGATCCATGGGT 0.383000 0 SO:0001583 missense ENST00000227758.2 0 1 hg19 CCDS8316.1 . . . . . . . . . . G 21.6 4.175075 0.78564 . . ENSG00000110330 ENST00000530675;ENST00000227758;ENST00000541741;ENST00000532672 T;T;T 0.05786 3.39;3.39;3.39 5.86 5.86 0.93980 Baculoviral inhibition of apoptosis protein repeat (5); 0.000000 0.85682 D 0.000000 T 0.39545 0.1082 H 0.94306 3.52 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.52238 -0.8602 10 0.87932 D 0 -17.6801 20.2019 0.98263 0.0:0.0:1.0:0.0 . 321 Q13490 BIRC2_HUMAN H 272;321;321;300 ENSP00000431723:D272H;ENSP00000227758:D321H;ENSP00000434979:D300H ENSP00000227758:D321H D + 1 0 BIRC2 101726850 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 6.428000 0.73383 2.776000 0.95493 0.655000 0.94253 GAT TCGA-FB-AAPU-01A-31D-A40W-08 BIRC2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000394170.1 0 0 0 11 683 0 163 1 5.249592e-01 3 102 0 163 2 0 0 0 0 0 2 1 0.998132 11 668 0 161 2 -2.584069 1 1 0 0 1 0 0 0 1.997612 0 0.700000 2 0.700000 0.040000 1.000000e-02 0.080000 0.040000 0.049344 0.040000 0 2.000000e-02 6.000000e-02 AMPD3 272 broad.mit.edu 37 11 10500085 10500085 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr11:10500085C>G ENST00000396554.3 + 3 602 c.261C>G c.(259-261)ttC>ttG p.F87L AMPD3_ENST00000444303.2_Intron NM_000480.2 NP_000471.1 Q01432 AMPD3_HUMAN adenosine monophosphate deaminase 3 25 AGAAAAGTTTCAAGATGATTC 0.537000 0 SO:0001583 missense ENST00000396554.3 1 1 hg19 CCDS7802.1 . . . . . . . . . . C 14.45 2.538677 0.45176 . . ENSG00000133805 ENST00000532250;ENST00000396554;ENST00000524866;ENST00000396553;ENST00000528723;ENST00000529507 T;T;T;T;T;T 0.52526 0.66;0.66;0.66;0.66;0.66;0.66 5.6 3.69 0.42338 . 0.092497 0.85682 D 0.000000 T 0.36441 0.0967 L 0.47716 1.5 0.80722 D 1 B;B;B 0.06786 0.001;0.0;0.001 B;B;B 0.06405 0.002;0.001;0.002 T 0.10917 -1.0609 10 0.18276 T 0.48 -21.7032 8.8973 0.35472 0.0:0.7682:0.0:0.2318 . 85;78;87 B7Z763;Q01432;A0AUX0 .;AMPD3_HUMAN;. L 78;87;78;78;85;78 ENSP00000432707:F78L;ENSP00000379802:F87L;ENSP00000433284:F78L;ENSP00000379801:F78L;ENSP00000436987:F85L;ENSP00000431648:F78L ENSP00000379801:F78L F + 3 2 AMPD3 10456661 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 1.165000 0.31822 0.690000 0.31570 0.643000 0.83706 TTC TCGA-FB-AAPU-01A-31D-A40W-08 AMPD3-001 PUTATIVE basic|CCDS protein_coding protein_coding OTTHUMT00000385783.2 0 0 0 33 1081 0 271 0 8.915581e-03 1 4 0 271 2 0 0 0 0 0 2 1 1.000000 33 1065 0 269 2 -3.058579 1 1 121410 1 40 1 0 0 0 2.001647 0 0.700000 2 0.700000 0.080000 4.000000e-02 0.120000 0.080000 0.087016 0.080000 0 6.000000e-02 1.000000e-01 KCNC1 3746 broad.mit.edu 37 11 17794037 17794037 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr11:17794037C>A ENST00000379472.3 + 2 1426 c.1396C>A c.(1396-1398)Ctg>Atg p.L466M KCNC1_ENST00000265969.6_Missense_Mutation_p.L466M NM_004976.4 NP_004967.1 P48547 KCNC1_HUMAN potassium voltage-gated channel, Shaw-related subfamily, member 1 33 Dalfampridine(DB06637) GCCACCGCAGCTGGGATCTCC 0.448000 0 SO:0001583 missense ENST00000379472.3 1 1 hg19 CCDS7827.1 . . . . . . . . . . C 11.44 1.639495 0.29157 . . ENSG00000129159 ENST00000265969;ENST00000379472 D;D 0.97279 -4.32;-4.3 5.24 5.24 0.73138 . 0.155348 0.45606 D 0.000355 D 0.96978 0.9013 L 0.39020 1.185 0.49915 D 0.999838 B;D 0.60160 0.116;0.987 B;P 0.61070 0.062;0.883 D 0.96559 0.9414 10 0.35671 T 0.21 . 18.8514 0.92232 0.0:1.0:0.0:0.0 . 466;466 Q3KNS8;P48547 .;KCNC1_HUMAN M 466 ENSP00000265969:L466M;ENSP00000368785:L466M ENSP00000265969:L466M L + 1 2 KCNC1 17750613 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.999000 0.70665 2.445000 0.82738 0.561000 0.74099 CTG TCGA-FB-AAPU-01A-31D-A40W-08 KCNC1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000389389.1 1 0 1 88 173 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1.000000 85 170 0 75 2 -20.000000 1 1 0 0 1 0 0 0 2.001647 0 0.700000 2 0.700000 0.950000 7.900000e-01 1.000000 1.000000 0.946332 0.950000 1 8.700000e-01 1 OR56A3 390083 broad.mit.edu 37 11 5969013 5969013 + Missense_Mutation SNP T T A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr11:5969013T>A ENST00000329564.6 + 1 444 c.437T>A c.(436-438)gTc>gAc p.V146D AC025016.1_ENST00000528915.1_lincRNA NM_001003443.2 NP_001003443.2 Q8NH54 O56A3_HUMAN olfactory receptor, family 56, subfamily A, member 3 41 Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114) CACTTTGTAGTCAAGGCTGCC 0.448000 0 SO:0001583 missense ENST00000329564.6 1 1 hg19 CCDS41614.1 . . . . . . . . . . T 4.194 0.034682 0.08101 . . ENSG00000184478 ENST00000329564 T 0.39406 1.08 5.13 -0.302 0.12796 GPCR, rhodopsin-like superfamily (1); 0.277746 0.18223 U 0.147820 T 0.43809 0.1264 M 0.82056 2.57 0.18873 N 0.999989 B 0.26041 0.14 B 0.34779 0.189 T 0.48927 -0.8991 10 0.72032 D 0.01 -6.0991 5.5314 0.16987 0.1326:0.4555:0.0:0.4119 . 146 Q8NH54 O56A3_HUMAN D 146 ENSP00000331572:V146D ENSP00000331572:V146D V + 2 0 OR56A3 5925589 0.000000 0.05858 0.001000 0.08648 0.001000 0.01503 -4.036000 0.00308 -0.225000 0.09913 -1.200000 0.01667 GTC TCGA-FB-AAPU-01A-31D-A40W-08 OR56A3-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383753.1 1 0 1 147 309 0 139 0 0 0 0 139 2 0 0 0 0 0 2 1 1.000000 146 304 0 137 2 -20.000000 1 1 0 0 1 0 0 0 2.001647 0 0.700000 2 0.700000 0.910000 7.900000e-01 1.000000 1.000000 0.918971 0.910000 1 8.500000e-01 9.800000e-01 UCP3 7352 broad.mit.edu 37 11 73718034 73718034 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr11:73718034C>T ENST00000314032.4 - 2 606 c.54G>A c.(52-54)ctG>ctA p.L18L UCP3_ENST00000348534.4_Silent_p.L18L|UCP3_ENST00000426995.2_Silent_p.L18L NM_003356.3 NP_003347.1 P55916 UCP3_HUMAN uncoupling protein 3 (mitochondrial, proton carrier) 12 Breast(11;2.08e-05) TGCCTGCCCCCAGGAACTTCA 0.597000 0 SO:0001819 synonymous_variant ENST00000314032.4 1 1 hg19 CCDS8229.1 TCGA-FB-AAPU-01A-31D-A40W-08 UCP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398200.1 1 0 1 42 84 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 1.000000 42 83 0 26 2 -20.000000 1 1 0 0 1 0 0 0 1.997612 0 0.700000 2 0.700000 0.940000 7.200000e-01 1.000000 1.000000 0.927447 0.940000 1 8.300000e-01 1 EIF3F 8665 broad.mit.edu 37 11 8014505 8014505 + Missense_Mutation SNP A A C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr11:8014505A>C ENST00000533626.1 + 6 1213 c.587A>C c.(586-588)aAc>aCc p.N196T EIF3F_ENST00000309828.4_Missense_Mutation_p.N196T|EIF3F_ENST00000449102.2_Missense_Mutation_p.N47T|EIF3F_ENST00000537635.1_Missense_Mutation_p.N211T eukaryotic translation initiation factor 3, subunit F 13 GAGGCCCCCAACCCCATCCAC 0.557000 0 SO:0001583 missense ENST00000533626.1 0 1 hg19 CCDS7785.1 . . . . . . . . . . A 24.9 4.586482 0.86851 . . ENSG00000175390 ENST00000533626;ENST00000537635;ENST00000309828;ENST00000538607;ENST00000449102 T;T;T;T 0.47869 1.39;1.39;1.39;0.83 4.97 4.97 0.65823 . 0.042963 0.85682 D 0.000000 T 0.67221 0.2870 M 0.77406 2.37 0.80722 D 1 D 0.56521 0.976 D 0.67725 0.953 T 0.71490 -0.4577 10 0.66056 D 0.02 -18.8904 13.2394 0.59987 1.0:0.0:0.0:0.0 . 196 O00303 EIF3F_HUMAN T 196;211;196;146;47 ENSP00000431800:N196T;ENSP00000442283:N211T;ENSP00000310040:N196T;ENSP00000396929:N47T ENSP00000310040:N196T N + 2 0 EIF3F 7971081 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.162000 0.58177 2.158000 0.67659 0.460000 0.39030 AAC TCGA-FB-AAPU-01A-31D-A40W-08 EIF3F-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000385713.2 0 0 0 9 370 1 83 0 1.390535e-01 19 578 1 83 23 0 0 0 0 0 2 0 0.105819 9 367 1 85 16 -9.057876 1 1 0 0 1 0 0 0 2.001647 0 0.700000 2 0.700000 0.060000 2.000000e-02 0.120000 0.070000 0.074884 0.060000 0 4.000000e-02 1.000000e-01 RAD52 5893 broad.mit.edu 37 12 1023204 1023204 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr12:1023204G>C ENST00000358495.3 - 11 1189 c.1051C>G c.(1051-1053)Cca>Gca p.P351A RAD52_ENST00000535376.1_5'UTR|RAD52_ENST00000430095.2_Missense_Mutation_p.P351A|RAD52_ENST00000539046.1_Missense_Mutation_p.P274A NM_134424.2 NP_602296.2 P43351 RAD52_HUMAN RAD52 homolog (S. cerevisiae) 19 all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987) OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323) GTCTGGGCTGGGTCTGCTCTA 0.527000 Homologous recombination 0 SO:0001583 missense ENST00000358495.3 0 1 hg19 CCDS8507.2 . . . . . . . . . . G 10.75 1.438716 0.25900 . . ENSG00000002016 ENST00000358495;ENST00000430095;ENST00000539046 T;T;T 0.36878 1.65;1.65;1.23 5.11 1.13 0.20643 . 0.341611 0.34245 N 0.004125 T 0.28001 0.0690 L 0.52364 1.645 0.19300 N 0.999976 B 0.09022 0.002 B 0.08055 0.003 T 0.23332 -1.0191 10 0.59425 D 0.04 -14.8336 6.5135 0.22234 0.163:0.2837:0.5532:0.0 . 351 P43351 RAD52_HUMAN A 351;351;274 ENSP00000351284:P351A;ENSP00000387901:P351A;ENSP00000445245:P274A ENSP00000351284:P351A P - 1 0 RAD52 893465 0.000000 0.05858 0.014000 0.15608 0.007000 0.05969 -0.129000 0.10515 0.378000 0.24764 0.561000 0.74099 CCA TCGA-FB-AAPU-01A-31D-A40W-08 RAD52-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206733.2 0 0 0 10 350 0 73 0 1.466164e-01 0 22 0 73 2 0 0 0 0 0 2 1 0.996758 9 346 0 72 2 -2.988197 1 1 0 0 1 1 3 4 2.833998 1 0.700000 2 0.786629 0.120000 5.000000e-02 1.000000 0.120000 0.329215 0.120000 0 8.000000e-02 1 CABP1 9478 broad.mit.edu 37 12 121098645 121098645 + Splice_Site SNP T T C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr12:121098645T>C ENST00000316803.3 + 4 1073 c.e4+2 CABP1_ENST00000453000.1_Splice_Site|CABP1_ENST00000351200.2_Splice_Site|CABP1_ENST00000288616.3_Splice_Site NM_001033677.1 NP_001028849.1 Q9NZU7 CABP1_HUMAN calcium binding protein 1 9 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) TTCCGAGAGGTAACGGACAGA 0.498000 0 SO:0001630 splice_region_variant ENST00000316803.3 1 1 hg19 CCDS31913.1 . . . . . . . . . . T 16.63 3.177845 0.57692 . . ENSG00000157782 ENST00000316803;ENST00000288616;ENST00000351200;ENST00000453000 . . . 5.25 4.11 0.48088 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 7.0835 0.25244 0.1314:0.0726:0.0:0.796 . . . . . -1 . . . + . . CABP1 119583028 0.809000 0.29036 0.875000 0.34327 0.825000 0.46686 0.594000 0.24014 0.850000 0.35239 0.528000 0.53228 . TCGA-FB-AAPU-01A-31D-A40W-08 CABP1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000345822.1 1 0 0 23 297 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 0.999999 23 294 0 101 2 -20.000000 1 1 0 0 1 0 0 0 1.987351 0 0.700000 2 0.697885 0.200000 1.300000e-01 0.290000 0.200000 0.211182 0.200000 0 1.600000e-01 2.500000e-01 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 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-FB-AAPU-01A-31D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 47 89 0 48 1 1 45 31 0 48 2 1 1 90 246 0 642 2 1 1.000000 47 89 0 48 2 -20.000000 1 1 0 0 1 1 2 3 2.011295 0 0.700000 2 0.701046 0.980000 7.600000e-01 1.000000 1.000000 0.950762 0.980000 1 8.700000e-01 1 TULP3 7289 broad.mit.edu 37 12 3042674 3042674 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr12:3042674G>A ENST00000448120.2 + 7 838 c.787G>A c.(787-789)Gaa>Aaa p.E263K TULP3_ENST00000397132.2_Missense_Mutation_p.E263K NM_003324.4 NP_003315.2 O75386 TULP3_HUMAN tubby like protein 3 22 OV - Ovarian serous cystadenocarcinoma(31;0.000818) TCGTGAAGGAGAAAGTTATGT 0.398000 0 SO:0001583 missense ENST00000448120.2 1 1 hg19 CCDS8519.1 . . . . . . . . . . G 21.0 4.082869 0.76642 . . ENSG00000078246 ENST00000228245;ENST00000542730;ENST00000448120;ENST00000397132 D;D 0.85702 -2.02;-2.02 5.3 3.42 0.39159 Tubby, C-terminal (4); 0.254970 0.46442 D 0.000292 D 0.88775 0.6528 M 0.72479 2.2 0.50632 D 0.999881 P;P;D 0.59357 0.755;0.868;0.985 P;P;P 0.59288 0.752;0.854;0.855 D 0.87634 0.2518 10 0.72032 D 0.01 -0.7952 9.1654 0.37048 0.0765:0.0:0.7778:0.1457 . 120;263;263 B7Z1E7;O75386;F8WBZ9 .;TULP3_HUMAN;. K 263;120;263;263 ENSP00000410051:E263K;ENSP00000380321:E263K ENSP00000228245:E263K E + 1 0 TULP3 2912935 1.000000 0.71417 0.878000 0.34440 0.654000 0.38779 7.869000 0.87170 0.573000 0.29400 0.561000 0.74099 GAA TCGA-FB-AAPU-01A-31D-A40W-08 TULP3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000398468.1 1 0 1 51 113 0 44 1 9.996761e-01 15 16 0 44 2 0 0 0 0 0 2 1 1.000000 51 110 0 44 2 -20.000000 1 1 0 0 1 0 0 0 1.997446 0 0.700000 2 0.700000 0.880000 6.900000e-01 1.000000 1.000000 0.884371 0.880000 1 7.800000e-01 9.900000e-01 OXGR1 27199 broad.mit.edu 37 13 97639242 97639242 + Missense_Mutation SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr13:97639242G>T ENST00000298440.1 - 4 1015 c.772C>A c.(772-774)Cat>Aat p.H258N OXGR1_ENST00000543457.1_Missense_Mutation_p.H258N NM_080818.3 NP_543008.3 Q96P68 OXGR1_HUMAN oxoglutarate (alpha-ketoglutarate) receptor 1 15 all_neural(89;0.0982)|Medulloblastoma(90;0.163) BRCA - Breast invasive adenocarcinoma(86;0.186) CTCAAGATATGGAAGGGTAAA 0.438000 0 SO:0001583 missense ENST00000298440.1 0 1 hg19 CCDS9482.1 . . . . . . . . . . G 18.41 3.617808 0.66787 . . ENSG00000165621 ENST00000298440;ENST00000543457 T;T 0.38077 1.16;1.16 5.83 5.83 0.93111 GPCR, rhodopsin-like superfamily (1); 0.000000 0.85682 D 0.000000 T 0.47911 0.1471 L 0.42581 1.335 0.39180 D 0.962769 D 0.89917 1.0 D 0.91635 0.999 T 0.22347 -1.0219 10 0.06757 T 0.87 . 15.3005 0.73945 0.0:0.0:0.8601:0.1399 . 258 Q96P68 OXGR1_HUMAN N 258 ENSP00000298440:H258N;ENSP00000438800:H258N ENSP00000298440:H258N H - 1 0 OXGR1 96437243 1.000000 0.71417 1.000000 0.80357 0.890000 0.51754 6.455000 0.73497 2.937000 0.99478 0.650000 0.86243 CAT TCGA-FB-AAPU-01A-31D-A40W-08 OXGR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045521.3 0 0 0 6 268 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 0.963408 6 263 0 68 2 -3.473646 1 1 0 0 1 1 2 3 2.101185 1 0.700000 2 0.721448 0.070000 2.000000e-02 1.000000 0.070000 0.228548 0.070000 0 4.000000e-02 1 POTEG 404785 broad.mit.edu 37 14 19566012 19566012 + Splice_Site SNP A A C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr14:19566012A>C ENST00000409832.3 + 6 1108 c.1056A>C c.(1054-1056)gtA>gtC p.V352V CTD-2311B13.5_ENST00000548748.1_lincRNA|RNU6-1239P_ENST00000391310.1_RNA NM_001005356.2 NP_001005356.1 Q6S5H5 POTEG_HUMAN POTE ankyrin domain family, member G 47 TTATACATAGAATTTGCCAGT 0.269000 0 SO:0001630 splice_region_variant ENST00000409832.3 0 1 hg19 CCDS32018.1 TCGA-FB-AAPU-01A-31D-A40W-08 POTEG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408579.1 0 0 0 4 313 0 114 0 0 0 0 114 2 0 0 0 0 0 2 0 0.650224 1 158 0 123 2 -5.541767 1 0 119882 5 26 1 0 0 0 1.422466 1 0.700000 2 0.579243 0.020000 0 0.060000 0.030000 0.031733 0.020000 0 1.000000e-02 5.000000e-02 MAP4K5 11183 broad.mit.edu 37 14 50911762 50911762 + Missense_Mutation SNP T T C rs55815015 byFrequency TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr14:50911762T>C ENST00000013125.4 - 18 1654 c.1336A>G c.(1336-1338)Att>Gtt p.I446V NM_006575.4|NM_198794.2 NP_006566.2|NP_942089.1 Q9Y4K4 M4K5_HUMAN mitogen-activated protein kinase kinase kinase kinase 5 15 all_epithelial(31;0.000415)|Breast(41;0.0102) GCCATACCAATAGAAGAAGTC 0.413000 0 SO:0001583 missense ENST00000013125.4 1 1 hg19 7 0.003205128205128205 0 0.0 0 0.0 7 0.012237762237762238 0 0.0 T 8.406 0.843090 0.16963 . . ENSG00000012983 ENST00000013125 T 0.13657 2.57 5.38 -0.756 0.11057 Protein kinase-like domain (1); 0.528155 0.20244 N 0.096221 T 0.03095 0.0091 N 0.08118 0 0.36535 D 0.870936 B;B;B 0.12013 0.005;0.005;0.005 B;B;B 0.09377 0.004;0.004;0.004 T 0.41305 -0.9516 10 0.15952 T 0.53 . 4.6228 0.12463 0.1045:0.0688:0.2378:0.5889 rs55815015 120;446;446 B3KWC4;B2R928;Q9Y4K4 .;.;M4K5_HUMAN V 446 ENSP00000013125:I446V ENSP00000013125:I446V I - 1 0 MAP4K5 49981512 0.750000 0.28316 0.991000 0.47740 0.887000 0.51463 -0.221000 0.09202 -0.008000 0.14320 -0.323000 0.08544 ATT TCGA-FB-AAPU-01A-31D-A40W-08 MAP4K5-001 KNOWN non_canonical_conserved|basic|appris_principal protein_coding protein_coding OTTHUMT00000410880.1 1 0 0 11 126 0 44 1 8.612261e-01 7 36 0 44 2 0 0 0 0 0 2 1 0.998366 11 123 0 44 2 -6.780243 1 1 0 0 1 0 0 0 1.985127 0 0.700000 2 0.697885 0.230000 1.200000e-01 0.380000 0.230000 0.244166 0.230000 0 1.700000e-01 3.100000e-01 BDKRB2 624 broad.mit.edu 37 14 96703485 96703485 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr14:96703485G>A ENST00000306005.3 + 2 237 c.41G>A c.(40-42)cGt>cAt p.R14H BDKRB2_ENST00000539359.1_5'UTR|BDKRB2_ENST00000542454.2_5'UTR|RP11-404P21.8_ENST00000553811.1_Missense_Mutation_p.R14H|BDKRB2_ENST00000554311.1_Missense_Mutation_p.R14H NM_000623.3 NP_000614.1 P30411 BKRB2_HUMAN bradykinin receptor B2 24 all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179) Icatibant(DB06196) CTGTCTGTTCGTGAGGACTCC 0.527000 0 SO:0001583 missense ENST00000306005.3 1 1 hg19 CCDS9942.1 . . . . . . . . . . G 13.47 2.247970 0.39697 . . ENSG00000168398;ENSG00000168398;ENSG00000258691 ENST00000554311;ENST00000306005;ENST00000553811 T;T;T 0.71934 -0.61;-0.61;1.71 3.71 -2.22 0.06952 . 2.399830 0.01945 N 0.042183 T 0.41050 0.1142 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.41787 -0.9489 10 0.05351 T 0.99 . 0.5426 0.00648 0.3331:0.1884:0.2948:0.1837 . 14 P30411 BKRB2_HUMAN H 14 ENSP00000450482:R14H;ENSP00000307713:R14H;ENSP00000450984:R14H ENSP00000307713:R14H R + 2 0 RP11-404P21.8;BDKRB2 95773238 0.019000 0.18553 0.000000 0.03702 0.002000 0.02628 -0.001000 0.12947 -0.415000 0.07484 -1.880000 0.00545 CGT TCGA-FB-AAPU-01A-31D-A40W-08 BDKRB2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413294.1 0 0 0 7 210 1 80 0 6.409125e-02 1 23 1 80 3 0 0 0 0 0 2 0 0.229490 7 209 1 80 11 -3.120890 1 1 121412 1 40 1 0 1 1 1.365525 1 0.700000 2 0.540933 0.060000 2.000000e-02 0.120000 0.060000 0.067943 0.060000 0 3.000000e-02 9.000000e-02 CPEB1 64506 broad.mit.edu 37 15 83215935 83215935 + Missense_Mutation SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr15:83215935G>T ENST00000562019.1 - 10 1783 c.1467C>A c.(1465-1467)agC>agA p.S489R RP11-152F13.10_ENST00000562833.1_Missense_Mutation_p.A219E|CPEB1_ENST00000563800.1_Missense_Mutation_p.S511R|RP11-379H8.1_ENST00000568285.1_Intron|CPEB1_ENST00000564522.1_Missense_Mutation_p.S409R|CPEB1_ENST00000398591.2_Missense_Mutation_p.S414R|CPEB1_ENST00000568128.1_Missense_Mutation_p.S484R|CPEB1_ENST00000568757.1_Missense_Mutation_p.S409R|CPEB1_ENST00000261723.6_Missense_Mutation_p.S487R|CPEB1_ENST00000398592.2_Missense_Mutation_p.S258R|CPEB1_ENST00000450751.2_Missense_Mutation_p.S409R|CPEB1_ENST00000423133.2_Missense_Mutation_p.S409R Q9BZB8 CPEB1_HUMAN cytoplasmic polyadenylation element binding protein 1 28 BRCA - Breast invasive adenocarcinoma(143;0.229) CAAAAGCAGCGCTGACTGCTT 0.463000 0 SO:0001583 missense ENST00000562019.1 1 1 hg19 . . . . . . . . . . g 14.03 2.412804 0.42817 . . ENSG00000214575 ENST00000450751;ENST00000398593;ENST00000423133;ENST00000398591;ENST00000261723;ENST00000398592 T;T;T;T 0.22539 1.95;1.95;1.95;1.95 5.18 -2.21 0.06973 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1); 0.284954 0.37348 U 0.002129 T 0.10723 0.0262 N 0.14661 0.345 0.44736 D 0.997731 B;B;B;B 0.25351 0.124;0.024;0.021;0.024 B;B;B;B 0.20184 0.015;0.01;0.028;0.01 T 0.08493 -1.0719 10 0.54805 T 0.06 -7.0429 11.4101 0.49921 0.5705:0.0:0.4295:0.0 . 487;484;489;484 B7Z237;Q9BZB8-3;Q9BZB8;E7ET70 .;.;CPEB1_HUMAN;. R 484;484;409;414;487;258 ENSP00000397526:S409R;ENSP00000381591:S414R;ENSP00000261723:S487R;ENSP00000381592:S258R ENSP00000261723:S487R S - 3 2 CPEB1 81012990 0.145000 0.22656 0.984000 0.44739 0.985000 0.73830 -0.371000 0.07513 -0.518000 0.06452 -0.423000 0.05987 AGC TCGA-FB-AAPU-01A-31D-A40W-08 CPEB1-006 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000421102.1 1 0 0 207 169 0 83 0 3.002625e-01 0 2 0 83 2 0 0 0 0 0 2 1 1.000000 205 168 0 83 2 -20.000000 1 1 0 0 1 1 3 4 3.164811 1 0.700000 2 0.813549 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CDH8 1006 broad.mit.edu 37 16 62055298 62055298 + Missense_Mutation SNP G G A rs139797882 TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr16:62055298G>A ENST00000577390.1 - 2 964 c.10C>T c.(10-12)Cgg>Tgg p.R4W CDH8_ENST00000577730.1_Missense_Mutation_p.R4W|CDH8_ENST00000299345.6_Missense_Mutation_p.R4W|CDH8_ENST00000584337.1_Missense_Mutation_p.R4W NM_001796.4 NP_001787.2 P55286 CADH8_HUMAN cadherin 8, type 2 112 Ovarian(137;0.0799)|Melanoma(118;0.16) TCCGCTAGCCGTTCTGGCATG 0.443000 0 SO:0001583 missense ENST00000577390.1 1 1 hg19 CCDS10802.1 . . . . . . . . . . G 19.94 3.920100 0.73098 . . ENSG00000150394 ENST00000299345 T 0.59083 0.29 6.17 5.2 0.72013 . 0.068663 0.64402 D 0.000020 T 0.69360 0.3102 L 0.47716 1.5 0.39308 D 0.965029 D 0.89917 1.0 D 0.77557 0.99 T 0.73792 -0.3871 10 0.87932 D 0 . 13.5257 0.61593 0.0:0.0:0.5605:0.4395 . 4 P55286 CADH8_HUMAN W 4 ENSP00000299345:R4W ENSP00000299345:R4W R - 1 2 CDH8 60612799 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 2.750000 0.47500 1.564000 0.49628 0.655000 0.94253 CGG TCGA-FB-AAPU-01A-31D-A40W-08 CDH8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268754.3 1 0 1 35 290 0 103 0 0 0 0 103 2 0 0 0 0 0 2 1 1.000000 33 285 0 102 2 -3.318796 1 1 0 0 1 0 0 0 2.004961 0 0.700000 2 0.700000 0.300000 2.100000e-01 0.410000 0.300000 0.314121 0.300000 0 2.500000e-01 3.600000e-01 MEOX1 4222 broad.mit.edu 37 17 41738449 41738449 + Missense_Mutation SNP T T C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:41738449T>C ENST00000318579.4 - 1 873 c.454A>G c.(454-456)Aga>Gga p.R152G MEOX1_ENST00000329168.3_Missense_Mutation_p.R152G|MEOX1_ENST00000549132.1_Silent_p.G122G|MEOX1_ENST00000393661.2_Missense_Mutation_p.R37G NM_001040002.1|NM_004527.3 NP_001035091.1|NP_004518.1 P50221 MEOX1_HUMAN mesenchyme homeobox 1 8 Breast(137;0.00908) CTCTCCTTTCTCCGCCTGGAT 0.572000 0 SO:0001583 missense ENST00000318579.4 1 1 hg19 CCDS11466.1 . . . . . . . . . . T 15.52 2.857712 0.51376 . . ENSG00000005102 ENST00000318579;ENST00000329168;ENST00000393661 D;T;D 0.91180 -2.8;0.64;-2.78 4.99 4.99 0.66335 . 0.048523 0.85682 D 0.000000 T 0.82135 0.4971 N 0.14661 0.345 0.37695 D 0.923982 B;B 0.29835 0.152;0.258 B;B 0.26969 0.023;0.075 T 0.83253 -0.0052 10 0.48119 T 0.1 -25.6858 13.4121 0.60948 0.0:0.0:0.0:1.0 . 152;152 Q15069;P50221 .;MEOX1_HUMAN G 152;152;37 ENSP00000321684:R152G;ENSP00000328678:R152G;ENSP00000377271:R37G ENSP00000321684:R152G R - 1 2 MEOX1 39093975 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 6.734000 0.74801 2.092000 0.63282 0.533000 0.62120 AGA TCGA-FB-AAPU-01A-31D-A40W-08 MEOX1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409452.1 0 0 0 19 790 0 178 0 3.690088e-03 0 4 0 178 2 0 0 0 0 0 2 1 0.999989 19 781 0 174 2 -14.375500 1 1 0 0 1 0 0 0 1.996979 0 0.700000 2 0.700000 0.060000 3.000000e-02 0.100000 0.060000 0.070436 0.060000 0 4.000000e-02 9.000000e-02 B4GALNT2 124872 broad.mit.edu 37 17 47230177 47230177 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:47230177C>T ENST00000300404.2 + 4 608 c.549C>T c.(547-549)cgC>cgT p.R183R B4GALNT2_ENST00000393354.2_Silent_p.R123R|B4GALNT2_ENST00000504681.1_Silent_p.R97R NM_153446.2 NP_703147.2 Q8NHY0 B4GN2_HUMAN beta-1,4-N-acetyl-galactosaminyl transferase 2 24 all cancers(6;0.000316) GGCTGCCCCGCCCACTGCCCC 0.617000 GBM(124;244 1635 8663 18097 33175) 0 SO:0001819 synonymous_variant ENST00000300404.2 1 1 hg19 CCDS11544.1 TCGA-FB-AAPU-01A-31D-A40W-08 B4GALNT2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000364477.1 1 0 1 13 27 0 20 0 0 0 0 20 2 0 0 0 0 0 2 1 0.999740 13 25 0 20 2 -20.000000 1 1 0 0 1 0 0 0 1.996979 0 0.700000 2 0.700000 0.920000 5.600000e-01 1.000000 1.000000 0.885801 0.920000 1 7.300000e-01 1 HELZ 9931 broad.mit.edu 37 17 65163782 65163782 + Missense_Mutation SNP T T A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:65163782T>A ENST00000358691.5 - 14 1727 c.1561A>T c.(1561-1563)Act>Tct p.T521S HELZ_ENST00000580168.1_Missense_Mutation_p.T521S NM_014877.3 NP_055692 P42694 HELZ_HUMAN helicase with zinc finger 69 all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13) CCAGCCAAAGTATCTTCAGAA 0.433000 0 SO:0001583 missense ENST00000358691.5 1 1 hg19 CCDS42374.1 . . . . . . . . . . T 15.61 2.885504 0.51908 . . ENSG00000198265 ENST00000358691 D 0.85484 -1.99 5.4 5.4 0.78164 . 0.000000 0.85682 D 0.000000 D 0.89955 0.6865 L 0.56280 1.765 0.80722 D 1 D;P 0.76494 0.999;0.922 D;P 0.68192 0.956;0.655 D 0.90316 0.4341 10 0.52906 T 0.07 -16.6549 15.4547 0.75302 0.0:0.0:0.0:1.0 . 521;521 B7ZLW2;P42694 .;HELZ_HUMAN S 521 ENSP00000351524:T521S ENSP00000351524:T521S T - 1 0 HELZ 62594244 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.662000 0.68032 2.045000 0.60652 0.460000 0.39030 ACT TCGA-FB-AAPU-01A-31D-A40W-08 HELZ-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000447068.1 0 0 0 11 379 0 99 0 1.370005e-01 1 20 0 99 2 0 0 0 0 0 2 1 0.998292 11 375 0 99 2 -11.152460 1 1 0 0 1 1 2 3 2.677864 1 0.700000 2 0.777778 0.110000 4.000000e-02 0.190000 0.120000 0.117974 0.110000 0 7.000000e-02 1.500000e-01 WIPI1 55062 broad.mit.edu 37 17 66430712 66430712 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:66430712C>A ENST00000262139.5 - 7 676 c.677G>T c.(676-678)cGg>cTg p.R226L WIPI1_ENST00000546360.1_Missense_Mutation_p.R144L|WIPI1_ENST00000589459.1_5'UTR NM_017983.5 NP_060453.3 Q5MNZ9 WIPI1_HUMAN WD repeat domain, phosphoinositide interacting 1 18 CATCCCTCTCCGGAACTCATA 0.512000 0 SO:0001583 missense ENST00000262139.5 1 1 hg19 CCDS11677.1 . . . . . . . . . . C 22.7 4.322237 0.81580 . . ENSG00000070540 ENST00000262139;ENST00000546360 T;T 0.52057 0.68;2.32 5.32 5.32 0.75619 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.116368 0.56097 D 0.000025 T 0.65565 0.2703 H 0.95043 3.615 0.80722 D 1 P 0.35328 0.495 B 0.35931 0.214 T 0.75673 -0.3236 10 0.72032 D 0.01 -15.4145 19.0599 0.93085 0.0:1.0:0.0:0.0 . 226 Q5MNZ9 WIPI1_HUMAN L 226;144 ENSP00000262139:R226L;ENSP00000437345:R144L ENSP00000262139:R226L R - 2 0 WIPI1 63942307 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.326000 0.79133 2.505000 0.84491 0.485000 0.47835 CGG TCGA-FB-AAPU-01A-31D-A40W-08 WIPI1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448739.1 1 0 1 57 182 0 39 1 1 22 70 0 39 2 0 0 0 0 0 2 1 1.000000 57 180 0 39 2 -3.828835 1 1 0 0 1 1 2 3 2.677864 1 0.700000 2 0.777778 0.910000 7.200000e-01 1.000000 1.000000 0.910945 0.910000 1 8.100000e-01 1 WIPI1 55062 broad.mit.edu 37 17 66430734 66430734 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:66430734C>A ENST00000262139.5 - 7 654 c.655G>T c.(655-657)Ggg>Tgg p.G219W WIPI1_ENST00000546360.1_Missense_Mutation_p.G137W|WIPI1_ENST00000589459.1_5'UTR NM_017983.5 NP_060453.3 Q5MNZ9 WIPI1_HUMAN WD repeat domain, phosphoinositide interacting 1 18 AGCTTTTGCCCATCAGGGACA 0.498000 0 SO:0001583 missense ENST00000262139.5 1 1 hg19 CCDS11677.1 . . . . . . . . . . C 24.7 4.559525 0.86335 . . ENSG00000070540 ENST00000262139;ENST00000546360 T;T 0.57595 0.39;2.03 5.32 5.32 0.75619 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.105797 0.64402 D 0.000004 T 0.80788 0.4690 M 0.93720 3.45 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 D 0.85997 0.1492 10 0.87932 D 0 -22.2488 19.0599 0.93085 0.0:1.0:0.0:0.0 . 219 Q5MNZ9 WIPI1_HUMAN W 219;137 ENSP00000262139:G219W;ENSP00000437345:G137W ENSP00000262139:G219W G - 1 0 WIPI1 63942329 1.000000 0.71417 0.936000 0.37596 0.891000 0.51852 7.326000 0.79133 2.505000 0.84491 0.485000 0.47835 GGG TCGA-FB-AAPU-01A-31D-A40W-08 WIPI1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448739.1 1 0 1 51 174 0 35 1 9.999994e-01 24 54 0 35 2 0 0 0 0 0 2 1 1.000000 51 173 0 35 2 -3.496361 1 0 0 0 1 1 2 3 2.677864 1 0.700000 2 0.777778 0.870000 6.700000e-01 1.000000 1.000000 0.874206 0.870000 1 7.600000e-01 9.900000e-01 KIAA0195 9772 broad.mit.edu 37 17 73488859 73488859 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr17:73488859C>T ENST00000314256.7 + 15 2295 c.1901C>T c.(1900-1902)gCc>gTc p.A634V KIAA0195_ENST00000579208.1_Missense_Mutation_p.A285V|KIAA0195_ENST00000375248.5_Missense_Mutation_p.A644V NM_014738.4 NP_055553.3 Q12767 K0195_HUMAN KIAA0195 42 all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246) all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154) TGCGAGCTTGCCCGCCTCATT 0.647000 0 SO:0001583 missense ENST00000314256.7 0 1 hg19 CCDS32732.1 . . . . . . . . . . C 16.32 3.088956 0.55968 . . ENSG00000177728 ENST00000314256;ENST00000375248 D;D 0.87650 -2.28;-2.28 5.77 5.77 0.91146 . 0.053643 0.85682 D 0.000000 D 0.86251 0.5888 L 0.54323 1.7 0.80722 D 1 B;B;B 0.34329 0.079;0.449;0.321 B;B;B 0.33960 0.043;0.173;0.084 D 0.85706 0.1316 10 0.62326 D 0.03 -29.8003 19.9787 0.97318 0.0:1.0:0.0:0.0 . 644;644;634 B4DGC6;C9JL75;Q12767 .;.;K0195_HUMAN V 634;644 ENSP00000313885:A634V;ENSP00000364397:A644V ENSP00000313885:A634V A + 2 0 KIAA0195 71000454 1.000000 0.71417 1.000000 0.80357 0.637000 0.38172 5.785000 0.68998 2.733000 0.93635 0.561000 0.74099 GCC TCGA-FB-AAPU-01A-31D-A40W-08 KIAA0195-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447303.1 0 0 0 5 435 0 69 0 2.092269e-01 0 62 0 69 2 0 0 0 0 0 2 1 0.935599 5 429 0 68 2 -2.686105 1 1 0 0 1 1 2 3 2.677864 1 0.700000 2 0.777778 0.040000 0 0.100000 0.050000 0.051290 0.040000 0 2.000000e-02 7.000000e-02 RNF125 54941 broad.mit.edu 37 18 29622203 29622203 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr18:29622203G>C ENST00000217740.3 + 3 872 c.380G>C c.(379-381)gGa>gCa p.G127A RNF125_ENST00000583384.1_3'UTR|RP11-53I6.2_ENST00000583184.1_RNA NM_017831.3 NP_060301.2 Q96EQ8 RN125_HUMAN ring finger protein 125, E3 ubiquitin protein ligase 6 GATAAGTATGGACCACTACAA 0.328000 0 SO:0001583 missense ENST00000217740.3 0 1 hg19 CCDS11902.1 . . . . . . . . . . G 14.94 2.686264 0.47991 . . ENSG00000101695 ENST00000217740 D 0.82255 -1.59 5.55 5.55 0.83447 . 0.000000 0.56097 D 0.000024 D 0.88040 0.6330 L 0.54323 1.7 0.50813 D 0.999893 D 0.76494 0.999 D 0.83275 0.996 T 0.83353 -0.0002 10 0.13853 T 0.58 0.442 16.7717 0.85539 0.0:0.0:1.0:0.0 . 127 Q96EQ8 RN125_HUMAN A 127 ENSP00000217740:G127A ENSP00000217740:G127A G + 2 0 RNF125 27876201 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 5.059000 0.64306 2.767000 0.95098 0.563000 0.77884 GGA TCGA-FB-AAPU-01A-31D-A40W-08 RNF125-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255354.1 0 0 0 4 88 0 40 0 0 0 1 0 40 2 0 0 0 0 0 2 1 0.881200 4 84 0 40 2 -7.348601 1 1 0 0 1 0 1 1 1.369046 1 0.700000 2 0.538462 0.080000 2.000000e-02 0.190000 0.080000 0.097865 0.080000 0 5.000000e-02 1.400000e-01 CARM1 10498 broad.mit.edu 37 19 11022882 11022882 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr19:11022882G>A ENST00000327064.4 + 5 771 c.581G>A c.(580-582)gGc>gAc p.G194D CARM1_ENST00000344150.4_Missense_Mutation_p.G194D NM_199141.1 NP_954592.1 Q86X55 CARM1_HUMAN coactivator-associated arginine methyltransferase 1 13 GTTGGCTGTGGCTCTGGGATC 0.592000 0 SO:0001583 missense ENST00000327064.4 1 1 hg19 CCDS12250.1 . . . . . . . . . . G 29.2 4.987583 0.93106 . . ENSG00000142453 ENST00000327064;ENST00000344150 T;T 0.77620 -1.11;-1.11 5.67 4.64 0.57946 . 0.058076 0.64402 N 0.000002 D 0.93354 0.7881 H 0.99770 4.765 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.95477 0.8557 10 0.87932 D 0 -4.2354 13.3148 0.60401 0.077:0.0:0.923:0.0 . 194 Q86X55 CARM1_HUMAN D 194 ENSP00000325690:G194D;ENSP00000340934:G194D ENSP00000325690:G194D G + 2 0 CARM1 10883882 1.000000 0.71417 1.000000 0.80357 0.955000 0.61496 9.233000 0.95337 1.403000 0.46800 0.655000 0.94253 GGC TCGA-FB-AAPU-01A-31D-A40W-08 CARM1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000452625.1 0 0 0 29 1232 0 314 1 8.384789e-01 3 139 0 314 2 0 0 0 0 0 2 1 1.000000 29 1206 0 310 2 -2.655911 1 1 0 0 1 0 0 0 1.983682 0 0.700000 2 0.697885 0.060000 3.000000e-02 0.090000 0.060000 0.067300 0.060000 0 4.000000e-02 8.000000e-02 AKAP8 10270 broad.mit.edu 37 19 15483674 15483674 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr19:15483674C>T ENST00000269701.2 - 5 909 c.849G>A c.(847-849)cgG>cgA p.R283R NM_005858.3 NP_005849.1 O43823 AKAP8_HUMAN A kinase (PRKA) anchor protein 8 26 GATCCCGATCCCGCATCCGAG 0.592000 GBM(190;1671 2163 3274 27186 30476) 0 SO:0001819 synonymous_variant ENST00000269701.2 1 1 hg19 CCDS12329.1 TCGA-FB-AAPU-01A-31D-A40W-08 AKAP8-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461293.3 1 0 1 27 92 0 23 1 9.998683e-01 20 33 0 23 2 0 0 0 0 0 2 1 1.000000 26 89 0 23 2 -20.000000 1 1 0 0 1 0 0 0 1.983682 0 0.700000 2 0.697885 0.640000 4.400000e-01 0.860000 0.640000 0.654099 0.640000 0 5.400000e-01 7.600000e-01 UPK1A 11045 broad.mit.edu 37 19 36168781 36168781 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr19:36168781C>G ENST00000222275.2 + 6 716 c.716C>G c.(715-717)gCc>gGc p.A239G UPK1A_ENST00000379013.2_Missense_Mutation_p.P272A NM_007000.2 NP_008931.1 O00322 UPK1A_HUMAN uroplakin 1A 9 all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) TTTGGGTTTGCCATCCTGATG 0.657000 0 SO:0001583 missense ENST00000222275.2 0 1 hg19 CCDS12470.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 18.45|18.45 3.625613|3.625613 0.66901|0.66901 .|. .|. ENSG00000105668|ENSG00000105668 ENST00000222275|ENST00000379013 T|T 0.77750|0.07216 -1.12|3.21 5.61|5.61 5.61|5.61 0.85477|0.85477 .|. .|. .|. .|. .|. T|T 0.09423|0.09423 0.0232|0.0232 L|L 0.48642|0.48642 1.525|1.525 0.39783|0.39783 D|D 0.97232|0.97232 P|P 0.35328|0.37330 0.495|0.59 B|B 0.39339|0.30572 0.297|0.117 T|T 0.04607|0.04607 -1.0939|-1.0939 9|9 0.06236|0.87932 T|D 0.91|0 -5.748|-5.748 15.1232|15.1232 0.72460|0.72460 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 239|272 O00322|O00322-2 UPK1A_HUMAN|. G|A 239|272 ENSP00000222275:A239G|ENSP00000368298:P272A ENSP00000222275:A239G|ENSP00000368298:P272A A|P +|+ 2|1 0|0 UPK1A|UPK1A 40860621|40860621 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.967000|0.967000 0.64934|0.64934 5.013000|5.013000 0.64023|0.64023 2.643000|2.643000 0.89663|0.89663 0.462000|0.462000 0.41574|0.41574 GCC|CCA TCGA-FB-AAPU-01A-31D-A40W-08 UPK1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109486.3 0 0 0 5 103 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.932708 5 99 0 30 2 -3.272686 1 1 0 0 1 0 0 0 1.983682 0 0.700000 2 0.697885 0.140000 5.000000e-02 0.280000 0.130000 0.154139 0.140000 0 8.000000e-02 2.100000e-01 SIPA1L3 23094 broad.mit.edu 37 19 38590667 38590667 + Silent SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr19:38590667G>T ENST00000222345.6 + 5 2240 c.1731G>T c.(1729-1731)ggG>ggT p.G577G NM_015073.1 NP_055888.1 O60292 SI1L3_HUMAN signal-induced proliferation-associated 1 like 3 59 Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292) ATGGGACCGGGCGGGGCCTGC 0.632000 0 SO:0001819 synonymous_variant ENST00000222345.6 1 1 hg19 CCDS33007.1 TCGA-FB-AAPU-01A-31D-A40W-08 SIPA1L3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000156294.2 0 0 1 87 179 0 68 1 9.999996e-01 28 21 0 68 2 0 0 0 0 0 2 1 1.000000 88 176 0 68 2 -20.000000 1 1 0 0 1 0 0 0 1.983682 0 0.700000 2 0.697885 0.920000 7.600000e-01 1.000000 1.000000 0.920984 0.920000 1 8.400000e-01 1 ZNF600 162966 broad.mit.edu 37 19 53270312 53270312 + Missense_Mutation SNP G G T rs150744538 TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr19:53270312G>T ENST00000338230.3 - 3 964 c.697C>A c.(697-699)Ctt>Att p.L233I NM_198457.2 NP_940859 Q6ZNG1 ZN600_HUMAN zinc finger protein 600 30 TGGCATGTAAGGGATGATACC 0.408000 Esophageal Squamous(196;1235 2112 2375 33339 34207) 0 SO:0001583 missense ENST00000338230.3 1 1 hg19 CCDS12856.1 . . . . . . . . . . . 16.90 3.250086 0.59212 . . ENSG00000189190 ENST00000338230 T 0.10860 2.83 1.62 1.62 0.23740 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.37019 0.0988 M 0.89715 3.055 0.09310 N 1 D 0.69078 0.997 D 0.85130 0.997 T 0.08066 -1.0740 9 0.87932 D 0 . 10.1661 0.42882 0.0:0.0:1.0:0.0 . 233 Q6ZNG1 ZN600_HUMAN I 233 ENSP00000344791:L233I ENSP00000344791:L233I L - 1 0 ZNF600 57962124 0.152000 0.22762 0.093000 0.20910 0.519000 0.34347 2.239000 0.43079 0.888000 0.36160 0.313000 0.20887 CTT TCGA-FB-AAPU-01A-31D-A40W-08 ZNF600-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463093.1 1 0 0 36 525 0 208 0 4.704596e-01 1 23 0 208 2 0 0 0 0 0 2 1 1.000000 35 518 0 205 2 -2.619816 1 1 0 0 1 1 2 3 2.023319 0 0.700000 2 0.701046 0.180000 1.200000e-01 0.250000 0.180000 0.188282 0.180000 0 1.500000e-01 2.200000e-01 DCST2 127579 broad.mit.edu 37 1 154998864 154998864 + Missense_Mutation SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:154998864G>T ENST00000368424.3 - 10 1583 c.1525C>A c.(1525-1527)Cta>Ata p.L509I DCST2_ENST00000295536.5_Missense_Mutation_p.L509I NM_144622.2 NP_653223.2 Q5T1A1 DCST2_HUMAN DC-STAMP domain containing 2 38 all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) BRCA - Breast invasive adenocarcinoma(34;0.00034) AAGAAGCATAGGCCATACATG 0.637000 0 SO:0001583 missense ENST00000368424.3 1 1 hg19 CCDS1082.2 . . . . . . . . . . G 14.24 2.477203 0.44044 . . ENSG00000163354 ENST00000368424;ENST00000295536 T;T 0.34667 1.35;1.35 4.75 4.75 0.60458 Dendritic cell-specific transmembrane protein-like (1); 0.218950 0.30392 N 0.009722 T 0.25082 0.0609 M 0.78637 2.42 0.28184 N 0.92805 P 0.47604 0.898 B 0.42138 0.377 T 0.12993 -1.0526 10 0.36615 T 0.2 -8.1492 10.3498 0.43927 0.0:0.0:0.8042:0.1958 . 509 Q5T1A1 DCST2_HUMAN I 509 ENSP00000357409:L509I;ENSP00000295536:L509I ENSP00000295536:L509I L - 1 2 DCST2 153265488 0.483000 0.25956 0.991000 0.47740 0.961000 0.63080 0.167000 0.16602 2.466000 0.83321 0.655000 0.94253 CTA TCGA-FB-AAPU-01A-31D-A40W-08 DCST2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090953.3 1 0 1 98 344 0 80 1 6.852107e-01 4 6 0 80 2 0 0 0 0 1 2 1 1.000000 98 342 0 80 2 -20.000000 1 1 0 0 1 2 2 4 3.240808 1 0.700000 2 0.815157 0.990000 8.500000e-01 1.000000 1.000000 0.979592 0.990000 1 9.400000e-01 1 CCDC19 0 broad.mit.edu 37 1 159850480 159850480 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:159850480C>T ENST00000368099.4 - 8 972 c.908G>A c.(907-909)cGa>cAa p.R303Q CCDC19_ENST00000426543.2_Missense_Mutation_p.R218Q|CCDC19_ENST00000476696.1_5'UTR NM_012337.2 NP_036469.2 26 all_hematologic(112;0.0597) BRCA - Breast invasive adenocarcinoma(70;0.151) TTGCTGCCTTCGTTCCATGTC 0.478000 0 SO:0001583 missense ENST00000368099.4 0 1 hg19 CCDS30914.1 . . . . . . . . . . C 1.086 -0.665561 0.03428 . . ENSG00000213085 ENST00000368099;ENST00000426543 T;T 0.10099 2.91;2.91 4.94 -0.338 0.12651 . 0.596147 0.17329 N 0.178193 T 0.01730 0.0055 N 0.16567 0.415 0.21915 N 0.999471 B;B 0.11235 0.004;0.004 B;B 0.10450 0.005;0.005 T 0.45629 -0.9248 9 . . . -0.0898 11.3354 0.49500 0.0:0.6301:0.0:0.3699 . 303;303 A8K884;Q9UL16 .;CCD19_HUMAN Q 303;218 ENSP00000357079:R303Q;ENSP00000403044:R218Q . R - 2 0 CCDC19 158117104 0.000000 0.05858 0.194000 0.23346 0.168000 0.22595 -0.761000 0.04751 -0.337000 0.08426 -1.786000 0.00637 CGA TCGA-FB-AAPU-01A-31D-A40W-08 CCDC19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085979.1 0 0 0 5 306 0 63 0 1.367304e-02 0 9 0 63 2 0 0 0 0 0 2 1 0.934788 5 300 0 63 2 -3.091975 1 1 121412 1 27 1 2 2 4 3.264818 1 0.700000 2 0.815951 0.080000 1.000000e-02 1.000000 0.080000 0.162526 0.080000 0 4.000000e-02 1.400000e-01 ADCY10 55811 broad.mit.edu 37 1 167830232 167830232 + Silent SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:167830232G>T ENST00000367851.4 - 15 1870 c.1686C>A c.(1684-1686)gcC>gcA p.A562A ADCY10_ENST00000367848.1_Silent_p.A470A|ADCY10_ENST00000545172.1_Silent_p.A409A NM_018417.4 NP_060887.2 Q96PN6 ADCYA_HUMAN adenylate cyclase 10 (soluble) 63 CTAGGACATTGGCCATGAACA 0.373000 0 SO:0001819 synonymous_variant ENST00000367851.4 1 1 hg19 CCDS1265.1 TCGA-FB-AAPU-01A-31D-A40W-08 ADCY10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083663.1 0 0 0 9 425 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 0.993951 10 418 0 77 2 -3.044378 1 1 0 0 1 2 2 4 3.264818 1 0.700000 2 0.815951 0.100000 4.000000e-02 1.000000 0.110000 0.179126 0.100000 0 6.000000e-02 1.600000e-01 PAPPA2 60676 broad.mit.edu 37 1 176564265 176564265 + Silent SNP T T C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:176564265T>C ENST00000367662.3 + 3 2689 c.1525T>C c.(1525-1527)Ttg>Ctg p.L509L PAPPA2_ENST00000367661.3_Silent_p.L509L NM_020318.2 NP_064714.2 Q9BXP8 PAPP2_HUMAN pappalysin 2 226 CAATGTGGAATTGATCTCCCA 0.537000 0 SO:0001819 synonymous_variant ENST00000367662.3 1 1 hg19 CCDS41438.1 TCGA-FB-AAPU-01A-31D-A40W-08 PAPPA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084763.1 0 0 1 67 236 1 50 0 0 0 1 50 2 0 0 0 0 0 2 1 1.000000 67 234 1 50 19 -20.000000 1 1 0 0 1 2 2 4 3.310555 1 0.700000 2 0.819059 0.990000 8.300000e-01 1.000000 1.000000 0.978593 0.990000 1 9.400000e-01 1 PAPPA2 60676 broad.mit.edu 37 1 176659486 176659486 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:176659486G>A ENST00000367662.3 + 5 3515 c.2351G>A c.(2350-2352)cGg>cAg p.R784Q PAPPA2_ENST00000367661.3_Missense_Mutation_p.R784Q NM_020318.2 NP_064714.2 Q9BXP8 PAPP2_HUMAN pappalysin 2 226 GAGCTGTGCCGGGAACCAGAG 0.577000 0 SO:0001583 missense ENST00000367662.3 1 1 hg19 CCDS41438.1 . . . . . . . . . . G 2.709 -0.269311 0.05716 . . ENSG00000116183 ENST00000367662;ENST00000367661 T;T 0.29917 4.8;1.55 5.51 -1.73 0.08081 Peptidase M43, pregnancy-associated plasma-A (1); 0.652550 0.16106 N 0.229335 T 0.17704 0.0425 N 0.25647 0.755 0.30128 N 0.805098 B;B 0.24483 0.104;0.024 B;B 0.21917 0.037;0.012 T 0.34750 -0.9816 10 0.09843 T 0.71 -0.187 13.3144 0.60399 0.3731:0.0:0.6269:0.0 . 784;784 Q9BXP8;A9Z1Y8 PAPP2_HUMAN;. Q 784 ENSP00000356634:R784Q;ENSP00000356633:R784Q ENSP00000356633:R784Q R + 2 0 PAPPA2 174926109 1.000000 0.71417 0.863000 0.33907 0.014000 0.08584 1.367000 0.34204 -0.594000 0.05836 -0.251000 0.11542 CGG TCGA-FB-AAPU-01A-31D-A40W-08 PAPPA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084763.1 1 0 1 252 382 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1.000000 252 373 0 83 2 -20.000000 1 1 120900 5 39 1 2 2 4 3.310555 1 0.700000 2 0.819059 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TMEM52 339456 broad.mit.edu 37 1 1849760 1849760 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:1849760G>A ENST00000310991.3 - 4 288 c.281C>T c.(280-282)gCa>gTa p.A94V TMEM52_ENST00000378602.3_Missense_Mutation_p.A79V NM_178545.3 NP_848640.1 Q8NDY8 TMM52_HUMAN transmembrane protein 52 3 all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217) GGGCTGCCGTGCTGGTGGCAG 0.637000 0 SO:0001583 missense ENST00000310991.3 1 1 hg19 CCDS35.1 . . . . . . . . . . . 10.32 1.317752 0.23994 . . ENSG00000178821 ENST00000378602;ENST00000310991 T;T 0.38401 1.14;1.14 3.71 1.75 0.24633 . 1.039220 0.07675 N 0.936067 T 0.33294 0.0858 L 0.40543 1.245 0.09310 N 1 P;P 0.50819 0.884;0.939 B;P 0.48524 0.396;0.58 T 0.16660 -1.0395 10 0.48119 T 0.1 -8.9629 2.56 0.04770 0.1093:0.1857:0.5143:0.1906 . 94;79 Q8NDY8;Q8NDY8-2 TMM52_HUMAN;. V 79;94 ENSP00000367865:A79V;ENSP00000311122:A94V ENSP00000311122:A94V A - 2 0 TMEM52 1839620 0.010000 0.17322 0.000000 0.03702 0.009000 0.06853 1.727000 0.38095 0.188000 0.20168 0.511000 0.50034 GCA TCGA-FB-AAPU-01A-31D-A40W-08 TMEM52-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000002781.1 0 0 0 72 54 1 35 1 9.393969e-01 6 0 1 35 2 0 0 0 0 0 2 1 1.000000 68 52 1 35 12 -20.000000 1 1 0 0 1 0 1 1 1.359352 1 0.700000 2 0.540933 0.960000 8.500000e-01 1.000000 1.000000 0.961243 0.960000 1 9.100000e-01 1 C1QB 713 broad.mit.edu 37 1 22986137 22986137 + Splice_Site SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:22986137G>A ENST00000314933.6 + 2 319 c.e2+1 C1QB_ENST00000509305.1_Splice_Site NM_000491.3 NP_000482.3 P02746 C1QB_HUMAN complement component 1, q subcomponent, B chain 14 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072) GGAGAGAAAGGTACCATGGGA 0.577000 0 SO:0001630 splice_region_variant ENST00000314933.6 0 1 hg19 CCDS228.1 . . . . . . . . . . G 17.23 3.336484 0.60963 . . ENSG00000173369 ENST00000510260;ENST00000509305;ENST00000432749;ENST00000314933 . . . 4.71 4.71 0.59529 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 13.6031 0.62031 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . C1QB 22858724 1.000000 0.71417 1.000000 0.80357 0.728000 0.41692 6.184000 0.72008 2.350000 0.79820 0.549000 0.68633 . TCGA-FB-AAPU-01A-31D-A40W-08 C1QB-201 KNOWN basic|CCDS protein_coding protein_coding 1 0 1 21 18 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 1.000000 21 17 0 13 2 -20.000000 1 1 0 0 1 0 1 1 1.339633 1 0.700000 2 0.540933 0.890000 6.600000e-01 1.000000 1.000000 0.887354 0.890000 1 7.800000e-01 9.800000e-01 FH 2271 broad.mit.edu 37 1 241671912 241671912 + Silent SNP A A G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:241671912A>G ENST00000366560.3 - 5 767 c.729T>C c.(727-729)acT>acC p.T243T NM_000143.3 NP_000134.2 P07954 FUMH_HUMAN fumarate hydratase 26 Ovarian(103;0.103) all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118) OV - Ovarian serous cystadenocarcinoma(106;0.0214) CCTGCCCAAGAGTAAGTGGAA 0.398000 Mis, N, F lieomyomatosis, renal Hereditary Leiomyomatosis and Renal Cell Cancer Melanoma(148;1573 2486 7381 46575) yes Rec hereditary leiomyomatosis and renal cell cancer 1 1q42.1 2271 fumarate hydratase E, M 0 SO:0001819 synonymous_variant Familial Cancer Database HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus ENST00000366560.3 1 1 hg19 CCDS1617.1 TCGA-FB-AAPU-01A-31D-A40W-08 FH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095490.1 1 0 1 130 128 0 66 1 1 226 138 0 66 2 0 0 0 0 0 2 1 1.000000 130 128 0 66 2 -20.000000 1 1 0 0 1 1 2 3 2.592080 1 0.700000 2 0.771254 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TMEM53 79639 broad.mit.edu 37 1 45120689 45120689 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:45120689G>C ENST00000372237.3 - 3 539 c.376C>G c.(376-378)Ctc>Gtc p.L126V TMEM53_ENST00000372242.3_Missense_Mutation_p.L126V|TMEM53_ENST00000476724.1_5'UTR|TMEM53_ENST00000372235.3_Missense_Mutation_p.L96V|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372243.3_Intron NM_024587.2 NP_078863.2 Q6P2H8 TMM53_HUMAN transmembrane protein 53 10 Acute lymphoblastic leukemia(166;0.155) GTCTGCAGGAGCTCCAGCACG 0.612000 OREG0013446 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000372237.3 1 1 hg19 CCDS511.1 . . . . . . . . . . G 17.98 3.521758 0.64747 . . ENSG00000126106 ENST00000372242;ENST00000372237;ENST00000372235;ENST00000420706 . . . 5.67 5.67 0.87782 . 0.129271 0.52532 D 0.000064 T 0.69305 0.3096 M 0.67953 2.075 0.58432 D 0.999997 D 0.69078 0.997 D 0.70716 0.97 T 0.65278 -0.6207 9 0.22706 T 0.39 . 10.263 0.43438 0.0751:0.1477:0.7771:0.0 . 126 Q6P2H8 TMM53_HUMAN V 126;126;96;95 . ENSP00000361309:L96V L - 1 0 TMEM53 44893276 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.322000 0.52007 2.687000 0.91594 0.563000 0.77884 CTC TCGA-FB-AAPU-01A-31D-A40W-08 TMEM53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021599.1 0 0 0 6 157 0 58 1 7.227515e-01 5 61 0 58 2 0 0 0 0 0 2 1 0.963820 6 154 0 57 2 -8.650731 1 1 0 0 1 1 2 3 2.031693 0 0.700000 2 0.702085 0.110000 4.000000e-02 0.240000 0.100000 0.130346 0.110000 0 7.000000e-02 1.700000e-01 ZZZ3 26009 broad.mit.edu 37 1 78031331 78031331 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:78031331G>C ENST00000370801.3 - 15 3181 c.2706C>G c.(2704-2706)aaC>aaG p.N902K ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Missense_Mutation_p.N408K NM_015534.4 NP_056349.1 Q8IYH5 ZZZ3_HUMAN zinc finger, ZZ-type containing 3 39 CATGTCATCTGTTTGCTGGAA 0.388000 0 SO:0001583 missense ENST00000370801.3 1 1 hg19 CCDS677.1 . . . . . . . . . . G 14.68 2.607382 0.46527 . . ENSG00000036549 ENST00000370801;ENST00000370798 . . . 5.15 4.23 0.50019 . 0.000000 0.85682 D 0.000000 T 0.59252 0.2180 L 0.50333 1.59 0.58432 D 0.999999 D;D;D 0.89917 0.996;1.0;1.0 D;D;D 0.87578 0.991;0.996;0.998 T 0.65067 -0.6258 9 0.87932 D 0 . 9.2332 0.37450 0.2136:0.0:0.7864:0.0 . 408;902;901 Q8IYH5-3;Q8IYH5;Q8IYH5-2 .;ZZZ3_HUMAN;. K 902;408 . ENSP00000359834:N408K N - 3 2 ZZZ3 77803919 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 3.295000 0.51794 1.500000 0.48636 -0.218000 0.12543 AAC TCGA-FB-AAPU-01A-31D-A40W-08 ZZZ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026615.1 1 0 1 62 133 0 47 1 9.999991e-01 23 27 0 47 2 0 0 0 0 0 2 1 1.000000 62 131 0 47 2 -20.000000 1 1 0 0 1 1 2 3 2.031693 0 0.700000 2 0.702085 0.910000 7.300000e-01 1.000000 1.000000 0.908258 0.910000 1 8.100000e-01 1 MCOLN2 255231 broad.mit.edu 37 1 85417986 85417986 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:85417986G>A ENST00000370608.3 - 6 754 c.687C>T c.(685-687)ggC>ggT p.G229G MCOLN2_ENST00000531325.1_5'UTR|MCOLN2_ENST00000284027.5_Silent_p.G201G NM_153259.2 NP_694991.2 Q8IZK6 MCLN2_HUMAN mucolipin 2 18 GTAGGTCAATGCCTTTAAGAT 0.328000 0 SO:0001819 synonymous_variant ENST00000370608.3 1 1 hg19 CCDS30762.1 TCGA-FB-AAPU-01A-31D-A40W-08 MCOLN2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000027567.2 1 0 0 13 167 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 0.999548 13 164 0 44 2 -6.052750 1 1 0 0 1 1 2 3 2.031693 0 0.700000 2 0.702085 0.210000 1.100000e-01 0.360000 0.200000 0.228433 0.210000 0 1.500000e-01 2.800000e-01 ABCA4 24 broad.mit.edu 37 1 94578575 94578575 + Silent SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr1:94578575G>C ENST00000370225.3 - 2 200 c.114C>G c.(112-114)gtC>gtG p.V38V ABCA4_ENST00000535735.1_Silent_p.V38V NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) ACCAGATCAAGACCAGAAATA 0.443000 0 SO:0001819 synonymous_variant ENST00000370225.3 1 1 hg19 CCDS747.1 TCGA-FB-AAPU-01A-31D-A40W-08 ABCA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029320.1 1 0 1 60 288 0 101 0 0 0 0 101 2 0 0 0 0 0 2 1 1.000000 60 285 0 100 2 -20.000000 1 1 0 0 1 1 2 3 2.031693 0 0.700000 2 0.702085 0.490000 3.800000e-01 0.630000 0.500000 0.505724 0.490000 0 4.300000e-01 5.600000e-01 CASS4 57091 broad.mit.edu 37 20 55033569 55033569 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr20:55033569C>T ENST00000360314.3 + 7 2352 c.2127C>T c.(2125-2127)gtC>gtT p.V709V AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000371336.3_Silent_p.V709V|CASS4_ENST00000434344.1_Silent_p.V272V NM_001164116.1 NP_001157588.1 Q9NQ75 CASS4_HUMAN Cas scaffolding protein family member 4 54 GCAAGCTGGTCATCATGGTGG 0.617000 0 SO:0001819 synonymous_variant ENST00000360314.3 1 1 hg19 CCDS33492.1 TCGA-FB-AAPU-01A-31D-A40W-08 CASS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079789.2 1 0 1 79 152 0 44 0 0 0 1 0 44 2 0 0 0 0 0 2 1 1.000000 78 150 0 44 2 -20.000000 1 1 0 0 1 0 0 0 2.006393 0 0.700000 2 0.700000 0.970000 8.000000e-01 1.000000 1.000000 0.953038 0.970000 1 8.800000e-01 1 CDH4 1002 broad.mit.edu 37 20 60511862 60511862 + Missense_Mutation SNP A A G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr20:60511862A>G ENST00000360469.5 + 16 2700 c.2612A>G c.(2611-2613)gAg>gGg p.E871G CDH4_ENST00000543233.1_Missense_Mutation_p.E797G NM_001794.3 NP_001785.2 P55283 CADH4_HUMAN cadherin 4, type 1, R-cadherin (retinal) 74 BRCA - Breast invasive adenocarcinoma(19;2.36e-08) TTCGACTACGAGGGGAGCGGC 0.627000 0 SO:0001583 missense ENST00000360469.5 1 1 hg19 CCDS13488.1 . . . . . . . . . . A 23.6 4.433272 0.83776 . . ENSG00000179242 ENST00000360469;ENST00000536643;ENST00000543233 D;D 0.87966 -2.32;-2.32 4.49 4.49 0.54785 Cadherin, cytoplasmic domain (1); 0.000000 0.85682 D 0.000000 D 0.94827 0.8329 M 0.93150 3.385 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.95944 0.8949 9 . . . . 13.8037 0.63218 1.0:0.0:0.0:0.0 . 871 P55283 CADH4_HUMAN G 871;779;797 ENSP00000353656:E871G;ENSP00000443301:E797G . E + 2 0 CDH4 59945257 1.000000 0.71417 0.695000 0.30226 0.635000 0.38103 9.016000 0.93645 1.681000 0.50988 0.383000 0.25322 GAG TCGA-FB-AAPU-01A-31D-A40W-08 CDH4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079965.2 1 0 1 25 158 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 25 156 0 38 2 -20.000000 1 1 0 0 1 0 0 0 2.006393 0 0.700000 2 0.700000 0.390000 2.600000e-01 0.540000 0.390000 0.400597 0.390000 0 3.200000e-01 4.700000e-01 LSM14B 149986 broad.mit.edu 37 20 60701454 60701454 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr20:60701454G>A ENST00000279068.6 + 3 546 c.386G>A c.(385-387)aGc>aAc p.S129N LSM14B_ENST00000370915.1_Missense_Mutation_p.S129N|LSM14B_ENST00000253001.4_Missense_Mutation_p.S129N NM_144703.2 NP_653304.2 Q9BX40 LS14B_HUMAN LSM14B, SCD6 homolog B (S. cerevisiae) 8 Breast(26;3.97e-09) BRCA - Breast invasive adenocarcinoma(19;1.28e-07) CTGGCGGCCAGCTCCCTGCTC 0.627000 0 SO:0001583 missense ENST00000279068.6 1 1 hg19 CCDS46626.1 . . . . . . . . . . G 18.92 3.724866 0.68959 . . ENSG00000149657 ENST00000370915;ENST00000279068;ENST00000253001;ENST00000444156;ENST00000400318;ENST00000279069;ENST00000370906;ENST00000361670 T;T;T;T 0.55588 0.88;0.87;0.9;0.51 5.42 5.42 0.78866 . 0.162938 0.64402 D 0.000002 T 0.56001 0.1956 M 0.75264 2.295 0.40246 D 0.978013 B;P;P;P;B 0.44429 0.134;0.647;0.799;0.835;0.047 B;B;B;B;B 0.41666 0.037;0.146;0.156;0.363;0.031 T 0.63056 -0.6722 10 0.49607 T 0.09 . 14.7797 0.69756 0.0:0.144:0.856:0.0 . 10;10;129;155;129 E9PG81;C9J454;Q9BX40;Q5TBQ0;Q9BX40-2 .;.;LS14B_HUMAN;.;. N 129;129;129;10;155;129;10;10 ENSP00000279068:S129N;ENSP00000253001:S129N;ENSP00000383172:S155N;ENSP00000355209:S10N ENSP00000253001:S129N S + 2 0 LSM14B 60134849 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.436000 0.66538 2.529000 0.85273 0.511000 0.50034 AGC TCGA-FB-AAPU-01A-31D-A40W-08 LSM14B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079996.4 1 0 1 43 78 0 26 1 9.999999e-01 25 28 0 26 2 0 0 0 0 0 2 1 1.000000 43 75 0 26 2 -20.000000 1 1 0 0 1 0 0 0 2.006393 0 0.700000 2 0.700000 0.990000 7.700000e-01 1.000000 1.000000 0.959764 0.990000 1 8.900000e-01 1 ADAMTS1 9510 broad.mit.edu 37 21 28214913 28214913 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr21:28214913G>A ENST00000284984.3 - 2 1276 c.822C>T c.(820-822)caC>caT p.H274H NM_006988.3 NP_008919.3 Q9UHI8 ATS1_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 1 42 Breast(209;0.000962) GACCACTGCCGTGGAATTCTG 0.483000 0 SO:0001819 synonymous_variant ENST00000284984.3 1 1 hg19 CCDS33524.1 . . . . . . . . . . G 9.460 1.092734 0.20471 . . ENSG00000154734 ENST00000451462 . . . 5.44 -1.59 0.08453 . . . . . T 0.58509 0.2127 . . . 0.80722 D 1 . . . . . . T 0.56481 -0.7972 4 . . . . 12.2727 0.54716 0.6587:0.0:0.3413:0.0 . . . . M 56 . . T - 2 0 ADAMTS1 27136784 0.097000 0.21791 0.993000 0.49108 0.987000 0.75469 -0.483000 0.06536 -0.211000 0.10124 -0.768000 0.03414 ACG TCGA-FB-AAPU-01A-31D-A40W-08 ADAMTS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171650.2 0 0 0 9 327 0 85 0 1.409441e-01 0 22 0 85 2 0 0 0 0 0 2 1 0.993546 9 317 0 85 2 -3.475365 1 1 0 0 1 1 2 3 2.013662 0 0.700000 2 0.701046 0.070000 3.000000e-02 0.150000 0.080000 0.084719 0.070000 0 5.000000e-02 1.100000e-01 TMPRSS3 64699 broad.mit.edu 37 21 43815480 43815480 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr21:43815480C>T ENST00000291532.3 - 2 1002 c.47G>A c.(46-48)cGa>cAa p.R16Q TMPRSS3_ENST00000380399.1_Missense_Mutation_p.R100Q|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.R16Q|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.R16Q|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.R16Q NM_032404.2 NP_115780.1 P57727 TMPS3_HUMAN transmembrane protease, serine 3 13 AAAAAGCGATCGGAATGAGAA 0.517000 0 SO:0001583 missense ENST00000291532.3 1 1 hg19 CCDS13686.1 . . . . . . . . . . C 19.92 3.916630 0.73098 2.27E-4 0.0 ENSG00000160183 ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397 D;D;D;D;D 0.88354 -2.33;-2.33;-2.33;-2.37;-2.33 5.39 4.5 0.54988 . 0.132141 0.36628 N 0.002499 T 0.80276 0.4593 N 0.19112 0.55 0.28577 N 0.910325 D;P;P 0.57899 0.981;0.948;0.913 B;B;B 0.43916 0.436;0.237;0.12 T 0.74551 -0.3628 9 . . . . 9.3585 0.38182 0.0:0.904:0.0:0.096 . 16;16;16 P57727-3;P57727-5;P57727 .;.;TMPS3_HUMAN Q 16;16;16;100;16 ENSP00000291532:R16Q;ENSP00000411013:R16Q;ENSP00000381442:R16Q;ENSP00000369762:R100Q;ENSP00000381434:R16Q . R - 2 0 TMPRSS3 42688549 0.993000 0.37304 0.956000 0.39512 0.959000 0.62525 1.712000 0.37940 2.691000 0.91804 0.655000 0.94253 CGA TCGA-FB-AAPU-01A-31D-A40W-08 TMPRSS3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000195347.1 1 0 1 47 91 0 44 1 9.999965e-01 8 35 0 44 2 0 0 0 0 0 2 1 1.000000 46 87 0 43 2 -7.570966 1 1 121412 5 41 1 1 2 3 2.013662 0 0.700000 2 0.701046 0.970000 7.500000e-01 1.000000 1.000000 0.943428 0.970000 1 8.600000e-01 1 TRMT2A 27037 broad.mit.edu 37 22 20103778 20103778 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:20103778C>T ENST00000252136.7 - 2 770 c.382G>A c.(382-384)Gtt>Att p.V128I RANBP1_ENST00000331821.3_5'Flank|RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000403707.3_Missense_Mutation_p.V128I|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000404751.3_Missense_Mutation_p.V128I|TRMT2A_ENST00000439169.2_Missense_Mutation_p.V128I|RANBP1_ENST00000430524.1_5'UTR NM_001257994.1|NM_022727.5|NM_182984.4 NP_001244923.1|NP_073564.3|NP_892029.2 Q8IZ69 TRM2A_HUMAN tRNA methyltransferase 2 homolog A (S. cerevisiae) 9 CCATGCAAAACGCGCAGGGCC 0.647000 0 SO:0001583 missense ENST00000252136.7 0 1 hg19 CCDS13774.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 15.87|15.87 2.960083|2.960083 0.53400|0.53400 .|. .|. ENSG00000099901|ENSG00000099899 ENST00000432879|ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169;ENST00000445045 .|T;T;T;T;T .|0.41758 .|3.17;3.17;3.17;3.17;0.99 5.68|5.68 4.67|4.67 0.58626|0.58626 .|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2); .|0.189905 .|0.47093 .|D .|0.000254 T|T 0.33962|0.33962 0.0881|0.0881 L|L 0.31065|0.31065 0.9|0.9 0.80722|0.80722 D|D 1|1 .|P;B;B .|0.50369 .|0.934;0.003;0.0 .|B;B;B .|0.43478 .|0.421;0.005;0.003 T|T 0.05402|0.05402 -1.0887|-1.0887 6|10 0.54805|0.27785 T|T 0.06|0.31 -28.7311|-28.7311 14.5387|14.5387 0.67979|0.67979 0.0:0.9287:0.0:0.0713|0.0:0.9287:0.0:0.0713 .|. .|128;128;128 .|B4E213;F2Z2W7;Q8IZ69 .|.;.;TRM2A_HUMAN M|I 24|128;128;128;128;116 .|ENSP00000252136:V128I;ENSP00000385807:V128I;ENSP00000384968:V128I;ENSP00000395738:V128I;ENSP00000393911:V116I ENSP00000404724:T24M|ENSP00000252136:V128I T|V +|- 2|1 0|0 RANBP1|TRMT2A 18483778|18483778 0.851000|0.851000 0.29673|0.29673 0.928000|0.928000 0.36995|0.36995 0.657000|0.657000 0.38888|0.38888 2.040000|2.040000 0.41203|0.41203 1.422000|1.422000 0.47177|0.47177 -0.424000|-0.424000 0.05967|0.05967 ACG|GTT TCGA-FB-AAPU-01A-31D-A40W-08 TRMT2A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318168.3 1 0 1 62 152 0 43 1 9.999310e-01 13 26 0 43 2 0 0 0 0 0 2 1 1.000000 62 152 0 43 2 -20.000000 1 1 121382 1 33 1 1 2 3 2.029302 0 0.700000 2 0.702085 0.830000 6.600000e-01 1.000000 0.830000 0.837693 0.830000 0 7.400000e-01 9.300000e-01 TOP3B 8940 broad.mit.edu 37 22 22316871 22316871 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:22316871C>T ENST00000398793.2 - 13 1889 c.1455G>A c.(1453-1455)gaG>gaA p.E485E TOP3B_ENST00000357179.5_Silent_p.E485E|TOP3B_ENST00000413067.2_Silent_p.E214E NM_003935.3 NP_003926.1 O95985 TOP3B_HUMAN topoisomerase (DNA) III beta 26 Colorectal(54;0.105) TCGTCTGCTTCTCCAGCATCT 0.662000 0 SO:0001819 synonymous_variant ENST00000398793.2 1 1 hg19 CCDS13797.1 . . . . . . . . . . C 8.858 0.946274 0.18356 . . ENSG00000100038 ENST00000457270 . . . 5.12 4.1 0.47936 . . . . . T 0.58438 0.2122 . . . 0.80722 D 1 . . . . . . T 0.55231 -0.8173 4 . . . . 8.1485 0.31126 0.0:0.7409:0.0:0.2591 . . . . K 280 . . R - 2 0 TOP3B 20646871 1.000000 0.71417 1.000000 0.80357 0.805000 0.45488 3.352000 0.52239 1.141000 0.42275 0.563000 0.77884 AGA TCGA-FB-AAPU-01A-31D-A40W-08 TOP3B-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320251.1 1 0 0 14 213 0 49 1 5.946364e-01 3 28 0 49 2 0 0 0 0 0 2 1 0.999745 13 209 0 48 2 -17.527500 1 1 0 0 1 1 2 3 2.029302 0 0.700000 2 0.702085 0.180000 1.000000e-01 0.300000 0.180000 0.196061 0.180000 0 1.300000e-01 2.400000e-01 SUSD2 56241 broad.mit.edu 37 22 24579094 24579094 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:24579094C>G ENST00000358321.3 + 2 407 c.146C>G c.(145-147)tCt>tGt p.S49C NM_019601.3 NP_062547.1 Q9UGT4 SUSD2_HUMAN sushi domain containing 2 26 CCGACGTGCTCTGGCCTTGGC 0.632000 0 SO:0001583 missense ENST00000358321.3 1 1 hg19 CCDS13824.1 . . . . . . . . . . C 7.214 0.596096 0.13875 . . ENSG00000099994 ENST00000358321 T 0.44482 0.92 3.76 1.58 0.23477 Somatomedin B domain (4); 1.140860 0.06462 N 0.729556 T 0.38931 0.1059 L 0.44542 1.39 0.09310 N 1 P 0.40731 0.728 P 0.44732 0.459 T 0.30679 -0.9970 10 0.51188 T 0.08 -8.1814 3.3614 0.07188 0.1932:0.5932:0.0:0.2136 . 49 Q9UGT4 SUSD2_HUMAN C 49 ENSP00000351075:S49C ENSP00000351075:S49C S + 2 0 SUSD2 22909094 0.000000 0.05858 0.353000 0.25747 0.062000 0.15995 -3.602000 0.00418 0.371000 0.24564 0.449000 0.29647 TCT TCGA-FB-AAPU-01A-31D-A40W-08 SUSD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320088.1 1 0 1 58 554 0 145 0 2.861161e-01 0 11 0 145 2 0 0 0 0 0 2 1 1.000000 58 536 0 148 2 -16.320620 1 0 0 0 1 1 2 3 2.029302 0 0.700000 2 0.702085 0.270000 2.000000e-01 0.360000 0.270000 0.283363 0.270000 0 2.300000e-01 3.100000e-01 THOC5 8563 broad.mit.edu 37 22 29915009 29915009 + Missense_Mutation SNP T T C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:29915009T>C ENST00000490103.1 - 15 1597 c.1475A>G c.(1474-1476)cAg>cGg p.Q492R THOC5_ENST00000397873.2_Missense_Mutation_p.Q492R|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.Q492R|THOC5_ENST00000397872.1_Missense_Mutation_p.Q492R NM_003678.4 NP_003669.4 Q13769 THOC5_HUMAN THO complex 5 21 GGATGCAAACTGTTTGTGGAG 0.507000 0 SO:0001583 missense ENST00000490103.1 1 1 hg19 CCDS13859.1 . . . . . . . . . . T 27.7 4.858213 0.91433 . . ENSG00000100296 ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873 T;T;T;T 0.20881 2.04;2.04;2.04;2.04 5.76 5.76 0.90799 . 0.000000 0.85682 D 0.000000 T 0.43743 0.1261 M 0.71581 2.175 0.80722 D 1 D 0.76494 0.999 D 0.63488 0.915 T 0.29274 -1.0017 10 0.45353 T 0.12 -17.1228 15.0502 0.71862 0.0:0.0:0.0:1.0 . 492 Q13769 THOC5_HUMAN R 492 ENSP00000420306:Q492R;ENSP00000380970:Q492R;ENSP00000380969:Q492R;ENSP00000380971:Q492R ENSP00000380969:Q492R Q - 2 0 THOC5 28245009 1.000000 0.71417 1.000000 0.80357 0.951000 0.60555 7.779000 0.85648 2.201000 0.70794 0.533000 0.62120 CAG TCGA-FB-AAPU-01A-31D-A40W-08 THOC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322097.1 1 0 1 59 583 0 147 1 8.901238e-01 5 35 0 147 2 0 0 0 0 0 2 1 1.000000 59 571 0 145 2 -20.000000 1 1 0 0 1 1 2 3 2.029302 0 0.700000 2 0.702085 0.260000 2.000000e-01 0.350000 0.260000 0.275048 0.260000 0 2.200000e-01 3.000000e-01 TMPRSS6 164656 broad.mit.edu 37 22 37466587 37466587 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:37466587C>A ENST00000346753.3 - 15 1921 c.1805G>T c.(1804-1806)tGt>tTt p.C602F TMPRSS6_ENST00000406725.1_Missense_Mutation_p.C593F|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.C593F|TMPRSS6_ENST00000381792.2_Missense_Mutation_p.C593F NM_153609.2 NP_705837.1 Q8IU80 TMPS6_HUMAN transmembrane protease, serine 6 40 GGCCCCCCCACAGATGTGTCG 0.662000 0 SO:0001583 missense ENST00000346753.3 1 1 hg19 CCDS13941.1 . . . . . . . . . . C 28.5 4.928706 0.92389 . . ENSG00000187045 ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856 D;D;D;D 0.98701 -5.08;-5.08;-5.08;-5.08 5.44 5.44 0.79542 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.000000 0.85682 D 0.000000 D 0.99579 0.9848 H 0.98786 4.33 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.999 D 0.97650 1.0154 10 0.87932 D 0 . 19.2437 0.93893 0.0:1.0:0.0:0.0 . 593;602 Q8IU80-5;Q8IU80 .;TMPS6_HUMAN F 593;602;593;593 ENSP00000371211:C593F;ENSP00000334962:C602F;ENSP00000385453:C593F;ENSP00000384964:C593F ENSP00000334962:C602F C - 2 0 TMPRSS6 35796533 1.000000 0.71417 0.998000 0.56505 0.997000 0.91878 7.741000 0.84997 2.540000 0.85666 0.591000 0.81541 TGT TCGA-FB-AAPU-01A-31D-A40W-08 TMPRSS6-003 NOVEL basic|CCDS protein_coding protein_coding OTTHUMT00000318822.1 1 0 0 16 352 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 0.999923 16 344 0 84 2 -16.663560 1 1 0 0 1 1 2 3 2.029302 0 0.700000 2 0.702085 0.120000 6.000000e-02 0.210000 0.120000 0.140540 0.120000 0 9.000000e-02 1.700000e-01 JOSD1 9929 broad.mit.edu 37 22 39084975 39084975 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:39084975C>A ENST00000216039.5 - 3 1153 c.474G>T c.(472-474)aaG>aaT p.K158N NM_014876.5 NP_055691.1 Q15040 JOS1_HUMAN Josephin domain containing 1 5 Melanoma(58;0.04) ACTCGGGCATCTTGAGTTTGG 0.547000 0 SO:0001583 missense ENST00000216039.5 1 1 hg19 CCDS13976.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 15.42|15.42 2.826872|2.826872 0.50739|0.50739 .|. .|. ENSG00000100221|ENSG00000100221 ENST00000545590|ENST00000216039 .|T .|0.42900 .|0.96 5.64|5.64 5.64|5.64 0.86602|0.86602 .|. .|0.046800 .|0.85682 .|D .|0.000000 T|T 0.33990|0.33990 0.0882|0.0882 L|L 0.38953|0.38953 1.18|1.18 0.58432|0.58432 D|D 0.999998|0.999998 .|B .|0.14438 .|0.01 .|B .|0.19666 .|0.026 T|T 0.08006|0.08006 -1.0743|-1.0743 5|10 .|0.27082 .|T .|0.32 .|. 12.9775|12.9775 0.58546|0.58546 0.0:0.9262:0.0:0.0738|0.0:0.9262:0.0:0.0738 .|. .|158 .|Q15040 .|JOS1_HUMAN Y|N 110|158 .|ENSP00000216039:K158N .|ENSP00000216039:K158N D|K -|- 1|3 0|2 JOSD1|JOSD1 37414921|37414921 0.999000|0.999000 0.42202|0.42202 1.000000|1.000000 0.80357|0.80357 0.897000|0.897000 0.52465|0.52465 2.113000|2.113000 0.41902|0.41902 2.647000|2.647000 0.89833|0.89833 0.655000|0.655000 0.94253|0.94253 GAT|AAG TCGA-FB-AAPU-01A-31D-A40W-08 JOSD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321047.1 0 0 0 18 421 0 91 1 9.998689e-01 13 333 0 91 2 0 0 0 0 0 2 1 0.999980 18 413 0 90 2 -4.200902 1 1 0 0 1 1 2 3 2.029302 0 0.700000 2 0.702085 0.110000 6.000000e-02 0.190000 0.120000 0.132417 0.110000 0 9.000000e-02 1.500000e-01 L3MBTL2 83746 broad.mit.edu 37 22 41620150 41620150 + Missense_Mutation SNP T T A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:41620150T>A ENST00000216237.5 + 9 1227 c.1069T>A c.(1069-1071)Tac>Aac p.Y357N NM_031488.4 NP_113676.2 Q969R5 LMBL2_HUMAN l(3)mbt-like 2 (Drosophila) 24 ACGGCTCCTCTACGAGGATGG 0.612000 0 SO:0001583 missense ENST00000216237.5 1 1 hg19 CCDS14011.1 . . . . . . . . . . T 29.2 4.987915 0.93106 . . ENSG00000100395 ENST00000216237 T 0.35789 1.29 5.26 5.26 0.73747 . 0.000000 0.85682 D 0.000000 T 0.65512 0.2698 M 0.87682 2.9 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.72947 -0.4137 10 0.87932 D 0 . 15.1768 0.72920 0.0:0.0:0.0:1.0 . 357;357 Q969R5-3;Q969R5 .;LMBL2_HUMAN N 357 ENSP00000216237:Y357N ENSP00000216237:Y357N Y + 1 0 L3MBTL2 39950096 1.000000 0.71417 1.000000 0.80357 0.963000 0.63663 6.305000 0.72805 2.008000 0.58898 0.533000 0.62120 TAC TCGA-FB-AAPU-01A-31D-A40W-08 L3MBTL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320613.1 1 0 1 125 169 0 53 1 1 24 31 0 53 2 0 0 0 0 0 2 1 1.000000 118 166 0 52 2 -20.000000 1 1 0 0 1 0 0 0 2.007508 0 0.700000 2 0.700000 0.990000 9.900000e-01 1.000000 1.000000 0.999904 0.990000 1 9.900000e-01 1 BIK 638 broad.mit.edu 37 22 43524566 43524566 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr22:43524566G>C ENST00000216115.2 + 4 388 c.325G>C c.(325-327)Gac>Cac p.D109H NM_001197.4 NP_001188.1 Q13323 BIK_HUMAN BCL2-interacting killer (apoptosis-inducing) 5 Ovarian(80;0.0694) AAGTTTCATGGACGGTTTCAC 0.517000 0 SO:0001583 missense ENST00000216115.2 1 1 hg19 CCDS14044.1 . . . . . . . . . . G 12.41 1.929535 0.34096 . . ENSG00000100290 ENST00000216115 T 0.25414 1.8 3.65 -1.33 0.09172 . . . . . T 0.24160 0.0585 N 0.19112 0.55 0.09310 N 1 D 0.61080 0.989 P 0.59948 0.866 T 0.16958 -1.0385 9 0.38643 T 0.18 2.1384 4.952 0.14019 0.2262:0.357:0.4168:0.0 . 109 Q13323 BIK_HUMAN H 109 ENSP00000216115:D109H ENSP00000216115:D109H D + 1 0 BIK 41854510 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.703000 0.01900 -0.087000 0.12528 0.462000 0.41574 GAC TCGA-FB-AAPU-01A-31D-A40W-08 BIK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319676.1 1 0 1 141 136 0 122 1 1 120 0 0 122 2 0 0 0 0 0 2 1 1.000000 141 136 0 120 2 -20.000000 1 1 0 0 1 0 1 1 1.359079 1 0.700000 2 0.540933 0.930000 8.300000e-01 1.000000 0.950000 0.934386 0.930000 1 8.800000e-01 9.800000e-01 STEAP3 55240 broad.mit.edu 37 2 120005698 120005698 + Silent SNP C C T rs145832236 TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:120005698C>T ENST00000354888.5 + 4 1440 c.936C>T c.(934-936)tgC>tgT p.C312C STEAP3_ENST00000409811.1_Silent_p.C312C|STEAP3_ENST00000393106.2_Silent_p.C312C|STEAP3_ENST00000393107.2_Silent_p.C312C|STEAP3_ENST00000425223.2_Silent_p.C312C|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000450943.2_Silent_p.C312C|STEAP3_ENST00000393110.2_Silent_p.C322C|STEAP3_ENST00000393108.2_Silent_p.C312C NM_182915.2 NP_878919.2 Q658P3 STEA3_HUMAN STEAP family member 3, metalloreductase 17 GCTTCTTCTGCGCCGCCCTGC 0.677000 0 SO:0001819 synonymous_variant ENST00000354888.5 1 1 hg19 CCDS2125.1 TCGA-FB-AAPU-01A-31D-A40W-08 STEAP3-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254193.1 1 0 1 70 55 0 33 1 9.999974e-01 21 1 0 33 2 0 0 0 0 0 2 1 1.000000 68 54 0 33 2 -19.992270 1 1 121074 8 38 1 0 1 1 1.343218 1 0.700000 2 0.538462 0.950000 8.300000e-01 1.000000 0.990000 0.947925 0.950000 1 8.900000e-01 9.900000e-01 RND3 390 broad.mit.edu 37 2 151326505 151326505 + Missense_Mutation SNP A A G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:151326505A>G ENST00000375734.2 - 5 980 c.731T>C c.(730-732)aTg>aCg p.M244T RND3_ENST00000472416.1_5'Flank|RND3_ENST00000409557.1_Missense_Mutation_p.M115T|RND3_ENST00000263895.4_Missense_Mutation_p.M244T NM_001254738.1 NP_001241667.1 P61587 RND3_HUMAN Rho family GTPase 3 13 AAAGATTCACATCACAGTGCA 0.423000 0 SO:0001583 missense ENST00000375734.2 1 1 hg19 CCDS2190.1 . . . . . . . . . . A 17.89 3.498553 0.64298 . . ENSG00000115963 ENST00000375734;ENST00000263895;ENST00000409557 T;T;T 0.68624 -0.34;-0.34;2.26 5.81 5.81 0.92471 . 0.033764 0.85682 D 0.000000 T 0.75517 0.3860 M 0.64404 1.975 0.80722 D 1 P;D;D 0.55800 0.597;0.973;0.973 P;P;P 0.55345 0.774;0.663;0.663 T 0.78560 -0.2157 10 0.87932 D 0 -26.2874 15.3525 0.74399 1.0:0.0:0.0:0.0 . 107;243;244 B4DSG7;D3DP96;P61587 .;.;RND3_HUMAN T 244;244;115 ENSP00000364886:M244T;ENSP00000263895:M244T;ENSP00000386576:M115T ENSP00000263895:M244T M - 2 0 RND3 151034751 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.335000 0.96500 2.221000 0.72209 0.528000 0.53228 ATG TCGA-FB-AAPU-01A-31D-A40W-08 RND3-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254809.1 1 0 1 91 82 0 98 1 1 35 14 0 98 2 0 0 0 0 0 2 1 1.000000 91 82 0 97 2 -20.000000 1 1 0 0 1 0 1 1 1.350572 1 0.700000 2 0.538462 0.930000 8.100000e-01 1.000000 0.970000 0.934666 0.930000 1 8.800000e-01 9.800000e-01 PXDN 7837 broad.mit.edu 37 2 1653014 1653014 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:1653014G>A ENST00000252804.4 - 17 2588 c.2538C>T c.(2536-2538)caC>caT p.H846H NM_012293.1 NP_036425.1 Q92626 PXDN_HUMAN peroxidasin homolog (Drosophila) 112 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) CGTTGCTGCAGTGCTGTCCGT 0.647000 0 SO:0001819 synonymous_variant ENST00000252804.4 1 1 hg19 CCDS46221.1 TCGA-FB-AAPU-01A-31D-A40W-08 PXDN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322505.1 1 0 1 34 57 0 38 0 9.638596e-01 0 12 0 38 2 0 0 0 0 0 2 1 1.000000 32 54 0 36 2 -20.000000 1 1 0 0 1 0 0 0 1.996559 0 0.700000 2 0.700000 0.990000 7.900000e-01 1.000000 1.000000 0.971952 0.990000 1 9.200000e-01 1 SGOL2 151246 broad.mit.edu 37 2 201436126 201436126 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:201436126G>A ENST00000357799.4 + 7 1155 c.1057G>A c.(1057-1059)Gac>Aac p.D353N NM_001160033.1|NM_001160046.1|NM_152524.5 NP_001153505.1|NP_001153518.1|NP_689737.4 Q562F6 SGOL2_HUMAN shugoshin-like 2 (S. pombe) 46 GGATAATGATGACTTTCAATT 0.373000 0 SO:0001583 missense ENST00000357799.4 0 1 hg19 CCDS42796.1 . . . . . . . . . . G 12.84 2.057581 0.36277 . . ENSG00000163535 ENST00000357799 T 0.12984 2.63 5.45 3.63 0.41609 . 0.200831 0.35436 N 0.003203 T 0.11324 0.0276 L 0.46157 1.445 0.22457 N 0.999084 P;P;P 0.40332 0.713;0.713;0.713 B;B;B 0.36845 0.234;0.234;0.234 T 0.16247 -1.0409 10 0.25106 T 0.35 -3.3647 9.4882 0.38942 0.1632:0.0:0.8368:0.0 . 353;353;353 B7Z7S9;Q562F6-2;Q562F6 .;.;SGOL2_HUMAN N 353 ENSP00000350447:D353N ENSP00000350447:D353N D + 1 0 SGOL2 201144371 0.000000 0.05858 0.691000 0.30163 0.196000 0.23810 0.307000 0.19296 0.837000 0.34925 0.585000 0.79938 GAC TCGA-FB-AAPU-01A-31D-A40W-08 SGOL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335834.1 0 0 0 4 127 0 56 0 1.516314e-02 1 4 0 56 2 0 0 0 0 0 2 1 0.889737 4 126 0 56 2 -6.807310 1 1 0 0 1 0 2 2 2.074045 1 0.700000 2 0.700000 0.090000 2.000000e-02 0.210000 0.090000 0.107035 0.090000 0 5.000000e-02 1.500000e-01 UGT1A10 54575 broad.mit.edu 37 2 234545236 234545236 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:234545236C>T ENST00000344644.5 + 1 137 c.68C>T c.(67-69)gCc>gTc p.A23V UGT1A10_ENST00000373445.1_Missense_Mutation_p.A23V|UGT1A1_ENST00000373450.4_Intron NM_019075.2 NP_061948.1 Q9HAW8 UD110_HUMAN UDP glucuronosyltransferase 1 family, polypeptide A10 32 Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128) Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313) TGTGGCTTTGCCGAGGCAGGG 0.592000 0 SO:0001583 missense ENST00000344644.5 0 1 hg19 CCDS33403.1 . . . . . . . . . . C 9.852 1.194005 0.22037 . . ENSG00000242515 ENST00000344644;ENST00000373445 T;T 0.59224 0.28;0.36 3.83 1.94 0.25998 . . . . . T 0.40619 0.1124 L 0.31845 0.965 0.09310 N 1 B;B 0.17268 0.021;0.021 B;B 0.23852 0.02;0.049 T 0.28964 -1.0027 9 0.13470 T 0.59 . 5.5238 0.16947 0.0:0.6325:0.1827:0.1848 . 23;23 Q9HAW8;Q7Z6H8 UD110_HUMAN;. V 23 ENSP00000343838:A23V;ENSP00000362544:A23V ENSP00000343838:A23V A + 2 0 UGT1A10 234209975 0.000000 0.05858 0.001000 0.08648 0.071000 0.16799 0.183000 0.16919 0.376000 0.24707 0.537000 0.68136 GCC TCGA-FB-AAPU-01A-31D-A40W-08 UGT1A10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000130986.1 0 0 0 5 394 0 117 0 4.871960e-01 0 115 0 117 2 0 0 0 0 0 2 1 0.934098 5 385 0 115 2 -2.244575 0 1 0 0 1 0 2 2 2.182243 1 0.700000 2 0.700000 0.030000 0 0.080000 0.040000 0.042347 0.030000 0 1.000000e-02 6.000000e-02 SPP2 6694 broad.mit.edu 37 2 234959698 234959698 + Missense_Mutation SNP A A T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:234959698A>T ENST00000168148.3 + 2 257 c.169A>T c.(169-171)Agt>Tgt p.S57C SPP2_ENST00000373368.1_Missense_Mutation_p.S57C|SPP2_ENST00000492481.1_3'UTR NM_006944.2 NP_008875.1 Q13103 SPP24_HUMAN secreted phosphoprotein 2, 24kDa 12 Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182) CCAGTCACTGAGTCCGTATCT 0.468000 0 SO:0001583 missense ENST00000168148.3 1 1 hg19 CCDS2511.1 . . . . . . . . . . A 16.27 3.077136 0.55753 . . ENSG00000072080 ENST00000373368;ENST00000168148 T;T 0.51071 0.72;0.72 5.39 3.07 0.35406 . 0.136200 0.52532 D 0.000071 T 0.60392 0.2265 M 0.65975 2.015 0.09310 N 1 D 0.89917 1.0 D 0.78314 0.991 T 0.49341 -0.8950 10 0.62326 D 0.03 -31.8015 6.1693 0.20408 0.8066:0.0:0.1934:0.0 . 57 Q13103 SPP24_HUMAN C 57 ENSP00000362466:S57C;ENSP00000168148:S57C ENSP00000168148:S57C S + 1 0 SPP2 234624437 0.997000 0.39634 0.772000 0.31596 0.826000 0.46750 1.596000 0.36718 0.903000 0.36546 0.533000 0.62120 AGT TCGA-FB-AAPU-01A-31D-A40W-08 SPP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131313.3 1 0 1 94 130 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1.000000 93 125 0 69 2 -20.000000 1 1 0 0 1 0 2 2 2.182243 1 0.700000 2 0.700000 0.990000 9.900000e-01 1.000000 1.000000 0.999500 0.990000 1 9.900000e-01 1 ITSN2 50618 broad.mit.edu 37 2 24521586 24521586 + Missense_Mutation SNP A A G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:24521586A>G ENST00000355123.4 - 13 1885 c.1442T>C c.(1441-1443)aTt>aCt p.I481T ITSN2_ENST00000406921.3_Missense_Mutation_p.I481T|ITSN2_ENST00000361999.3_Missense_Mutation_p.I481T NM_006277.2 NP_006268.2 Q9NZM3 ITSN2_HUMAN intersectin 2 61 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TAACCTGACAATTTCTTCTTG 0.398000 0 SO:0001583 missense ENST00000355123.4 1 1 hg19 CCDS1710.2 . . . . . . . . . . A 17.24 3.339931 0.60963 . . ENSG00000198399 ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011 T;T;T;T;T 0.79653 0.08;0.13;0.08;0.56;-1.29 5.24 5.24 0.73138 . 0.000000 0.37577 U 0.002034 D 0.86531 0.5955 L 0.52011 1.625 0.52099 D 0.999941 D;D;D;D 0.89917 1.0;1.0;1.0;0.999 D;D;D;D 0.83275 0.996;0.996;0.996;0.991 D 0.85992 0.1489 10 0.40728 T 0.16 . 15.4385 0.75165 1.0:0.0:0.0:0.0 . 481;481;481;481 Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 .;.;.;ITSN2_HUMAN T 481;481;481;505;481;506 ENSP00000354561:I481T;ENSP00000347244:I481T;ENSP00000370250:I481T;ENSP00000384499:I481T;ENSP00000391224:I506T ENSP00000347244:I481T I - 2 0 ITSN2 24375090 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 8.614000 0.90917 2.123000 0.65237 0.397000 0.26171 ATT TCGA-FB-AAPU-01A-31D-A40W-08 ITSN2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000207620.2 0 0 1 119 263 0 112 1 9.998899e-01 17 16 0 112 2 0 0 0 0 0 2 1 1.000000 117 259 0 110 2 -20.000000 1 0 0 0 1 0 0 0 1.996559 0 0.700000 2 0.700000 0.880000 7.500000e-01 1.000000 1.000000 0.890100 0.880000 1 8.100000e-01 9.600000e-01 KCNG3 170850 broad.mit.edu 37 2 42719978 42719978 + Splice_Site SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr2:42719978C>G ENST00000306078.1 - 1 1259 c.664G>C c.(664-666)Ggg>Cgg p.G222R KCNG3_ENST00000394973.4_Intron|MTA3_ENST00000405592.1_5'Flank NM_133329.5|NM_172344.2 NP_579875.1|NP_758847.1 Q8TAE7 KCNG3_HUMAN potassium voltage-gated channel, subfamily G, member 3 6 GCGTCCTACCCGGAGGGCTCC 0.711000 0 SO:0001630 splice_region_variant ENST00000306078.1 1 0 hg19 CCDS1809.1 . . . . . . . . . . C 14.84 2.656292 0.47467 . . ENSG00000171126 ENST00000306078 D 0.97328 -4.34 4.85 3.97 0.46021 . 0.983145 0.08331 N 0.962294 D 0.91529 0.7325 N 0.08118 0 0.80722 D 1 P 0.45768 0.866 B 0.35278 0.199 D 0.86409 0.1747 10 0.54805 T 0.06 . 13.3731 0.60723 0.0:0.9238:0.0:0.0762 . 222 Q8TAE7 KCNG3_HUMAN R 222 ENSP00000304127:G222R ENSP00000304127:G222R G - 1 0 KCNG3 42573482 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 5.822000 0.69265 1.253000 0.44018 0.563000 0.77884 GGG TCGA-FB-AAPU-01A-31D-A40W-08 KCNG3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000250464.2 1 0 1 26 50 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 1.000000 26 48 0 14 2 -6.053581 1 1 118912 1 28 1 0 0 0 1.980529 0 0.700000 2 0.697885 0.960000 6.800000e-01 1.000000 1.000000 0.926902 0.960000 1 8.100000e-01 1 CCDC58 131076 broad.mit.edu 37 3 122081856 122081856 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr3:122081856C>T ENST00000291458.5 - 4 349 c.343G>A c.(343-345)Gaa>Aaa p.E115K CCDC58_ENST00000497726.1_Missense_Mutation_p.E24K|CCDC58_ENST00000466854.1_5'UTR|CCDC58_ENST00000479899.1_Missense_Mutation_p.E101K NM_001017928.2 NP_001017928.1 Q4VC31 CCD58_HUMAN coiled-coil domain containing 58 2 ACATTCAGTTCTGACTGCATC 0.313000 0 SO:0001583 missense ENST00000291458.5 1 1 hg19 CCDS33838.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 27.3|27.3 4.821041|4.821041 0.90873|0.90873 .|. .|. ENSG00000160124|ENSG00000160124 ENST00000291458;ENST00000497726;ENST00000479899|ENST00000479414 .|. .|. .|. 5.1|5.1 5.1|5.1 0.69264|0.69264 .|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.83008|0.83008 0.5161|0.5161 M|M 0.89287|0.89287 3.02|3.02 0.58432|0.58432 D|D 0.999994|0.999994 D|. 0.89917|. 1.0|. D|. 0.91635|. 0.999|. D|D 0.85748|0.85748 0.1341|0.1341 9|5 0.87932|. D|. 0|. .|. 15.8232|15.8232 0.78676|0.78676 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 115|. Q4VC31|. CCD58_HUMAN|. K|K 115;24;101|111 .|. ENSP00000291458:E115K|. E|R -|- 1|2 0|0 CCDC58|CCDC58 123564546|123564546 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.974000|0.974000 0.67602|0.67602 6.444000|6.444000 0.73452|0.73452 2.650000|2.650000 0.89964|0.89964 0.561000|0.561000 0.74099|0.74099 GAA|AGA TCGA-FB-AAPU-01A-31D-A40W-08 CCDC58-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355754.1 1 0 1 59 129 0 72 1 1 58 74 0 72 2 0 0 0 0 0 2 1 1.000000 58 128 0 72 2 -20.000000 1 1 0 0 1 0 0 0 1.997626 0 0.700000 2 0.700000 0.890000 7.100000e-01 1.000000 1.000000 0.892324 0.890000 1 7.900000e-01 9.900000e-01 MYLK 4638 broad.mit.edu 37 3 123418920 123418920 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr3:123418920G>A ENST00000475616.1 - 15 3394 c.3395C>T c.(3394-3396)aCg>aTg p.T1132M MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000360772.3_Missense_Mutation_p.T1132M|MYLK_ENST00000359169.1_Missense_Mutation_p.T1132M|MYLK_ENST00000346322.5_Missense_Mutation_p.T1063M|MYLK_ENST00000360304.3_Missense_Mutation_p.T1132M Q15746 MYLK_HUMAN myosin light chain kinase 113 Lung NSC(201;0.0496) TCCGTTCAGCGTCCAGATGAT 0.567000 0 SO:0001583 missense ENST00000475616.1 1 1 hg19 CCDS46896.1 . . . . . . . . . . G 11.53 1.664962 0.29604 . . ENSG00000065534 ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616 T;T;T;T;T 0.42131 0.98;0.98;0.98;0.98;0.98 5.76 3.98 0.46160 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.32526 0.0832 L 0.29908 0.895 0.32639 N 0.521 B;B;B;B;B;B 0.33512 0.237;0.157;0.379;0.362;0.415;0.279 B;B;B;B;B;B 0.34138 0.11;0.062;0.105;0.11;0.139;0.176 T 0.38308 -0.9667 9 0.33141 T 0.24 . 12.9494 0.58391 0.1201:0.0:0.8799:0.0 . 1132;210;1063;1132;1063;1132 Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746 .;.;.;.;.;MYLK_HUMAN M 1132;1132;1132;1063;1132 ENSP00000354004:T1132M;ENSP00000353452:T1132M;ENSP00000352088:T1132M;ENSP00000320622:T1063M;ENSP00000418335:T1132M ENSP00000320622:T1063M T - 2 0 MYLK 124901610 1.000000 0.71417 0.648000 0.29521 0.936000 0.57629 3.938000 0.56583 0.800000 0.34041 0.555000 0.69702 ACG TCGA-FB-AAPU-01A-31D-A40W-08 MYLK-004 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356464.1 1 0 1 148 295 0 127 0 9.926479e-01 0 18 0 127 2 0 0 0 0 0 2 1 1.000000 147 290 0 124 2 -20.000000 1 1 121412 8 39 1 0 0 0 1.997626 0 0.700000 2 0.700000 0.940000 8.200000e-01 1.000000 1.000000 0.946234 0.940000 1 8.800000e-01 1 XRN1 54464 broad.mit.edu 37 3 142094760 142094760 + Missense_Mutation SNP A A C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr3:142094760A>C ENST00000264951.4 - 25 2975 c.2858T>G c.(2857-2859)gTg>gGg p.V953G XRN1_ENST00000392981.2_Missense_Mutation_p.V953G NM_019001.3 NP_061874.3 Q8IZH2 XRN1_HUMAN 5'-3' exoribonuclease 1 61 ATTTAAACCCACATTTGCTTT 0.403000 0 SO:0001583 missense ENST00000264951.4 1 1 hg19 CCDS3123.1 . . . . . . . . . . A 22.9 4.344152 0.82022 . . ENSG00000114127 ENST00000264951;ENST00000392981 T;T 0.37752 1.18;1.18 5.78 5.78 0.91487 . 0.062617 0.64402 D 0.000006 T 0.58104 0.2099 M 0.70275 2.135 0.80722 D 1 D;D 0.69078 0.997;0.995 P;P 0.62649 0.905;0.806 T 0.62315 -0.6880 10 0.87932 D 0 -11.1021 16.0952 0.81114 1.0:0.0:0.0:0.0 . 953;953 Q8IZH2-2;Q8IZH2 .;XRN1_HUMAN G 953 ENSP00000264951:V953G;ENSP00000376707:V953G ENSP00000264951:V953G V - 2 0 XRN1 143577450 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.268000 0.95675 2.209000 0.71365 0.477000 0.44152 GTG TCGA-FB-AAPU-01A-31D-A40W-08 XRN1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000354087.2 1 0 1 63 163 0 96 1 9.101886e-01 6 7 0 96 2 0 0 0 0 0 2 1 1.000000 61 162 0 96 2 -20.000000 1 1 0 0 1 0 0 0 1.997626 0 0.700000 2 0.700000 0.790000 6.300000e-01 0.960000 0.800000 0.800110 0.790000 0 7.100000e-01 8.800000e-01 CCNL1 57018 broad.mit.edu 37 3 156866115 156866115 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr3:156866115C>T ENST00000295926.3 - 11 1614 c.1496G>A c.(1495-1497)cGt>cAt p.R499H CCNL1_ENST00000479052.1_5'Flank|CCNL1_ENST00000461804.1_Intron NM_020307.2 NP_064703.1 Q9UK58 CCNL1_HUMAN cyclin L1 18 LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308) AGATCGTTCACGCCTGTCCCT 0.512000 0 SO:0001583 missense ENST00000295926.3 1 1 hg19 CCDS3178.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 15.15 2.746831 0.49257 0.0 1.16E-4 ENSG00000163660 ENST00000295926 T 0.22945 1.93 5.2 4.32 0.51571 . 0.110120 0.53938 D 0.000041 T 0.24967 0.0606 L 0.54323 1.7 0.80722 D 1 P 0.42584 0.784 B 0.38616 0.277 T 0.03025 -1.1081 10 0.27785 T 0.31 -1.4904 13.7858 0.63108 0.0:0.9257:0.0:0.0743 . 499 Q9UK58 CCNL1_HUMAN H 499 ENSP00000295926:R499H ENSP00000295926:R499H R - 2 0 CCNL1 158348809 0.999000 0.42202 0.844000 0.33320 0.808000 0.45660 4.102000 0.57776 1.314000 0.45095 0.557000 0.71058 CGT TCGA-FB-AAPU-01A-31D-A40W-08 CCNL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351859.1 1 0 1 120 267 0 134 1 1 149 157 0 134 2 0 0 0 0 0 2 1 1.000000 120 260 0 133 2 -20.000000 1 1 121412 2 40 1 0 0 0 1.997626 0 0.700000 2 0.700000 0.880000 7.500000e-01 1.000000 0.880000 0.886264 0.880000 1 8.100000e-01 9.500000e-01 CYP8B1 1582 broad.mit.edu 37 3 42917299 42917299 + Missense_Mutation SNP A A C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr3:42917299A>C ENST00000316161.4 - 1 334 c.10T>G c.(10-12)Tgg>Ggg p.W4G KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.W4G|RP11-141M3.5_ENST00000471537.1_RNA NM_004391.2 NP_004382.2 Q9UNU6 CP8B1_HUMAN cytochrome P450, family 8, subfamily B, polypeptide 1 23 ACTGGACCCCAGAGAACCATG 0.592000 0 SO:0001583 missense ENST00000316161.4 1 1 hg19 CCDS2707.1 . . . . . . . . . . A 14.77 2.634875 0.47049 . . ENSG00000180432 ENST00000437102;ENST00000316161 T;T 0.74947 -0.73;-0.89 4.89 4.89 0.63831 . 0.287902 0.27513 N 0.019032 T 0.71281 0.3321 N 0.08118 0 0.32807 D 0.500855 D;D 0.76494 0.999;0.988 D;P 0.63488 0.915;0.779 T 0.80111 -0.1519 10 0.87932 D 0 -13.3635 13.6159 0.62108 1.0:0.0:0.0:0.0 . 4;4 C9JFR9;Q9UNU6 .;CP8B1_HUMAN G 4 ENSP00000404499:W4G;ENSP00000318867:W4G ENSP00000318867:W4G W - 1 0 CYP8B1 42892303 1.000000 0.71417 0.997000 0.53966 0.298000 0.27526 5.950000 0.70265 2.064000 0.61679 0.459000 0.35465 TGG TCGA-FB-AAPU-01A-31D-A40W-08 CYP8B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256653.1 1 0 0 58 82 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 1.000000 56 82 0 37 2 -20.000000 1 1 0 0 1 0 2 2 1.795195 1 0.700000 2 0.700000 0.990000 9.500000e-01 1.000000 1.000000 0.997571 0.990000 1 9.900000e-01 1 PLK4 10733 broad.mit.edu 37 4 128816239 128816239 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr4:128816239G>C ENST00000270861.5 + 14 2968 c.2694G>C c.(2692-2694)tgG>tgC p.W898C PLK4_ENST00000513090.1_Missense_Mutation_p.W866C|PLK4_ENST00000507249.1_Missense_Mutation_p.W837C|PLK4_ENST00000514379.1_Missense_Mutation_p.W857C|PLK4_ENST00000515069.1_Missense_Mutation_p.W820C NM_014264.4 NP_055079.3 O00444 PLK4_HUMAN polo-like kinase 4 31 ATGTTGGTTGGGCTACACAGG 0.323000 Colon(135;508 1718 19061 31832 42879) 0 SO:0001583 missense ENST00000270861.5 1 1 hg19 CCDS3735.1 . . . . . . . . . . G 14.48 2.548975 0.45383 . . ENSG00000142731 ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379;ENST00000508113 T;T;T;T;T;T 0.11712 2.75;2.75;2.75;2.75;2.75;2.75 5.25 4.37 0.52481 POLO box duplicated domain (2); 0.056561 0.85682 D 0.000000 T 0.12475 0.0303 L 0.35723 1.085 0.80722 D 1 B;B 0.33494 0.01;0.414 B;B 0.38378 0.034;0.272 T 0.06232 -1.0838 10 0.52906 T 0.07 -1.8738 15.0412 0.71793 0.0:0.0:0.8575:0.1425 . 866;898 O00444-2;O00444 .;PLK4_HUMAN C 898;820;866;837;857;144 ENSP00000270861:W898C;ENSP00000421774:W820C;ENSP00000427554:W866C;ENSP00000423412:W837C;ENSP00000423582:W857C;ENSP00000427568:W144C ENSP00000270861:W898C W + 3 0 PLK4 129035689 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 5.950000 0.70265 2.730000 0.93505 0.479000 0.44913 TGG TCGA-FB-AAPU-01A-31D-A40W-08 PLK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257095.3 1 0 1 77 183 0 80 1 9.925636e-01 8 13 0 80 2 0 0 0 0 0 2 1 1.000000 77 181 0 80 2 -6.870145 1 1 0 0 1 1 2 3 2.072253 0 0.700000 2 0.705160 0.860000 7.000000e-01 1.000000 1.000000 0.867412 0.860000 1 7.700000e-01 9.600000e-01 LIMCH1 22998 broad.mit.edu 37 4 41605916 41605916 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr4:41605916G>A ENST00000313860.7 + 5 423 c.369G>A c.(367-369)ctG>ctA p.L123L LIMCH1_ENST00000509638.1_5'UTR|LIMCH1_ENST00000508501.1_Silent_p.L123L|LIMCH1_ENST00000512820.1_Silent_p.L123L|LIMCH1_ENST00000512632.1_Silent_p.L123L|LIMCH1_ENST00000512946.1_Silent_p.L123L|LIMCH1_ENST00000513024.1_5'UTR|LIMCH1_ENST00000503057.1_5'UTR|LIMCH1_ENST00000511496.1_Intron NM_014988.2 NP_055803.2 Q9UPQ0 LIMC1_HUMAN LIM and calponin homology domains 1 41 GTAGGAAGCTGAAAAATGTAA 0.338000 0 SO:0001819 synonymous_variant ENST00000313860.7 1 1 hg19 CCDS33977.1 TCGA-FB-AAPU-01A-31D-A40W-08 LIMCH1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000361249.2 1 0 0 58 115 0 49 1 8.019111e-01 2 6 0 49 2 0 0 0 0 0 2 1 1.000000 57 115 0 48 2 -20.000000 1 1 0 0 1 1 2 3 2.072253 0 0.700000 2 0.705160 0.970000 7.700000e-01 1.000000 1.000000 0.948441 0.970000 1 8.700000e-01 1 FIP1L1 81608 broad.mit.edu 37 4 54248462 54248462 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr4:54248462G>C ENST00000337488.6 + 4 382 c.188G>C c.(187-189)gGa>gCa p.G63A FIP1L1_ENST00000507166.1_Missense_Mutation_p.G63A|FIP1L1_ENST00000510668.1_3'UTR|FIP1L1_ENST00000507922.1_Missense_Mutation_p.G48A|FIP1L1_ENST00000306932.6_Missense_Mutation_p.G48A|FIP1L1_ENST00000358575.5_Missense_Mutation_p.G48A NM_030917.3 NP_112179.2 Q6UN15 FIP1_HUMAN factor interacting with PAPOLA and CPSF1 6 GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134) CCTCCATCTGGAATTGAAGAT 0.333000 T PDGFRA idiopathic hypereosinophilic syndrome Dom yes 4 4q12 81608 FIP1 like 1 (S. cerevisiae) L 0 SO:0001583 missense ENST00000337488.6 1 1 hg19 CCDS3491.1 . . . . . . . . . . G 19.53 3.844491 0.71488 . . ENSG00000145216 ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166 T 0.76578 -1.03 5.48 5.48 0.80851 . 0.000000 0.64402 D 0.000003 D 0.82430 0.5035 L 0.36672 1.1 0.54753 D 0.999984 P;D;B;D 0.76494 0.955;0.999;0.217;0.958 P;D;B;P 0.80764 0.756;0.994;0.189;0.671 T 0.78175 -0.2306 10 0.20519 T 0.43 -21.7326 17.912 0.88937 0.0:0.0:1.0:0.0 . 48;48;63;48 G3XAD6;Q6UN15-3;Q6UN15;Q6UN15-4 .;.;FIP1_HUMAN;. A 63;48;48;48;63 ENSP00000423325:G63A ENSP00000302993:G48A G + 2 0 FIP1L1 53943219 1.000000 0.71417 1.000000 0.80357 0.933000 0.57130 2.540000 0.45727 2.556000 0.86216 0.655000 0.94253 GGA TCGA-FB-AAPU-01A-31D-A40W-08 FIP1L1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000250602.1 1 0 1 55 82 0 59 1 1 52 43 0 59 2 0 0 0 0 0 2 1 1.000000 54 81 0 59 2 -20.000000 1 1 0 0 1 1 2 3 2.072253 0 0.700000 2 0.705160 0.990000 9.300000e-01 1.000000 1.000000 0.995992 0.990000 1 9.900000e-01 1 ADAMTS3 9508 broad.mit.edu 37 4 73205337 73205337 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr4:73205337C>G ENST00000286657.4 - 5 771 c.735G>C c.(733-735)atG>atC p.M245I NM_014243.2 NP_055058.2 O15072 ATS3_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 3 76 Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154) TGCGGCGTCTCATTGTTTCAT 0.488000 NSCLC(168;1941 2048 2918 13048 43078) 0 SO:0001583 missense ENST00000286657.4 1 1 hg19 CCDS3553.1 . . . . . . . . . . C 3.124 -0.179799 0.06380 . . ENSG00000156140 ENST00000286657 T 0.60171 0.21 5.31 1.65 0.23941 . 1.075530 0.07192 N 0.855931 T 0.39572 0.1083 N 0.22421 0.69 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.26087 -1.0113 10 0.39692 T 0.17 . 2.8231 0.05477 0.2577:0.4819:0.1247:0.1357 . 245 O15072 ATS3_HUMAN I 245 ENSP00000286657:M245I ENSP00000286657:M245I M - 3 0 ADAMTS3 73424201 0.001000 0.12720 0.019000 0.16419 0.005000 0.04900 -0.034000 0.12225 0.093000 0.17368 -0.300000 0.09419 ATG TCGA-FB-AAPU-01A-31D-A40W-08 ADAMTS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252164.2 0 0 0 25 694 1 211 0 0 0 1 211 2 0 0 0 0 0 2 1 0.982958 25 687 1 209 13 -2.942243 1 1 0 0 1 1 2 3 2.072253 0 0.700000 2 0.705160 0.090000 6.000000e-02 1.000000 0.100000 0.138766 0.090000 0 7.000000e-02 1.300000e-01 ADAMTS3 9508 broad.mit.edu 37 4 73414444 73414444 + Silent SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr4:73414444C>G ENST00000286657.4 - 3 291 c.255G>C c.(253-255)acG>acC p.T85T ADAMTS3_ENST00000505193.1_5'UTR NM_014243.2 NP_055058.2 O15072 ATS3_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 3 76 Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154) TTCCAAATGCCGTGATGTTAA 0.493000 NSCLC(168;1941 2048 2918 13048 43078) 0 SO:0001819 synonymous_variant ENST00000286657.4 1 1 hg19 CCDS3553.1 TCGA-FB-AAPU-01A-31D-A40W-08 ADAMTS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252164.2 1 0 1 69 151 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 1.000000 69 150 0 60 2 -7.474031 1 1 0 0 1 1 2 3 2.072253 0 0.700000 2 0.705160 0.910000 7.300000e-01 1.000000 1.000000 0.909649 0.910000 1 8.200000e-01 1 TSSK1B 83942 broad.mit.edu 37 5 112769663 112769663 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:112769663G>A ENST00000390666.3 - 1 1065 c.874C>T c.(874-876)Cgg>Tgg p.R292W MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000416046.2_RNA NM_032028.3 NP_114417.1 Q9BXA7 TSSK1_HUMAN testis-specific serine kinase 1B 13 all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156) TCAGTTCCCCGGGAACTCTCC 0.637000 0 SO:0001583 missense ENST00000390666.3 1 1 hg19 CCDS4112.1 . . . . . . . . . . G 10.12 1.263874 0.23136 2.3E-4 0.0 ENSG00000212122 ENST00000390666 T 0.69806 -0.43 1.24 1.24 0.21308 Protein kinase-like domain (1); 0.657886 0.11189 U 0.590072 T 0.43211 0.1237 N 0.08118 0 0.09310 N 1 D 0.65815 0.995 B 0.43445 0.42 T 0.26883 -1.0090 10 0.41790 T 0.15 . 5.7504 0.18144 0.0:0.0:1.0:0.0 . 292 Q9BXA7 TSSK1_HUMAN W 292 ENSP00000375081:R292W ENSP00000375081:R292W R - 1 2 TSSK1B 112797562 0.980000 0.34600 0.001000 0.08648 0.004000 0.04260 4.334000 0.59291 0.653000 0.30826 0.462000 0.41574 CGG TCGA-FB-AAPU-01A-31D-A40W-08 TSSK1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250774.2 1 0 1 47 81 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 1.000000 46 79 0 39 2 -8.080114 1 1 121314 2 34 1 1 2 3 2.010798 0 0.700000 2 0.723247 0.990000 8.900000e-01 1.000000 1.000000 0.992649 0.990000 1 9.900000e-01 1 ZNF608 57507 broad.mit.edu 37 5 123984759 123984759 + Missense_Mutation SNP A A T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:123984759A>T ENST00000306315.5 - 4 1753 c.1318T>A c.(1318-1320)Tct>Act p.S440T ZNF608_ENST00000504926.1_Missense_Mutation_p.S13T NM_020747.2 NP_065798.2 Q9ULD9 ZN608_HUMAN zinc finger protein 608 46 all_cancers(142;0.186)|Prostate(80;0.081) KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221) GCAGCAGCAGACCTCGCTCTC 0.597000 0 SO:0001583 missense ENST00000306315.5 0 1 hg19 CCDS34219.1 . . . . . . . . . . A 12.74 2.027154 0.35797 . . ENSG00000168916 ENST00000504926;ENST00000306315;ENST00000509799;ENST00000513986 T;T 0.45276 0.93;0.9 5.26 5.26 0.73747 . 0.178789 0.50627 D 0.000117 T 0.22166 0.0534 N 0.14661 0.345 0.30518 N 0.768777 B 0.02656 0.0 B 0.06405 0.002 T 0.18304 -1.0341 10 0.08837 T 0.75 -13.6396 9.307 0.37881 0.7225:0.0:0.0:0.2775 . 440 Q9ULD9 ZN608_HUMAN T 13;440;440;440 ENSP00000427657:S13T;ENSP00000307746:S440T ENSP00000307746:S440T S - 1 0 ZNF608 124012658 0.999000 0.42202 0.853000 0.33588 0.600000 0.36913 1.070000 0.30653 1.989000 0.58080 0.445000 0.29226 TCT TCGA-FB-AAPU-01A-31D-A40W-08 ZNF608-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371300.1 1 0 0 11 302 0 61 1 1.251874e-01 2 14 0 61 2 0 0 0 0 0 2 1 0.998322 11 299 0 60 2 -12.025330 1 1 0 0 1 0 0 0 1.992331 0 0.700000 2 0.700000 0.100000 4.000000e-02 0.170000 0.100000 0.108677 0.100000 0 7.000000e-02 1.400000e-01 PCDHB15 56121 broad.mit.edu 37 5 140626038 140626038 + Missense_Mutation SNP T T A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:140626038T>A ENST00000231173.3 + 1 892 c.892T>A c.(892-894)Tca>Aca p.S298T NM_018935.2 NP_061758.1 Q9Y5E8 PCDBF_HUMAN protocadherin beta 15 61 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) AAGCAGCCTTTCAGGAGAAAT 0.403000 0 SO:0001583 missense ENST00000231173.3 0 1 hg19 CCDS4257.1 . . . . . . . . . . t 0.004 -2.283625 0.00251 . . ENSG00000113248 ENST00000231173 T 0.44482 0.92 5.07 2.17 0.27698 Cadherin (4);Cadherin-like (1); . . . . T 0.13927 0.0337 N 0.02357 -0.585 0.09310 N 1 B 0.12630 0.006 B 0.21546 0.035 T 0.36187 -0.9758 9 0.02654 T 1 . 4.5546 0.12130 0.4747:0.0948:0.0:0.4306 . 298 Q9Y5E8 PCDBF_HUMAN T 298 ENSP00000231173:S298T ENSP00000231173:S298T S + 1 0 PCDHB15 140606222 0.004000 0.15560 0.091000 0.20842 0.376000 0.30014 1.902000 0.39848 0.853000 0.35312 -0.669000 0.03829 TCA TCGA-FB-AAPU-01A-31D-A40W-08 PCDHB15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251804.2 0 0 0 10 429 0 98 0 2.126693e-02 0 9 0 98 2 0 0 0 0 0 2 1 0.996845 10 426 0 98 2 -9.530774 1 1 0 0 1 1 2 3 2.593277 1 0.700000 2 0.768786 0.080000 3.000000e-02 1.000000 0.090000 0.200189 0.080000 0 5.000000e-02 1.500000e-01 PCDHGA10 56106 broad.mit.edu 37 5 140793564 140793564 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:140793564C>T ENST00000398610.2 + 1 822 c.822C>T c.(820-822)gaC>gaT p.D274D PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron NM_018913.2|NM_032090.1 NP_061736.1|NP_114479.1 Q9Y5H3 PCDGA_HUMAN protocadherin gamma subfamily A, 10 43 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CCGACAGGGACGAAGGTGCCA 0.458000 0 SO:0001819 synonymous_variant ENST00000398610.2 0 1 hg19 CCDS47292.1 TCGA-FB-AAPU-01A-31D-A40W-08 PCDHGA10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374747.1 1 0 0 8 111 0 20 0 0 0 1 0 20 2 0 0 0 0 0 2 1 0.989825 8 110 0 20 2 -12.657840 1 1 0 0 1 1 2 3 2.593277 1 0.700000 2 0.768786 0.270000 1.200000e-01 1.000000 0.260000 0.361153 0.270000 0 1.800000e-01 4.400000e-01 JAKMIP2 9832 broad.mit.edu 37 5 147040819 147040819 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:147040819G>C ENST00000265272.5 - 3 786 c.319C>G c.(319-321)Cgt>Ggt p.R107G JAKMIP2_ENST00000507386.1_Missense_Mutation_p.R107G|JAKMIP2_ENST00000333010.6_Missense_Mutation_p.R65G NM_001270941.1|NM_014790.4 NP_001257870.1|NP_055605.2 Q96AA8 JKIP2_HUMAN janus kinase and microtubule interacting protein 2 64 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TCTCCATCACGTACCTTCACC 0.557000 0 SO:0001583 missense ENST00000265272.5 1 1 hg19 CCDS4285.1 . . . . . . . . . . G 9.591 1.126056 0.20959 . . ENSG00000176049 ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401 T;T;T 0.35421 1.31;1.31;1.31 4.67 3.71 0.42584 . 0.059973 0.64402 D 0.000003 T 0.24160 0.0585 N 0.24115 0.695 0.38983 D 0.95898 B;B;B;B 0.32396 0.15;0.369;0.369;0.239 B;B;B;B 0.29176 0.045;0.099;0.099;0.099 T 0.23013 -1.0200 10 0.66056 D 0.02 . 12.4034 0.55426 0.0:0.0:0.6863:0.3137 . 65;107;107;107 B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8 .;.;.;JKIP2_HUMAN G 107;107;65;107 ENSP00000421398:R107G;ENSP00000265272:R107G;ENSP00000328989:R65G ENSP00000265272:R107G R - 1 0 JAKMIP2 147021012 1.000000 0.71417 1.000000 0.80357 0.068000 0.16541 4.826000 0.62715 2.529000 0.85273 0.563000 0.77884 CGT TCGA-FB-AAPU-01A-31D-A40W-08 JAKMIP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251941.1 1 0 1 439 435 0 198 0 0 0 0 198 2 0 0 0 0 0 2 1 1.000000 438 429 0 197 2 -20.000000 1 1 0 0 1 1 2 3 2.593277 1 0.700000 2 0.768786 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ADRB2 154 broad.mit.edu 37 5 148206693 148206693 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:148206693C>G ENST00000305988.4 + 1 538 c.299C>G c.(298-300)aCt>aGt p.T100S NM_000024.5 NP_000015 P07550 ADRB2_HUMAN adrenoceptor beta 2, surface 14 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726) AAAATGTGGACTTTTGGCAAC 0.527000 0 SO:0001583 missense ENST00000305988.4 0 1 hg19 CCDS4292.1 . . . . . . . . . . C 0.963 -0.702511 0.03255 . . ENSG00000169252 ENST00000305988 T 0.19105 2.17 5.4 0.158 0.14942 GPCR, rhodopsin-like superfamily (1); 0.415884 0.28459 N 0.015270 T 0.06508 0.0167 N 0.04245 -0.25 0.09310 N 1 B 0.02656 0.0 B 0.06405 0.002 T 0.37549 -0.9701 10 0.09590 T 0.72 . 4.9026 0.13782 0.5116:0.2522:0.1675:0.0686 . 100 P07550 ADRB2_HUMAN S 100 ENSP00000305372:T100S ENSP00000305372:T100S T + 2 0 ADRB2 148186886 0.024000 0.19004 0.917000 0.36280 0.995000 0.86356 0.638000 0.24674 -0.152000 0.11156 0.655000 0.94253 ACT TCGA-FB-AAPU-01A-31D-A40W-08 ADRB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252189.1 0 0 0 9 234 0 50 0 0 0 1 0 50 2 0 0 0 0 0 2 1 0.994030 9 230 0 50 2 -10.688220 1 1 0 0 1 1 2 3 2.593277 1 0.700000 2 0.768786 0.140000 6.000000e-02 1.000000 0.140000 0.251945 0.140000 0 1.000000e-01 2.400000e-01 PLK2 10769 broad.mit.edu 37 5 57750426 57750426 + Nonsense_Mutation SNP A A C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:57750426A>C ENST00000274289.3 - 14 2342 c.2042T>G c.(2041-2043)tTa>tGa p.L681* PLK2_ENST00000502671.1_Intron NM_001252226.1|NM_006622.3 NP_001239155.1|NP_006613.2 Q9NYY3 PLK2_HUMAN polo-like kinase 2 26 all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182) ACATCTTTGTAAGAGCATGTT 0.408000 0 SO:0001587 stop_gained ENST00000274289.3 0 1 hg19 CCDS3974.1 . . . . . . . . . . A 40 8.531226 0.98852 . . ENSG00000145632 ENST00000274289 . . . 5.92 5.92 0.95590 . 0.000000 0.85682 D 0.000000 . . . . . . 0.54753 D 0.999981 . . . . . . . . . . 0.15066 T 0.55 -9.6175 16.3662 0.83325 1.0:0.0:0.0:0.0 . . . . X 681 . ENSP00000274289:L681X L - 2 0 PLK2 57786183 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 6.962000 0.76048 2.274000 0.75844 0.533000 0.62120 TTA TCGA-FB-AAPU-01A-31D-A40W-08 PLK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214150.1 0 0 0 9 259 0 82 1 9.369305e-01 7 134 0 82 2 0 0 0 0 0 2 1 0.994040 9 255 0 80 2 -3.855942 1 1 0 0 1 1 2 3 2.047411 0 0.700000 2 0.704142 0.100000 4.000000e-02 1.000000 0.100000 0.132833 0.100000 0 6.000000e-02 1.500000e-01 F2RL1 2150 broad.mit.edu 37 5 76129526 76129526 + Missense_Mutation SNP G G A rs149001132 TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr5:76129526G>A ENST00000296677.4 + 2 1300 c.1094G>A c.(1093-1095)cGc>cAc p.R365H NM_005242.4 NP_005233 P55085 PAR2_HUMAN coagulation factor II (thrombin) receptor-like 1 p.R365H(1) 13 all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11) CGAAGTGTCCGCACTGTAAAG 0.448000 1 Substitution - Missense(1) SO:0001583 missense ENST00000296677.4 0 1 hg19 CCDS4033.1 . . . . . . . . . . G 16.69 3.192238 0.58017 2.27E-4 0.0 ENSG00000164251 ENST00000296677 T 0.40225 1.04 5.3 4.43 0.53597 . 0.111618 0.64402 D 0.000013 T 0.62405 0.2425 M 0.69823 2.125 0.58432 D 0.999999 D 0.89917 1.0 D 0.91635 0.999 T 0.63726 -0.6572 9 . . . -18.6704 13.8882 0.63721 0.0735:0.0:0.9265:0.0 . 365 P55085 PAR2_HUMAN H 365 ENSP00000296677:R365H . R + 2 0 F2RL1 76165282 1.000000 0.71417 0.640000 0.29408 0.271000 0.26615 9.808000 0.99193 1.236000 0.43740 -0.136000 0.14681 CGC TCGA-FB-AAPU-01A-31D-A40W-08 F2RL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219957.2 0 0 0 7 544 0 229 0 9.071567e-01 0 330 0 229 2 0 0 0 0 0 2 1 0.980211 7 540 0 228 2 -1.762392 0 1 121412 2 38 1 0 1 1 1.320364 1 0.700000 2 0.538462 0.020000 0 0.050000 0.020000 0.026853 0.020000 0 1.000000e-02 4.000000e-02 HACE1 57531 broad.mit.edu 37 6 105198307 105198307 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr6:105198307C>G ENST00000262903.4 - 20 2528 c.2252G>C c.(2251-2253)aGa>aCa p.R751T HACE1_ENST00000369125.2_Missense_Mutation_p.R536T|HACE1_ENST00000517995.1_5'UTR NM_020771.3 NP_065822.2 Q8IYU2 HACE1_HUMAN HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 44 all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202) CTGAATGGCTCTTGTCATTCG 0.368000 0 SO:0001583 missense ENST00000262903.4 1 1 hg19 CCDS5050.1 . . . . . . . . . . C 19.68 3.872626 0.72180 . . ENSG00000085382 ENST00000262903;ENST00000369125 T;T 0.56776 0.44;0.44 5.0 5.0 0.66597 HECT (4); 0.000000 0.85682 D 0.000000 T 0.47210 0.1433 N 0.25286 0.73 0.34010 D 0.651392 B;P;D;D 0.59357 0.347;0.901;0.985;0.981 B;P;D;D 0.69824 0.387;0.453;0.966;0.943 T 0.36456 -0.9747 10 0.17369 T 0.5 . 18.6385 0.91386 0.0:1.0:0.0:0.0 . 536;240;751;404 E9PGP0;B4DFM6;Q8IYU2;Q8IYU2-3 .;.;HACE1_HUMAN;. T 751;536 ENSP00000262903:R751T;ENSP00000358121:R536T ENSP00000262903:R751T R - 2 0 HACE1 105305000 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.358000 0.79466 2.473000 0.83533 0.563000 0.77884 AGA TCGA-FB-AAPU-01A-31D-A40W-08 HACE1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041643.2 1 0 0 12 159 0 54 0 9.527409e-02 1 6 0 54 2 0 0 0 0 0 2 1 0.999196 12 158 0 54 2 -3.319756 1 1 0 0 1 0 2 2 1.969417 1 0.700000 2 0.700000 0.200000 1.100000e-01 0.350000 0.200000 0.221846 0.200000 0 1.500000e-01 2.700000e-01 THBS2 7058 broad.mit.edu 37 6 169639743 169639743 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr6:169639743G>A ENST00000366787.3 - 8 1329 c.1080C>T c.(1078-1080)tgC>tgT p.C360C XXyac-YX65C7_A.2_ENST00000444188.1_RNA NM_003247.2 NP_003238.2 P35442 TSP2_HUMAN thrombospondin 2 111 Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247) ATGGACTGGCGCAGGTTGCAG 0.512000 Esophageal Squamous(91;219 1934 18562 44706) 0 SO:0001819 synonymous_variant ENST00000366787.3 0 1 hg19 CCDS34574.1 TCGA-FB-AAPU-01A-31D-A40W-08 THBS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000105439.1 0 0 0 5 54 0 12 0 9.764975e-01 0 81 0 12 2 0 0 0 0 0 2 1 0.937599 5 53 0 12 2 -5.260740 1 1 121146 1 30 1 1 2 3 2.051905 0 0.700000 2 0.704142 0.260000 1.000000e-01 1.000000 0.240000 0.303608 0.260000 0 1.700000e-01 4.000000e-01 RBM24 221662 broad.mit.edu 37 6 17292038 17292038 + Silent SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr6:17292038C>G ENST00000379052.5 + 4 635 c.399C>G c.(397-399)gtC>gtG p.V133V RBM24_ENST00000318204.5_Silent_p.V88V|RBM24_ENST00000425446.2_Silent_p.V75V|RBM24_ENST00000508508.1_3'UTR NM_001143942.1 NP_001137414.1 Q9BX46 RBM24_HUMAN RNA binding motif protein 24 13 Breast(50;0.0615)|Ovarian(93;0.0733) all_hematologic(90;0.062) all cancers(50;0.131)|Epithelial(50;0.15) CGGGAGTGGTCATTCCACACG 0.542000 0 SO:0001819 synonymous_variant ENST00000379052.5 0 1 hg19 CCDS47378.1 . . . . . . . . . . C 10.36 1.329137 0.24167 . . ENSG00000112183 ENST00000503965 . . . 5.71 1.34 0.21922 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -4.3684 3.4813 0.07603 0.3218:0.4196:0.1748:0.0839 . . . . X 98 . . S + 2 0 RBM24 17400017 0.303000 0.24463 0.997000 0.53966 0.998000 0.95712 -0.217000 0.09253 0.020000 0.15106 0.591000 0.81541 TCA TCGA-FB-AAPU-01A-31D-A40W-08 RBM24-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039946.2 0 0 0 11 522 0 123 0 5.419828e-04 0 2 0 123 2 0 0 0 0 0 2 1 0.998291 11 519 0 120 2 -2.801395 1 1 0 0 1 0 0 0 1.955452 0 0.700000 2 0.695740 0.050000 2.000000e-02 0.100000 0.060000 0.063108 0.050000 0 3.000000e-02 8.000000e-02 DAAM2 23500 broad.mit.edu 37 6 39866704 39866704 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr6:39866704G>A ENST00000398904.2 + 22 2852 c.2670G>A c.(2668-2670)gcG>gcA p.A890A RP11-61I13.3_ENST00000606829.1_RNA|DAAM2_ENST00000274867.4_Silent_p.A890A|RP11-61I13.3_ENST00000430595.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000538976.1_Silent_p.A890A Q86T65 DAAM2_HUMAN dishevelled associated activator of morphogenesis 2 49 Ovarian(28;0.0355)|Colorectal(47;0.196) GCCTGAGAGCGGTGGAGGTGG 0.577000 0 SO:0001819 synonymous_variant ENST00000398904.2 1 1 hg19 CCDS56426.1 TCGA-FB-AAPU-01A-31D-A40W-08 DAAM2-003 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000280648.1 1 0 1 11 41 0 12 0 3.106473e-01 0 5 0 12 2 0 0 0 0 0 2 1 0.998675 11 39 0 12 2 -10.489340 1 1 121040 5 39 1 0 0 0 1.969283 0 0.700000 2 0.695740 0.600000 3.300000e-01 0.930000 0.590000 0.619950 0.600000 0 4.500000e-01 7.700000e-01 KLHL32 114792 broad.mit.edu 37 6 97423967 97423967 + Missense_Mutation SNP A A G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr6:97423967A>G ENST00000369261.4 + 3 481 c.118A>G c.(118-120)Atc>Gtc p.I40V KLHL32_ENST00000544166.1_5'UTR|KLHL32_ENST00000539200.1_Missense_Mutation_p.I40V|KLHL32_ENST00000536676.1_Missense_Mutation_p.I40V NM_052904.3 NP_443136.2 Q96NJ5 KLH32_HUMAN kelch-like family member 32 38 all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122) GAGTGATGGCATCCTCTGCGA 0.507000 0 SO:0001583 missense ENST00000369261.4 0 1 hg19 CCDS5038.1 . . . . . . . . . . A 12.19 1.865093 0.32977 . . ENSG00000186231 ENST00000369261;ENST00000536676;ENST00000539200;ENST00000369254 T;T;T;T 0.66638 -0.22;-0.22;-0.22;-0.22 5.14 3.98 0.46160 BTB/POZ (1);BTB/POZ fold (2); 0.319047 0.33834 N 0.004507 T 0.35158 0.0922 N 0.25201 0.72 0.80722 D 1 B;B;B;B 0.15719 0.0;0.0;0.014;0.008 B;B;B;B 0.19666 0.0;0.0;0.015;0.026 T 0.26744 -1.0094 10 0.30854 T 0.27 . 11.1181 0.48273 0.917:0.0:0.083:0.0 . 40;40;40;40 B7Z4E2;B7Z346;Q96NJ5;Q6IQ08 .;.;KLH32_HUMAN;. V 40 ENSP00000358265:I40V;ENSP00000440382:I40V;ENSP00000441527:I40V;ENSP00000358258:I40V ENSP00000358258:I40V I + 1 0 KLHL32 97530688 0.997000 0.39634 1.000000 0.80357 0.961000 0.63080 2.905000 0.48727 2.159000 0.67721 0.482000 0.46254 ATC TCGA-FB-AAPU-01A-31D-A40W-08 KLHL32-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041570.1 0 0 0 4 118 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.887695 4 116 0 61 2 -7.262399 1 1 0 0 1 0 1 1 1.315272 1 0.700000 2 0.540933 0.060000 1.000000e-02 0.140000 0.060000 0.074769 0.060000 0 3.000000e-02 1.100000e-01 GIMAP1 170575 broad.mit.edu 37 7 150417597 150417597 + Missense_Mutation SNP A A C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr7:150417597A>C ENST00000307194.5 + 3 645 c.505A>C c.(505-507)Aca>Cca p.T169P NM_130759.3 NP_570115.1 Q8WWP7 GIMA1_HUMAN GTPase, IMAP family member 1 28 OV - Ovarian serous cystadenocarcinoma(82;0.0145) CGTGAGCAACACAGAGAACCG 0.647000 0 SO:0001583 missense ENST00000307194.5 1 1 hg19 CCDS5906.1 . . . . . . . . . . A 10.64 1.407461 0.25378 . . ENSG00000213203 ENST00000307194 T 0.60672 0.17 4.81 1.04 0.20106 AIG1 (1); 0.325956 0.28431 U 0.015380 T 0.63307 0.2500 M 0.64170 1.965 0.09310 N 1 P 0.47910 0.902 P 0.61397 0.888 T 0.53493 -0.8431 10 0.56958 D 0.05 . 3.4499 0.07494 0.5502:0.0:0.0968:0.353 . 169 Q8WWP7 GIMA1_HUMAN P 169 ENSP00000302833:T169P ENSP00000302833:T169P T + 1 0 GIMAP1 150048530 0.000000 0.05858 0.008000 0.14137 0.009000 0.06853 0.636000 0.24644 0.033000 0.15463 -0.309000 0.09137 ACA TCGA-FB-AAPU-01A-31D-A40W-08 GIMAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348951.2 1 0 1 87 331 0 60 0 1.962864e-01 0 4 0 60 2 0 0 0 0 0 2 1 1.000000 85 325 0 60 2 -20.000000 1 1 0 0 1 1 2 3 2.507732 1 0.700000 2 0.760383 0.760000 6.100000e-01 1.000000 0.740000 0.797536 0.760000 0 6.800000e-01 1 NOS3 4846 broad.mit.edu 37 7 150699033 150699033 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr7:150699033C>T ENST00000484524.1 + 12 1627 c.1627C>T c.(1627-1629)Cgg>Tgg p.R543W NOS3_ENST00000297494.3_Missense_Mutation_p.R543W|NOS3_ENST00000467517.1_Missense_Mutation_p.R543W|NOS3_ENST00000461406.1_Missense_Mutation_p.R337W NM_001160111.1 NP_001153583.1 P60323 NANO3_HUMAN nitric oxide synthase 3 (endothelial cell) 50 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) GAGACTCTTCCGGAAGGCTTT 0.632000 0 SO:0001583 missense ENST00000484524.1 1 1 hg19 CCDS55182.1 . . . . . . . . . . C 18.61 3.660722 0.67700 . . ENSG00000164867 ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517 T;T;T;T 0.74106 -0.81;-0.81;-0.81;-0.81 4.8 3.9 0.45041 Flavodoxin/nitric oxide synthase (2); 0.118708 0.35772 N 0.002998 D 0.86230 0.5883 M 0.88377 2.95 0.33655 D 0.609001 D;D;D;D;D 0.76494 0.999;0.999;0.988;0.997;0.997 D;D;D;D;P 0.70716 0.917;0.97;0.97;0.948;0.892 D 0.90621 0.4559 10 0.72032 D 0.01 -20.3273 10.4856 0.44719 0.3522:0.6478:0.0:0.0 . 543;543;543;337;543 A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474 .;.;.;.;NOS3_HUMAN W 543;337;543;543 ENSP00000297494:R543W;ENSP00000417143:R337W;ENSP00000420215:R543W;ENSP00000420551:R543W ENSP00000297494:R543W R + 1 2 NOS3 150329966 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 0.991000 0.29654 1.123000 0.41961 0.655000 0.94253 CGG TCGA-FB-AAPU-01A-31D-A40W-08 NOS3-004 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000351550.1 1 0 1 165 212 0 64 0 8.191065e-01 0 6 0 64 2 0 0 0 0 0 2 1 1.000000 164 207 0 63 2 -20.000000 1 1 121398 6 36 1 1 2 3 2.507732 1 0.700000 2 0.760383 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SDK1 221935 broad.mit.edu 37 7 4247761 4247761 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr7:4247761G>A ENST00000404826.2 + 37 5384 c.5245G>A c.(5245-5247)Gaa>Aaa p.E1749K SDK1_ENST00000389531.3_Missense_Mutation_p.E1729K 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) CAGCCAGAACGAAACGGAGAA 0.552000 0 SO:0001583 missense ENST00000404826.2 1 1 hg19 CCDS34590.1 . . . . . . . . . . G 10.26 1.302508 0.23736 . . ENSG00000146555 ENST00000404826;ENST00000389531 T;T 0.53640 0.61;0.61 4.67 3.77 0.43336 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.667620 0.13455 N 0.386599 T 0.41604 0.1166 M 0.66560 2.04 0.28442 N 0.916768 P;B;B 0.37158 0.585;0.034;0.249 B;B;B 0.29524 0.103;0.015;0.082 T 0.33394 -0.9870 10 0.22706 T 0.39 . 12.5036 0.55970 0.0817:0.0:0.9183:0.0 . 1729;236;1749 F8W6X9;F2Z3E9;Q7Z5N4 .;.;SDK1_HUMAN K 1749;1729 ENSP00000385899:E1749K;ENSP00000374182:E1729K ENSP00000374182:E1729K E + 1 0 SDK1 4214287 1.000000 0.71417 0.571000 0.28486 0.426000 0.31534 4.633000 0.61318 2.302000 0.77476 0.655000 0.94253 GAA TCGA-FB-AAPU-01A-31D-A40W-08 SDK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323702.1 1 0 0 16 271 0 44 0 0 0 1 0 44 2 0 0 0 0 0 2 1 0.999936 15 270 0 43 2 -18.313940 1 1 0 0 1 1 2 3 2.068427 0 0.700000 2 0.705160 0.160000 9.000000e-02 1.000000 0.160000 0.202249 0.160000 0 1.200000e-01 2.200000e-01 PEG10 23089 broad.mit.edu 37 7 94293789 94293789 + Missense_Mutation SNP T T A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr7:94293789T>A ENST00000482108.1 + 2 1400 c.921T>A c.(919-921)aaT>aaA p.N307K PEG10_ENST00000488574.1_Missense_Mutation_p.N307K NM_001040152.1|NM_001172438.1|NM_001184962.1 NP_001035242.1|NP_001165909.1|NP_001171891.1 Q86TG7 PEG10_HUMAN paternally expressed 10 21 all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215) STAD - Stomach adenocarcinoma(171;0.0031) ACGCTGACAATTGTCCTGCCA 0.582000 0 SO:0001583 missense ENST00000482108.1 0 1 hg19 CCDS55126.1 . . . . . . . . . . T 10.18 1.279380 0.23307 . . ENSG00000242265 ENST00000482108;ENST00000488574 T;T 0.76186 -1.0;-1.0 4.42 1.51 0.23008 Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (2); . . . . T 0.54013 0.1832 N 0.19112 0.55 0.22684 N 0.998851 B;B 0.13145 0.007;0.001 B;B 0.12156 0.007;0.002 T 0.36163 -0.9759 9 0.29301 T 0.29 . 4.0781 0.09914 0.0:0.5347:0.1743:0.291 . 383;307 B4DSP0;Q86TG7 .;PEG10_HUMAN K 307 ENSP00000417587:N307K;ENSP00000418944:N307K ENSP00000417587:N307K N + 3 2 PEG10 94131725 0.214000 0.23563 0.998000 0.56505 0.920000 0.55202 0.218000 0.17622 0.203000 0.20529 -0.262000 0.10625 AAT TCGA-FB-AAPU-01A-31D-A40W-08 PEG10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340751.1 1 0 1 11 41 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 0.998946 11 41 0 8 2 -20.000000 1 1 0 0 1 2 2 4 3.465305 1 0.700000 2 0.823529 0.990000 5.800000e-01 1.000000 1.000000 0.926655 0.990000 1 7.900000e-01 1 KCNQ3 3786 broad.mit.edu 37 8 133184899 133184899 + Missense_Mutation SNP T T A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr8:133184899T>A ENST00000388996.4 - 7 1506 c.1086A>T c.(1084-1086)caA>caT p.Q362H KCNQ3_ENST00000521134.1_Missense_Mutation_p.Q242H|KCNQ3_ENST00000519445.1_Missense_Mutation_p.Q362H NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) TCTGACGGTGTTGCTCCTGCA 0.587000 0 SO:0001583 missense ENST00000388996.4 1 1 hg19 CCDS34943.1 . . . . . . . . . . T 18.00 3.525173 0.64747 . . ENSG00000184156 ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790 D;D;D 0.99186 -5.52;-5.44;-5.53 5.0 -2.3 0.06785 . 0.000000 0.85682 D 0.000000 D 0.98611 0.9535 L 0.56396 1.775 0.46654 D 0.999145 D;D 0.71674 0.998;0.998 D;D 0.79784 0.993;0.993 D 0.97346 0.9960 10 0.87932 D 0 -21.3538 11.8756 0.52546 0.0:0.3411:0.0:0.6589 . 362;362 E7ET42;O43525 .;KCNQ3_HUMAN H 362;242;362;351;241 ENSP00000373648:Q362H;ENSP00000429799:Q242H;ENSP00000428790:Q362H ENSP00000373648:Q362H Q - 3 2 KCNQ3 133254081 0.890000 0.30428 0.991000 0.47740 0.984000 0.73092 0.009000 0.13219 -0.300000 0.08895 -0.315000 0.08773 CAA TCGA-FB-AAPU-01A-31D-A40W-08 KCNQ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268621.2 1 0 1 157 231 0 79 1 6.687366e-01 2 3 0 79 2 0 0 0 0 0 2 1 1.000000 151 228 0 79 2 -20.000000 1 1 0 0 1 1 2 3 2.284464 1 0.700000 2 0.735216 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ADRA1A 148 broad.mit.edu 37 8 26722090 26722090 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr8:26722090G>A ENST00000519229.1 - 1 403 c.397C>T c.(397-399)Cgc>Tgc p.R133C ADRA1A_ENST00000380572.3_Missense_Mutation_p.R133C|ADRA1A_ENST00000380581.2_Missense_Mutation_p.R133C|ADRA1A_ENST00000380573.3_Missense_Mutation_p.R133C|ADRA1A_ENST00000380582.3_Missense_Mutation_p.R133C|ADRA1A_ENST00000354550.4_Missense_Mutation_p.R133C|ADRA1A_ENST00000380587.1_Missense_Mutation_p.R133C|ADRA1A_ENST00000380586.1_Missense_Mutation_p.R133C|ADRA1A_ENST00000358857.5_Missense_Mutation_p.R133C|ADRA1A_ENST00000276393.4_Missense_Mutation_p.R133C P25100 ADA1D_HUMAN adrenoceptor alpha 1A 36 all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118) 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) GTTGGGTAGCGCAGCGGGTAG 0.617000 0 SO:0001583 missense ENST00000519229.1 1 1 hg19 . . . . . . . . . . G 18.33 3.599366 0.66332 . . ENSG00000120907 ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857 T;T;T;T;T;T;T;T;T;T 0.43294 0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95 4.94 4.94 0.65067 GPCR, rhodopsin-like superfamily (1); 0.058843 0.64402 D 0.000001 T 0.67429 0.2892 M 0.89214 3.015 0.54753 D 0.999985 D;D;D;D;D;D 0.89917 1.0;1.0;0.999;1.0;1.0;1.0 D;D;D;D;D;D 0.75020 0.975;0.975;0.973;0.975;0.95;0.985 T 0.73585 -0.3936 10 0.87932 D 0 . 11.6903 0.51512 0.0:0.0:0.7031:0.2969 . 133;133;133;133;133;133 P35348-9;P35348-8;P35348;P35348-4;P35348-3;B0ZBD3 .;.;ADA1A_HUMAN;.;.;. C 133 ENSP00000369960:R133C;ENSP00000369961:R133C;ENSP00000369956:R133C;ENSP00000369955:R133C;ENSP00000430793:R133C;ENSP00000346557:R133C;ENSP00000276393:R133C;ENSP00000369947:R133C;ENSP00000369946:R133C;ENSP00000351725:R133C ENSP00000276393:R133C R - 1 0 ADRA1A 26778007 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 5.027000 0.64109 2.423000 0.82170 0.563000 0.77884 CGC TCGA-FB-AAPU-01A-31D-A40W-08 ADRA1A-009 PUTATIVE not_organism_supported|basic|exp_conf protein_coding protein_coding OTTHUMT00000376207.1 1 0 1 48 149 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 47 147 0 53 2 -20.000000 1 1 0 0 1 0 1 1 1.873826 1 0.700000 2 0.674973 0.630000 4.900000e-01 0.800000 0.640000 0.647766 0.630000 0 5.600000e-01 7.300000e-01 EXTL3 2137 broad.mit.edu 37 8 28575489 28575489 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr8:28575489C>A ENST00000220562.4 + 3 2815 c.1913C>A c.(1912-1914)cCt>cAt p.P638H EXTL3_ENST00000523149.1_Missense_Mutation_p.P254H|EXTL3_ENST00000519886.1_Intron NM_001440.2 NP_001431.1 O43909 EXTL3_HUMAN exostosin-like glycosyltransferase 3 36 Ovarian(32;0.069) GGCTTTCGGCCTATTGGTGGT 0.557000 0 SO:0001583 missense ENST00000220562.4 1 1 hg19 CCDS6070.1 . . . . . . . . . . C 19.81 3.896758 0.72639 . . ENSG00000012232 ENST00000523149;ENST00000220562 D;D 0.97016 -3.64;-4.21 5.74 5.74 0.90152 . 0.000000 0.85682 D 0.000000 D 0.97999 0.9341 M 0.71206 2.165 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 D 0.98335 1.0535 10 0.87932 D 0 -20.1467 20.2982 0.98569 0.0:1.0:0.0:0.0 . 638 O43909 EXTL3_HUMAN H 254;638 ENSP00000428691:P254H;ENSP00000220562:P638H ENSP00000220562:P638H P + 2 0 EXTL3 28631408 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.567000 0.82357 2.873000 0.98535 0.563000 0.77884 CCT TCGA-FB-AAPU-01A-31D-A40W-08 EXTL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219987.3 1 0 1 72 215 0 86 1 9.989941e-01 14 20 0 86 2 0 0 0 0 0 2 1 1.000000 72 212 0 83 2 -20.000000 1 1 0 0 1 0 1 1 1.873826 1 0.700000 2 0.674973 0.650000 5.300000e-01 0.790000 0.660000 0.665015 0.650000 0 5.900000e-01 7.300000e-01 INTS9 55756 broad.mit.edu 37 8 28717081 28717081 + Splice_Site SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr8:28717081C>A ENST00000521022.1 - 2 91 c.e2-1 INTS9_ENST00000397363.4_Intron|INTS9_ENST00000416984.2_Splice_Site|INTS9_ENST00000521777.1_Splice_Site NM_018250.3 NP_060720.2 Q9NV88 INT9_HUMAN integrator complex subunit 9 19 Ovarian(32;0.0439) ACAGGCAATACTGAAAAAAAT 0.383000 0 SO:0001630 splice_region_variant ENST00000521022.1 1 1 hg19 CCDS34873.1 . . . . . . . . . . C 16.58 3.162573 0.57368 . . ENSG00000104299 ENST00000521022;ENST00000416984;ENST00000541706;ENST00000523436 . . . 4.94 4.94 0.65067 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 18.5649 0.91113 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . INTS9 28773000 1.000000 0.71417 1.000000 0.80357 0.761000 0.43186 7.720000 0.84759 2.456000 0.83038 0.655000 0.94253 . TCGA-FB-AAPU-01A-31D-A40W-08 INTS9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376846.1 1 0 0 29 93 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 1.000000 29 93 0 29 2 -19.986440 1 1 0 0 1 0 1 1 1.873826 1 0.700000 2 0.674973 0.620000 4.400000e-01 0.830000 0.620000 0.635506 0.620000 0 5.200000e-01 7.300000e-01 TEX10 54881 broad.mit.edu 37 9 103090198 103090198 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:103090198G>C ENST00000374902.4 - 8 1848 c.1672C>G c.(1672-1674)Caa>Gaa p.Q558E TEX10_ENST00000535814.1_Missense_Mutation_p.Q561E NM_017746.3 NP_060216.2 Q9NXF1 TEX10_HUMAN testis expressed 10 38 Acute lymphoblastic leukemia(62;0.0527) TGAGCAAGTTGCAATGGTAAG 0.398000 0 SO:0001583 missense ENST00000374902.4 1 1 hg19 CCDS6748.1 . . . . . . . . . . G 25.0 4.593958 0.86953 . . ENSG00000136891 ENST00000535814;ENST00000374902;ENST00000444730 . . . 5.33 5.33 0.75918 . 0.000000 0.85682 D 0.000000 T 0.67097 0.2857 L 0.34521 1.04 0.80722 D 1 D;D;D 0.64830 0.994;0.99;0.993 D;D;P 0.72982 0.97;0.979;0.708 T 0.63171 -0.6697 9 0.29301 T 0.29 -6.3079 19.0215 0.92917 0.0:0.0:1.0:0.0 . 561;426;558 B4DYV2;E7ERG2;Q9NXF1 .;.;TEX10_HUMAN E 561;558;426 . ENSP00000364037:Q558E Q - 1 0 TEX10 102130019 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 8.932000 0.92897 2.494000 0.84150 0.655000 0.94253 CAA TCGA-FB-AAPU-01A-31D-A40W-08 TEX10-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053416.1 1 0 1 63 110 0 53 1 9.999999e-01 28 20 0 53 2 0 0 0 0 0 2 1 1.000000 62 108 0 52 2 -20.000000 1 1 0 0 1 1 2 3 2.013462 0 0.700000 2 0.701046 0.990000 8.400000e-01 1.000000 1.000000 0.977677 0.990000 1 9.300000e-01 1 EPB41L4B 54566 broad.mit.edu 37 9 111970268 111970268 + Missense_Mutation SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:111970268G>A ENST00000374566.3 - 18 2331 c.1814C>T c.(1813-1815)gCg>gTg p.A605V NM_019114.3 NP_061987.3 Q9H329 E41LB_HUMAN erythrocyte membrane protein band 4.1 like 4B 39 CACATGATCCGCAACAGGGGA 0.423000 0 SO:0001583 missense ENST00000374566.3 0 1 hg19 CCDS43859.1 . . . . . . . . . . G 15.03 2.711206 0.48517 0.0 4.86E-4 ENSG00000095203 ENST00000262536;ENST00000374566 D 0.84516 -1.86 5.49 5.49 0.81192 . 0.000000 0.39834 N 0.001248 T 0.78130 0.4235 N 0.22421 0.69 0.80722 D 1 B 0.22541 0.071 B 0.12156 0.007 T 0.75255 -0.3382 10 0.87932 D 0 . 16.9032 0.86118 0.0:0.0:1.0:0.0 . 605 Q9H329 E41LB_HUMAN V 290;605 ENSP00000363694:A605V ENSP00000262536:A290V A - 2 0 EPB41L4B 111010089 0.984000 0.35163 0.130000 0.21974 0.350000 0.29205 4.611000 0.61162 2.583000 0.87209 0.561000 0.74099 GCG TCGA-FB-AAPU-01A-31D-A40W-08 EPB41L4B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053592.1 0 0 0 5 356 1 90 0 0 0 1 90 2 0 0 0 0 0 2 0 0.026078 5 347 1 90 14 -1.970880 0 1 120806 18 46 1 1 2 3 2.013462 0 0.700000 2 0.701046 0.040000 0 0.090000 0.040000 0.047127 0.040000 0 2.000000e-02 7.000000e-02 AMBP 259 broad.mit.edu 37 9 116837247 116837247 + Missense_Mutation SNP G G C TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:116837247G>C ENST00000265132.3 - 3 592 c.330C>G c.(328-330)caC>caG p.H110Q NM_001633.3 NP_001624.1 P02760 AMBP_HUMAN alpha-1-microglobulin/bikunin precursor 11 Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064) TACTGGATTTGTGATAGAGAA 0.438000 0 SO:0001583 missense ENST00000265132.3 1 1 hg19 CCDS6800.1 . . . . . . . . . . G 16.70 3.195027 0.58017 . . ENSG00000106927 ENST00000265132;ENST00000540645 T 0.07444 3.19 5.43 2.45 0.29901 Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1); 0.579014 0.19553 N 0.111528 T 0.19406 0.0466 M 0.83953 2.67 0.37815 D 0.928163 D;D 0.60575 0.988;0.966 P;P 0.56343 0.796;0.617 T 0.05084 -1.0907 10 0.38643 T 0.18 . 4.7856 0.13223 0.1675:0.0:0.6611:0.1713 . 51;110 B7Z8R6;P02760 .;AMBP_HUMAN Q 110;51 ENSP00000265132:H110Q ENSP00000265132:H110Q H - 3 2 AMBP 115877068 0.031000 0.19500 0.934000 0.37439 0.845000 0.48019 0.132000 0.15891 0.686000 0.31488 0.561000 0.74099 CAC TCGA-FB-AAPU-01A-31D-A40W-08 AMBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053758.2 1 0 1 86 212 0 101 1 9.404316e-01 8 6 0 101 2 0 0 0 0 0 2 1 1.000000 85 206 0 100 2 -20.000000 1 1 0 0 1 1 2 3 2.013462 0 0.700000 2 0.701046 0.820000 6.800000e-01 0.980000 0.830000 0.829881 0.820000 0 7.500000e-01 9.100000e-01 ASTN2 23245 broad.mit.edu 37 9 120053699 120053699 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:120053699C>A ENST00000313400.4 - 2 636 c.536G>T c.(535-537)aGc>aTc p.S179I ASTN2_ENST00000373996.3_Missense_Mutation_p.S179I|ASTN2_ENST00000361209.2_Missense_Mutation_p.S179I|ASTN2_ENST00000361477.3_5'UTR O75129 ASTN2_HUMAN astrotactin 2 102 CTGCCCGGAGCTGCTCATGGA 0.592000 0 SO:0001583 missense ENST00000313400.4 1 1 hg19 . . . . . . . . . . C 21.8 4.209137 0.79240 . . ENSG00000148219 ENST00000313400;ENST00000373996;ENST00000361209 T;T;T 0.11495 2.8;2.8;2.77 5.58 5.58 0.84498 . 0.141111 0.56097 D 0.000032 T 0.15046 0.0363 N 0.19112 0.55 0.38032 D 0.935204 P;P;D 0.61080 0.911;0.855;0.989 P;B;P 0.58820 0.563;0.36;0.846 T 0.08126 -1.0737 9 . . . -29.8448 13.1929 0.59722 0.0:0.9271:0.0:0.0729 . 179;179;179 O75129-2;O75129;O75129-3 .;ASTN2_HUMAN;. I 179 ENSP00000314038:S179I;ENSP00000363108:S179I;ENSP00000354504:S179I . S - 2 0 ASTN2 119093520 0.998000 0.40836 1.000000 0.80357 0.998000 0.95712 3.132000 0.50523 2.782000 0.95742 0.655000 0.94253 AGC TCGA-FB-AAPU-01A-31D-A40W-08 ASTN2-201 KNOWN basic protein_coding protein_coding 1 0 1 53 344 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1.000000 52 335 0 68 2 -20.000000 1 1 121410 1 33 1 1 2 3 2.036802 0 0.700000 2 0.702085 0.380000 2.900000e-01 0.500000 0.380000 0.394958 0.380000 0 3.300000e-01 4.400000e-01 CCIN 881 broad.mit.edu 37 9 36170825 36170825 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:36170825C>T ENST00000335119.2 + 1 1437 c.1326C>T c.(1324-1326)gtC>gtT p.V442V NM_005893.2 NP_005884.2 Q13939 CALI_HUMAN calicin 21 STAD - Stomach adenocarcinoma(86;0.228) TCTCCCGGGTCGGGGTAGTGG 0.552000 0 SO:0001819 synonymous_variant ENST00000335119.2 1 1 hg19 CCDS6599.1 TCGA-FB-AAPU-01A-31D-A40W-08 CCIN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052418.1 1 0 1 80 193 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 1.000000 79 187 0 95 2 -20.000000 1 1 121412 2 34 1 0 0 0 1.909640 0 0.700000 2 0.684543 0.790000 6.500000e-01 0.940000 0.800000 0.798856 0.790000 0 7.100000e-01 8.700000e-01 RNF38 152006 broad.mit.edu 37 9 36351123 36351123 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:36351123C>G ENST00000259605.6 - 9 1359 c.1252G>C c.(1252-1254)Gaa>Caa p.E418Q RNF38_ENST00000377885.2_Missense_Mutation_p.E335Q|RNF38_ENST00000350199.4_Missense_Mutation_p.E335Q|RNF38_ENST00000353739.4_Missense_Mutation_p.E368Q|RNF38_ENST00000357058.3_Missense_Mutation_p.E335Q|RNF38_ENST00000377877.4_Missense_Mutation_p.E342Q NM_022781.4 NP_073618.3 Q9H0F5 RNF38_HUMAN ring finger protein 38 11 STAD - Stomach adenocarcinoma(86;0.228) TCGTAATTTTCTACTTCTCCA 0.378000 0 SO:0001583 missense ENST00000259605.6 1 1 hg19 CCDS6603.1 . . . . . . . . . . C 24.1 4.499260 0.85069 . . ENSG00000137075 ENST00000259605;ENST00000353739;ENST00000377885;ENST00000357058;ENST00000350199;ENST00000377876;ENST00000377870;ENST00000377877 T;T;T;T;T;T 0.16073 2.37;2.4;2.41;2.41;2.41;2.42 5.14 5.14 0.70334 . 0.000000 0.85682 D 0.000000 T 0.41534 0.1163 M 0.65498 2.005 0.80722 D 1 D;D;D 0.89917 1.0;0.987;0.999 D;D;D 0.87578 0.998;0.958;0.995 T 0.22138 -1.0225 10 0.66056 D 0.02 -6.4143 16.4624 0.84064 0.0:1.0:0.0:0.0 . 342;368;418 B1AM81;Q9H0F5-2;Q9H0F5 .;.;RNF38_HUMAN Q 418;368;335;335;335;235;342;342 ENSP00000259605:E418Q;ENSP00000335239:E368Q;ENSP00000367117:E335Q;ENSP00000349566:E335Q;ENSP00000343947:E335Q;ENSP00000367109:E342Q ENSP00000259605:E418Q E - 1 0 RNF38 36341123 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.103000 0.77014 2.553000 0.86117 0.563000 0.77884 GAA TCGA-FB-AAPU-01A-31D-A40W-08 RNF38-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000052422.3 1 0 1 20 45 0 26 1 9.965730e-01 13 11 0 26 2 0 0 0 0 0 2 1 0.999998 19 44 0 26 2 -20.000000 1 0 0 0 1 0.700000 2 0 0 RNF38 152006 broad.mit.edu 37 9 36351150 36351150 + Missense_Mutation SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:36351150C>T ENST00000259605.6 - 9 1332 c.1225G>A c.(1225-1227)Gaa>Aaa p.E409K RNF38_ENST00000377885.2_Missense_Mutation_p.E326K|RNF38_ENST00000350199.4_Missense_Mutation_p.E326K|RNF38_ENST00000353739.4_Missense_Mutation_p.E359K|RNF38_ENST00000357058.3_Missense_Mutation_p.E326K|RNF38_ENST00000377877.4_Missense_Mutation_p.E333K NM_022781.4 NP_073618.3 Q9H0F5 RNF38_HUMAN ring finger protein 38 11 STAD - Stomach adenocarcinoma(86;0.228) ACATCTAATTCAAAGCTGAAA 0.358000 0 SO:0001583 missense ENST00000259605.6 1 1 hg19 CCDS6603.1 . . . . . . . . . . C 23.7 4.451466 0.84209 . . ENSG00000137075 ENST00000259605;ENST00000353739;ENST00000377885;ENST00000357058;ENST00000350199;ENST00000377876;ENST00000377870;ENST00000377877 T;T;T;T;T;T 0.54675 0.56;0.56;0.56;0.56;0.56;0.56 5.14 5.14 0.70334 . 0.000000 0.85682 D 0.000000 T 0.51381 0.1671 L 0.40543 1.245 0.80722 D 1 P;B;P 0.47910 0.82;0.38;0.902 P;B;P 0.46110 0.504;0.291;0.504 T 0.54596 -0.8270 10 0.54805 T 0.06 -6.5436 16.4624 0.84064 0.0:1.0:0.0:0.0 . 333;359;409 B1AM81;Q9H0F5-2;Q9H0F5 .;.;RNF38_HUMAN K 409;359;326;326;326;226;333;333 ENSP00000259605:E409K;ENSP00000335239:E359K;ENSP00000367117:E326K;ENSP00000349566:E326K;ENSP00000343947:E326K;ENSP00000367109:E333K ENSP00000259605:E409K E - 1 0 RNF38 36341150 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.061000 0.76699 2.553000 0.86117 0.563000 0.77884 GAA TCGA-FB-AAPU-01A-31D-A40W-08 RNF38-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000052422.3 1 0 1 26 53 0 28 1 9.990121e-01 16 11 0 28 2 0 0 0 0 0 2 1 1.000000 25 53 0 28 2 -20.000000 1 0 0 0 1 0.700000 2 0 0 PCSK5 5125 broad.mit.edu 37 9 78686787 78686787 + Silent SNP G G A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chr9:78686787G>A ENST00000545128.1 + 7 1405 c.867G>A c.(865-867)cgG>cgA p.R289R PCSK5_ENST00000376767.3_Silent_p.R289R|PCSK5_ENST00000376752.4_Silent_p.R289R NM_001190482.1 NP_001177411.1 Q92824 PCSK5_HUMAN proprotein convertase subtilisin/kexin type 5 55 CCCTCACCCGGCAAGCCTTTG 0.507000 0 SO:0001819 synonymous_variant ENST00000545128.1 0 1 hg19 CCDS55320.1 TCGA-FB-AAPU-01A-31D-A40W-08 PCSK5-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 7 651 1 166 0 4.506040e-02 0 27 1 166 2 0 0 0 0 0 2 0 0.062121 7 645 1 165 15 -1.976864 0 1 0 0 1 1 2 3 2.013462 0 0.700000 2 0.701046 0.020000 0 0.070000 0.040000 0.034049 0.020000 0 1.000000e-02 5.000000e-02 RNF128 79589 broad.mit.edu 37 X 105970227 105970227 + Silent SNP C C T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chrX:105970227C>T ENST00000255499.2 + 1 334 c.84C>T c.(82-84)gcC>gcT p.A28A RNF128_ENST00000324342.3_Intron NM_194463.1 NP_919445.1 Q8TEB7 RN128_HUMAN ring finger protein 128, E3 ubiquitin protein ligase 11 TCCTGCTGGCCCTGAGTCCGC 0.711000 0 SO:0001819 synonymous_variant ENST00000255499.2 1 1 hg19 CCDS14521.1 TCGA-FB-AAPU-01A-31D-A40W-08 RNF128-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057804.1 1 0 1 11 27 0 13 1 9.999999e-01 127 0 0 13 2 0 0 0 0 0 2 1 0.998614 11 24 0 13 2 -19.999880 1 1 0 0 1 0 1 1 0.700000 2 0.700000 0.830000 4.700000e-01 1.000000 1.000000 0.819220 0.830000 0 6.300000e-01 1 ACSL4 2182 broad.mit.edu 37 X 108921610 108921610 + Missense_Mutation SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chrX:108921610G>T ENST00000469796.2 - 7 1209 c.813C>A c.(811-813)gaC>gaA p.D271E ACSL4_ENST00000348502.6_Missense_Mutation_p.D230E|ACSL4_ENST00000340800.2_Missense_Mutation_p.D271E O60488 ACSL4_HUMAN acyl-CoA synthetase long-chain family member 4 22 Icosapent(DB00159)|Rosiglitazone(DB00412) CAATGGCCATGTCTGAAGGCG 0.378000 Pancreas(188;358 2127 38547 41466 45492) 0 SO:0001583 missense ENST00000469796.2 1 1 hg19 CCDS14548.1 . . . . . . . . . . G 19.69 3.875527 0.72180 . . ENSG00000068366 ENST00000348502;ENST00000469796;ENST00000340800 T;T;T 0.14893 2.47;2.47;2.47 5.57 3.8 0.43715 AMP-dependent synthetase/ligase (1); 0.000000 0.85682 D 0.000000 T 0.47637 0.1456 M 0.92412 3.305 0.58432 D 0.999997 D 0.89917 1.0 D 0.97110 1.0 T 0.50734 -0.8793 10 0.87932 D 0 -16.4258 8.8404 0.35137 0.2351:0.0:0.7649:0.0 . 271 O60488 ACSL4_HUMAN E 230;271;271 ENSP00000262835:D230E;ENSP00000419171:D271E;ENSP00000339787:D271E ENSP00000339787:D271E D - 3 2 ACSL4 108808266 1.000000 0.71417 0.998000 0.56505 0.997000 0.91878 2.011000 0.40922 0.533000 0.28675 0.600000 0.82982 GAC TCGA-FB-AAPU-01A-31D-A40W-08 ACSL4-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000358155.2 1 0 1 61 359 0 121 1 9.997582e-01 32 42 0 121 2 0 0 0 0 0 2 1 1.000000 60 354 0 120 2 -20.000000 1 1 0 0 1 0 1 1 0.700000 2 0.700000 0.410000 3.200000e-01 0.510000 0.420000 0.419331 0.410000 0 3.600000e-01 4.700000e-01 KIAA1210 57481 broad.mit.edu 37 X 118221500 118221500 + Missense_Mutation SNP C C A TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chrX:118221500C>A ENST00000402510.2 - 11 3692 c.3693G>T c.(3691-3693)aaG>aaT p.K1231N NM_020721.1 NP_065772.1 Q9ULL0 K1210_HUMAN KIAA1210 64 TGACTTCAGGCTTTGATAAAG 0.448000 0 SO:0001583 missense ENST00000402510.2 1 1 hg19 CCDS48156.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 8.176|8.176 0.792717|0.792717 0.16327|0.16327 .|. .|. ENSG00000248857|ENSG00000250423 ENST00000440399|ENST00000402510 .|T .|0.14516 .|2.5 4.38|4.38 -2.02|-2.02 0.07388|0.07388 .|. .|. .|. .|. .|. T|T 0.07052|0.07052 0.0179|0.0179 L|L 0.27053|0.27053 0.805|0.805 0.09310|0.09310 N|N 1|1 .|P .|0.37573 .|0.6 .|B .|0.36289 .|0.221 T|T 0.22977|0.22977 -1.0201|-1.0201 5|9 .|0.40728 .|T .|0.16 .|. 0.6478|0.6478 0.00821|0.00821 0.292:0.2336:0.2834:0.191|0.292:0.2336:0.2834:0.191 .|. .|1231 .|Q9ULL0 .|K1210_HUMAN S|N 638|1231 .|ENSP00000384670:K1231N .|ENSP00000384670:K1231N A|K -|- 1|3 0|2 KIAA1210|RP13-347D8.6 118105528|118105528 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.003000|0.003000 0.03518|0.03518 -0.729000|-0.729000 0.04920|0.04920 -0.638000|-0.638000 0.05509|0.05509 -0.192000|-0.192000 0.12808|0.12808 GCC|AAG TCGA-FB-AAPU-01A-31D-A40W-08 KIAA1210-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371251.2 1 0 1 23 97 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 1.000000 23 97 0 36 2 -20.000000 1 1 0 0 1 0 1 1 0.700000 2 0.700000 0.540000 3.600000e-01 0.760000 0.540000 0.560059 0.540000 0 4.500000e-01 6.600000e-01 CXorf27 0 broad.mit.edu 37 X 37850202 37850202 + Missense_Mutation SNP A A T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chrX:37850202A>T ENST00000341016.3 + 1 133 c.110A>T c.(109-111)cAa>cTa p.Q37L TM4SF2_ENST00000465127.1_Intron NM_012274.1 NP_036406.1 O75409 HYPM_HUMAN 8 CGCGTTGTGCAAGATGAACGA 0.478000 0 SO:0001583 missense ENST00000341016.3 1 1 hg19 CCDS43929.1 . . . . . . . . . . A 14.71 2.616948 0.46736 . . ENSG00000187516 ENST00000341016 T 0.48836 0.8 3.7 -3.49 0.04724 Histone-fold (2); . . . . T 0.53238 0.1784 L 0.48642 1.525 0.09310 N 1 D 0.65815 0.995 D 0.63877 0.919 T 0.52305 -0.8593 9 0.59425 D 0.04 . 9.1117 0.36732 0.443:0.0:0.557:0.0 . 37 O75409 HYPM_HUMAN L 37 ENSP00000339511:Q37L ENSP00000339511:Q37L Q + 2 0 CXorf27 37735146 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 0.197000 0.17197 -0.845000 0.04179 0.417000 0.27973 CAA TCGA-FB-AAPU-01A-31D-A40W-08 CXorf27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080888.1 1 0 1 62 120 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 60 120 0 53 2 -20.000000 1 1 0 0 1 0 1 1 0.700000 2 0.700000 0.960000 7.700000e-01 1.000000 1.000000 0.946865 0.960000 1 8.700000e-01 1 DGKK 139189 broad.mit.edu 37 X 50136189 50136189 + RNA SNP G G T TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chrX:50136189G>T ENST00000376025.2 - 0 1615 Q5KSL6 DGKK_HUMAN diacylglycerol kinase, kappa 45 Ovarian(276;0.236) GAACACTTGAGATGGGTTAAG 0.453000 0 ENST00000376025.2 1 1 hg19 TCGA-FB-AAPU-01A-31D-A40W-08 DGKK-001 KNOWN basic processed_transcript processed_transcript OTTHUMT00000368187.1 0 0 0 7 86 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.979708 7 83 0 23 2 -11.980330 1 1 0 0 1 0 1 1 0.700000 2 0.700000 0.220000 1.000000e-01 0.400000 0.220000 0.239489 0.220000 0 1.500000e-01 3.200000e-01 SHROOM4 57477 broad.mit.edu 37 X 50378166 50378166 + Missense_Mutation SNP C C G TCGA-FB-AAPU-01A-31D-A40W-08 TCGA-FB-AAPU-11A-12D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c40787c-0278-4af4-9040-ab073ef2287b 6d31d43e-5e3f-4c55-a7b2-1188f82ab4f8 g.chrX:50378166C>G ENST00000289292.7 - 4 1190 c.907G>C c.(907-909)Gtc>Ctc p.V303L SHROOM4_ENST00000460112.3_Missense_Mutation_p.V187L|SHROOM4_ENST00000376020.2_Missense_Mutation_p.V303L Q9ULL8 SHRM4_HUMAN shroom family member 4 52 Ovarian(276;0.236) GGCAAGGGGACCACAGGCTCA 0.587000 0 SO:0001583 missense ENST00000289292.7 1 1 hg19 CCDS35277.1 . . . . . . . . . . C 1.010 -0.688151 0.03328 . . ENSG00000158352 ENST00000289292;ENST00000376020;ENST00000460112 T;T;T 0.13538 2.99;2.99;2.58 5.95 5.1 0.69264 . 1.004360 0.08012 N 0.990475 T 0.08492 0.0211 N 0.08118 0 0.09310 N 1 B 0.17667 0.023 B 0.14023 0.01 T 0.32745 -0.9895 10 0.10636 T 0.68 . 13.1671 0.59577 0.0:0.9205:0.0:0.0795 . 303 Q9ULL8 SHRM4_HUMAN L 303;303;187 ENSP00000289292:V303L;ENSP00000365188:V303L;ENSP00000421450:V187L ENSP00000289292:V303L V - 1 0 SHROOM4 50394906 0.001000 0.12720 0.006000 0.13384 0.013000 0.08279 1.313000 0.33585 1.279000 0.44446 0.600000 0.82982 GTC TCGA-FB-AAPU-01A-31D-A40W-08 SHROOM4-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056564.4 1 0 1 23 48 0 21 0 1.110700e-01 0 2 0 21 2 0 0 0 0 0 2 1 1.000000 23 48 0 21 2 -20.000000 1 1 0 0 1 0 1 1 0.700000 2 0.700000 0.920000 6.300000e-01 1.000000 1.000000 0.898603 0.920000 1 7.700000e-01 1