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 OSBPL1A 114876 broad.mit.edu 37 18 21745087 21745087 + Frame_Shift_Del DEL C C - TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr18:21745087delC ENST00000319481.3 - 27 2898 c.2692delG c.(2692-2694)gaafs p.E898fs OSBPL1A_ENST00000357041.4_Frame_Shift_Del_p.E516fs|OSBPL1A_ENST00000399443.3_Frame_Shift_Del_p.E385fs|RP11-799B12.4_ENST00000583267.1_lincRNA NM_080597.3 NP_542164.2 Q9BXW6 OSBL1_HUMAN oxysterol binding protein-like 1A 36 all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17) CTTTGTTTTTCCTCAAGTCGT 0.473000 0 SO:0001589 frameshift_variant ENST00000319481.3 0 1 hg19 CCDS11884.1 TCGA-IB-7646-01A-11D-2154-08 OSBPL1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254902.1 1 0 0 58 1040 0 148 0 9.228337e-01 0 79 0 148 2 0 0 0 0 0 0 1 0.996784 67 1015 2 146 33 -6.859243 1 0 0 0 1 1 2 3 2.061329 1 0.320000 2.940000 0.413793 0.380000 0.280000 0.480000 0.390000 0.388360 0.380000 0 3.300000e-01 4.400000e-01 SLC5A3 6526 broad.mit.edu 37 21 35469260 35469274 + In_Frame_Del DEL ACGGGAAATCTGAAG ACGGGAAATCTGAAG - rs145773467 byFrequency TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr21:35469260_35469274delACGGGAAATCTGAAG ENST00000381151.3 + 2 2275_2289 c.1763_1777delACGGGAAATCTGAAG c.(1762-1779)aacgggaaatctgaagac>aac p.GKSED589del MRPS6_ENST00000399312.2_Intron|AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_In_Frame_Del_p.GKSED589del P53794 SC5A3_HUMAN solute carrier family 5 (sodium/myo-inositol cotransporter), member 3 20 ATCATTCCCAACGGGAAATCTGAAGACAGCATTAA 0.465000 0 SO:0001651 inframe_deletion ENST00000381151.3 1 1 hg19 CCDS33549.1 TCGA-IB-7646-01A-11D-2154-08 SLC5A3-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000141037.1 1 0 0 36 393 0 89 0 9.788634e-01 0 69 0 89 2 0 0 0 0 0 0 1 1.000000 58 413 0 89 2 -10.652510 1 0 0 0 1 0 1 1 1.551330 1 0.320000 2.940000 0.196597 0.440000 0.310000 0.590000 0.440000 0.449816 0.440000 0 3.700000e-01 5.200000e-01 GLRX3 10539 broad.mit.edu 37 10 131959074 131959074 + Silent SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr10:131959074C>T ENST00000368644.1 + 4 313 c.291C>T c.(289-291)atC>atT p.I97I GLRX3_ENST00000331244.5_Silent_p.I97I NM_001199868.1 NP_001186797.1 O76003 GLRX3_HUMAN glutaredoxin 3 13 all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222) CTCAGAAAATCGACCGATTAG 0.378000 0 SO:0001819 synonymous_variant ENST00000368644.1 1 1 hg19 CCDS7661.1 TCGA-IB-7646-01A-11D-2154-08 GLRX3-002 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051021.1 1 0 1 102 202 0 39 1 1 146 59 0 39 2 0 0 0 0 0 2 1 1.000000 99 200 0 39 2 -20.000000 1 1 121412 1 30 1 0 2 2 1.802623 1 0.320000 2.940000 0.320000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ANK3 288 broad.mit.edu 37 10 61833923 61833923 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr10:61833923C>T ENST00000280772.2 - 37 6907 c.6716G>A c.(6715-6717)cGt>cAt p.R2239H ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron NM_020987.3 NP_066267.2 Q12955 ANK3_HUMAN ankyrin 3, node of Ranvier (ankyrin G) 196 TTCTTTAACACGCATGCCTTT 0.413000 0 SO:0001583 missense ENST00000280772.2 1 1 hg19 CCDS7258.1 . . . . . . . . . . C 19.32 3.804751 0.70682 . . ENSG00000151150 ENST00000280772 T 0.67523 -0.27 6.05 6.05 0.98169 . 0.000000 0.42420 D 0.000701 T 0.64000 0.2559 L 0.56769 1.78 0.80722 D 1 P 0.52577 0.954 B 0.36666 0.23 T 0.69262 -0.5191 10 0.54805 T 0.06 . 20.6032 0.99464 0.0:1.0:0.0:0.0 . 2239 Q12955 ANK3_HUMAN H 2239 ENSP00000280772:R2239H ENSP00000280772:R2239H R - 2 0 ANK3 61503929 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 7.811000 0.86092 2.875000 0.98604 0.643000 0.83706 CGT TCGA-IB-7646-01A-11D-2154-08 ANK3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000048201.4 0 0 0 19 649 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 0.999990 20 645 0 90 2 -3.044431 1 1 121412 2 39 1 0 2 2 1.796771 1 0.320000 2.940000 0.320000 0.170000 0.100000 0.270000 0.180000 0.185958 0.170000 0 1.300000e-01 2.300000e-01 SEC24C 9632 broad.mit.edu 37 10 75530836 75530836 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr10:75530836C>T ENST00000339365.2 + 24 3430 c.3268C>T c.(3268-3270)Cgg>Tgg p.R1090W FUT11_ENST00000372841.3_5'Flank|SEC24C_ENST00000540668.1_Missense_Mutation_p.R338W|SEC24C_ENST00000345254.4_Missense_Mutation_p.R1090W|SEC24C_ENST00000535742.1_Missense_Mutation_p.R338W|SEC24C_ENST00000411652.2_Missense_Mutation_p.R971W|FUT11_ENST00000394790.1_5'Flank NM_004922.3 NP_004913.2 P53992 SC24C_HUMAN SEC24 family member C 32 Prostate(51;0.0112) CAAGGAGATTCGGCAGCTACT 0.488000 0 SO:0001583 missense ENST00000339365.2 1 1 hg19 CCDS7332.1 . . . . . . . . . . C 19.88 3.909189 0.72868 . . ENSG00000176986 ENST00000535742;ENST00000345254;ENST00000540668;ENST00000339365;ENST00000411652 T;T;T;T;T 0.32023 1.47;1.47;1.47;1.47;1.47 6.08 6.08 0.98989 . 0.000000 0.85682 D 0.000000 T 0.59662 0.2210 M 0.87456 2.885 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.64410 0.925;0.925 T 0.64132 -0.6479 10 0.66056 D 0.02 -11.7174 15.3963 0.74798 0.1392:0.8608:0.0:0.0 . 971;1090 E7EP00;P53992 .;SC24C_HUMAN W 338;1090;338;1090;971 ENSP00000446174:R338W;ENSP00000321845:R1090W;ENSP00000445023:R338W;ENSP00000343405:R1090W;ENSP00000402913:R971W ENSP00000343405:R1090W R + 1 2 SEC24C 75200842 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.767000 0.62286 2.894000 0.99253 0.591000 0.81541 CGG TCGA-IB-7646-01A-11D-2154-08 SEC24C-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048679.1 1 0 1 185 413 0 102 1 1 64 62 0 102 2 0 0 0 0 0 2 1 1.000000 185 408 0 102 2 -20.000000 1 1 121412 1 37 1 0 2 2 1.796771 1 0.320000 2.940000 0.320000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 DRD2 1813 broad.mit.edu 37 11 113281640 113281640 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr11:113281640C>T ENST00000362072.3 - 8 1485 c.1141G>A c.(1141-1143)Gtg>Atg p.V381M DRD2_ENST00000346454.3_Missense_Mutation_p.V352M|RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000538967.1_Missense_Mutation_p.V383M|DRD2_ENST00000544518.1_Missense_Mutation_p.V380M|DRD2_ENST00000355319.2_Missense_Mutation_p.V383M|DRD2_ENST00000542968.1_Missense_Mutation_p.V381M NM_000795.3 NP_000786.1 P14416 DRD2_HUMAN dopamine receptor D2 39 all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494) Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246) ATGATGAACACGCCTGGGGGA 0.617000 0 SO:0001583 missense ENST00000362072.3 1 0 hg19 CCDS8361.1 . . . . . . . . . . C 22.1 4.250906 0.80135 . . ENSG00000149295 ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967 T;T;T;T;T;T 0.75821 -0.97;-0.97;-0.97;-0.97;-0.97;-0.97 5.66 4.72 0.59763 GPCR, rhodopsin-like superfamily (1); 0.111037 0.64402 D 0.000009 D 0.87947 0.6306 M 0.89095 3.005 0.80722 D 1 D;D;D 0.89917 1.0;0.999;1.0 D;D;D 0.74674 0.984;0.917;0.979 D 0.90416 0.4413 10 0.87932 D 0 . 15.7176 0.77681 0.1378:0.8622:0.0:0.0 . 380;352;381 F8VUV1;P14416-2;P14416 .;.;DRD2_HUMAN M 383;352;381;380;381;383 ENSP00000347474:V383M;ENSP00000278597:V352M;ENSP00000354859:V381M;ENSP00000441068:V380M;ENSP00000442172:V381M;ENSP00000438215:V383M ENSP00000278597:V352M V - 1 0 DRD2 112786850 1.000000 0.71417 0.998000 0.56505 0.554000 0.35429 6.075000 0.71261 1.321000 0.45227 0.655000 0.94253 GTG TCGA-IB-7646-01A-11D-2154-08 DRD2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395834.1 1 0 0 35 257 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 35 249 0 43 2 -20.000000 1 1 121408 4 32 1 1 2 3 2.069473 1 0.320000 2.940000 0.413793 0.870000 0.620000 1.000000 1.000000 0.866728 0.870000 1 7.400000e-01 1 EFEMP2 30008 broad.mit.edu 37 11 65638816 65638816 + Missense_Mutation SNP G G T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr11:65638816G>T ENST00000307998.6 - 4 409 c.179C>A c.(178-180)aCc>aAc p.T60N EFEMP2_ENST00000528176.1_Missense_Mutation_p.T60N NM_016938.4 NP_058634.4 O95967 FBLN4_HUMAN EGF containing fibulin-like extracellular matrix protein 2 21 CTCAGGGATGGTCAGACACTC 0.642000 0 SO:0001583 missense ENST00000307998.6 1 1 hg19 CCDS8116.1 . . . . . . . . . . G 19.36 3.812097 0.70797 . . ENSG00000172638 ENST00000528176;ENST00000307998;ENST00000526624;ENST00000527378 D;D;D;D 0.92199 -2.99;-2.99;-2.99;-2.99 4.93 4.93 0.64822 EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1); 0.000000 0.40640 N 0.001054 D 0.94666 0.8280 M 0.69358 2.11 0.52501 D 0.999956 D;D 0.69078 0.997;0.997 D;P 0.80764 0.994;0.898 D 0.92380 0.5912 10 0.16896 T 0.51 . 15.6604 0.77182 0.0:0.0:1.0:0.0 . 60;60 E9PRU1;O95967 .;FBLN4_HUMAN N 60 ENSP00000434151:T60N;ENSP00000309953:T60N;ENSP00000435419:T60N;ENSP00000435963:T60N ENSP00000309953:T60N T - 2 0 EFEMP2 65395392 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.893000 0.63199 2.553000 0.86117 0.655000 0.94253 ACC TCGA-IB-7646-01A-11D-2154-08 EFEMP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391047.4 1 0 1 72 528 0 92 0 1 0 267 0 92 2 0 0 0 0 0 2 1 1.000000 71 526 0 92 2 -20.000000 1 1 0 0 1 1 2 3 2.069473 1 0.320000 2.940000 0.413793 0.860000 0.690000 1.000000 1.000000 0.871719 0.860000 1 7.700000e-01 9.700000e-01 CTSF 8722 broad.mit.edu 37 11 66333389 66333389 + Missense_Mutation SNP C C A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr11:66333389C>A ENST00000310325.5 - 7 986 c.877G>T c.(877-879)Ggc>Tgc p.G293C ACTN3_ENST00000513398.1_RNA|ACTN3_ENST00000502692.1_RNA|CTSF_ENST00000533168.1_5'Flank NM_003793.3 NP_003784.2 Q9UBX1 CATF_HUMAN cathepsin F 19 CAGCAGGAGCCACACATGCCC 0.622000 0 SO:0001583 missense ENST00000310325.5 1 1 hg19 CCDS8144.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 27.9|27.9 4.870856|4.870856 0.91587|0.91587 .|. .|. ENSG00000174080|ENSG00000174080 ENST00000310325|ENST00000524994 D|. 0.93659|. -3.26|. 5.54|5.54 5.54|5.54 0.83059|0.83059 Peptidase C1A, papain C-terminal (3);|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.90957|0.90957 0.7157|0.7157 H|H 0.99058|0.99058 4.415|4.415 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.97110|. 1.0|. D|D 0.94151|0.94151 0.7405|0.7405 10|5 0.87932|. D|. 0|. .|. 17.339|17.339 0.87291|0.87291 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 293|. Q9UBX1|. CATF_HUMAN|. C|L 293|140 ENSP00000310832:G293C|. ENSP00000310832:G293C|. G|W -|- 1|2 0|0 CTSF|CTSF 66089965|66089965 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.923000|0.923000 0.55619|0.55619 4.866000|4.866000 0.63005|0.63005 2.779000|2.779000 0.95612|0.95612 0.591000|0.591000 0.81541|0.81541 GGC|TGG TCGA-IB-7646-01A-11D-2154-08 CTSF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393047.1 1 0 1 76 174 0 32 0 1 0 119 0 32 2 0 0 0 0 0 2 1 1.000000 74 171 0 31 2 -20.000000 1 1 0 0 1 1 2 3 2.069473 1 0.320000 2.940000 0.413793 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 MRGPRF 116535 broad.mit.edu 37 11 68773653 68773653 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr11:68773653G>A ENST00000309099.6 - 3 507 c.125C>T c.(124-126)cCg>cTg p.P42L MRGPRF_ENST00000441623.1_Missense_Mutation_p.P42L|RP11-554A11.5_ENST00000562506.1_RNA NM_145015.4 NP_659452.3 Q96AM1 MRGRF_HUMAN MAS-related GPR, member F 7 STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713) GGCCGGAGGCGGCAGCATCGC 0.632000 0 SO:0001583 missense ENST00000309099.6 1 1 hg19 CCDS8188.1 . . . . . . . . . . G 13.76 2.332758 0.41297 . . ENSG00000172935 ENST00000441623;ENST00000309099;ENST00000421543 T;T 0.05447 3.44;3.44 4.35 4.35 0.52113 . 0.000000 0.44483 D 0.000457 T 0.08447 0.0210 N 0.19112 0.55 0.09310 N 0.999993 D 0.69078 0.997 P 0.56088 0.791 T 0.36237 -0.9756 10 0.19590 T 0.45 -45.2304 12.2679 0.54689 0.0:0.0:1.0:0.0 . 42 Q96AM1 MRGRF_HUMAN L 42 ENSP00000403660:P42L;ENSP00000309782:P42L ENSP00000309782:P42L P - 2 0 MRGPRF 68530229 0.661000 0.27430 0.135000 0.22099 0.425000 0.31504 1.452000 0.35156 2.261000 0.74972 0.561000 0.74099 CCG TCGA-IB-7646-01A-11D-2154-08 MRGPRF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396875.1 1 0 1 72 193 0 36 0 8.414213e-01 0 11 0 36 2 0 0 0 0 0 2 1 1.000000 70 190 0 35 2 -20.000000 1 1 0 0 1 1 2 3 2.069473 1 0.320000 2.940000 0.413793 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 P2RY6 5031 broad.mit.edu 37 11 73008405 73008405 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr11:73008405C>T ENST00000393590.2 + 2 1141 c.842C>T c.(841-843)gCg>gTg p.A281V P2RY6_ENST00000393592.2_Missense_Mutation_p.A281V|P2RY6_ENST00000393591.1_Missense_Mutation_p.A281V|P2RY6_ENST00000540342.1_Missense_Mutation_p.A281V|P2RY6_ENST00000538328.1_Missense_Mutation_p.A281V|P2RY6_ENST00000349767.2_Missense_Mutation_p.A281V|P2RY6_ENST00000540124.1_Missense_Mutation_p.A281V|P2RY6_ENST00000542092.1_Missense_Mutation_p.A281V NM_001277207.1|NM_001277208.1 NP_001264136.1|NP_001264137.1 Q15077 P2RY6_HUMAN pyrimidinergic receptor P2Y, G-protein coupled, 6 14 GCCTTTGCAGCGGCCTACAAA 0.602000 0 SO:0001583 missense ENST00000393590.2 1 1 hg19 CCDS8220.1 . . . . . . . . . . C 0.097 -1.157720 0.01686 . . ENSG00000171631 ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000538328 T;T;T;T;T;T;T;T 0.12984 2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63 4.81 3.9 0.45041 GPCR, rhodopsin-like superfamily (1); 0.302347 0.31734 N 0.007143 T 0.03608 0.0103 N 0.02247 -0.625 0.09310 N 1 B 0.24651 0.108 B 0.16289 0.015 T 0.41875 -0.9484 10 0.02654 T 1 . 6.2522 0.20852 0.0:0.7162:0.0:0.2838 . 281 Q15077 P2RY6_HUMAN V 281 ENSP00000443427:A281V;ENSP00000445652:A281V;ENSP00000309771:A281V;ENSP00000377217:A281V;ENSP00000377216:A281V;ENSP00000442551:A281V;ENSP00000377215:A281V;ENSP00000442990:A281V ENSP00000309771:A281V A + 2 0 P2RY6 72686053 0.964000 0.33143 0.016000 0.15963 0.306000 0.27790 3.836000 0.55813 1.383000 0.46405 0.655000 0.94253 GCG TCGA-IB-7646-01A-11D-2154-08 P2RY6-007 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397349.1 1 0 1 64 428 0 76 0 1.318110e-01 1 4 0 76 2 0 0 0 0 0 2 1 1.000000 64 419 0 75 2 -20.000000 1 1 121396 2 41 1 1 2 3 2.069473 1 0.320000 2.940000 0.413793 0.940000 0.730000 1.000000 1.000000 0.926770 0.940000 1 8.300000e-01 1 ARHGEF17 9828 broad.mit.edu 37 11 73020596 73020596 + Missense_Mutation SNP G G C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr11:73020596G>C ENST00000263674.3 + 1 1263 c.913G>C c.(913-915)Gac>Cac p.D305H RP11-800A3.7_ENST00000546324.1_RNA NM_014786.3 NP_055601.2 Q96PE2 ARHGH_HUMAN Rho guanine nucleotide exchange factor (GEF) 17 32 ATTGGATCAGGACTGCAGGCC 0.632000 0 SO:0001583 missense ENST00000263674.3 1 1 hg19 CCDS8221.1 . . . . . . . . . . G 9.597 1.127584 0.20959 . . ENSG00000110237 ENST00000263674 T 0.59083 0.29 4.48 2.59 0.31030 . 0.431022 0.17191 N 0.183499 T 0.37812 0.1017 N 0.19112 0.55 0.09310 N 1 B 0.25169 0.119 B 0.26517 0.07 T 0.19679 -1.0298 10 0.29301 T 0.29 -5.789 6.67 0.23064 0.3027:0.0:0.6973:0.0 . 305 Q96PE2 ARHGH_HUMAN H 305 ENSP00000263674:D305H ENSP00000263674:D305H D + 1 0 ARHGEF17 72698244 0.179000 0.23135 0.263000 0.24496 0.767000 0.43475 2.280000 0.43443 0.353000 0.24079 0.313000 0.20887 GAC TCGA-IB-7646-01A-11D-2154-08 ARHGEF17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397365.1 1 0 1 136 319 0 71 0 8.474749e-01 1 9 0 71 2 0 0 0 0 0 2 1 1.000000 135 313 0 69 2 -20.000000 1 1 0 0 1 1 2 3 2.069473 1 0.320000 2.940000 0.413793 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 NUAK1 9891 broad.mit.edu 37 12 106461627 106461627 + Silent SNP G G A rs143829749 TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr12:106461627G>A ENST00000261402.2 - 7 2318 c.939C>T c.(937-939)agC>agT p.S313S NM_014840.2 NP_055655.1 O60285 NUAK1_HUMAN NUAK family, SNF1-like kinase, 1 37 AGTCACACACGCTGCTCTTAT 0.587000 0 SO:0001819 synonymous_variant ENST00000261402.2 1 1 hg19 CCDS31892.1 TCGA-IB-7646-01A-11D-2154-08 NUAK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405767.2 1 0 1 71 264 0 45 1 9.729789e-01 2 22 0 45 2 0 0 0 0 0 2 1 1.000000 71 262 0 45 2 -3.878179 1 1 121412 7 40 1 2 2 4 2.086181 0 0.320000 2.940000 0.434088 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-7646-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 22 82 0 12 1 9.990578e-01 16 30 0 12 2 1 1 123 445 0 404 2 1 1.000000 21 82 0 12 2 -16.436940 1 1 121404 2 44 1 2 2 4 2.071951 0 0.320000 2.940000 0.431058 0.990000 0.990000 1.000000 1.000000 0.999248 0.990000 1 9.900000e-01 1 PRICKLE1 144165 broad.mit.edu 37 12 42854329 42854329 + Missense_Mutation SNP T T C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr12:42854329T>C ENST00000455697.1 - 8 2063 c.1778A>G c.(1777-1779)gAg>gGg p.E593G PRICKLE1_ENST00000552240.1_Missense_Mutation_p.E593G|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.E593G|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.E593G|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.E593G|RP11-328C8.4_ENST00000547824.1_RNA NM_001144882.1|NM_001144883.1 NP_001138354.1|NP_001138355.1 Q96MT3 PRIC1_HUMAN prickle homolog 1 (Drosophila) 47 all_cancers(12;4.25e-05)|Breast(8;0.176) CTTTAAGGACTCTGCACTCCT 0.438000 0 SO:0001583 missense ENST00000455697.1 1 1 hg19 CCDS8742.1 . . . . . . . . . . T 17.03 3.284911 0.59867 . . ENSG00000139174 ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240 T;T;T;T;T 0.69806 -0.43;-0.43;-0.43;-0.43;-0.43 5.56 5.56 0.83823 . 0.198871 0.52532 D 0.000063 T 0.62648 0.2445 L 0.61218 1.895 0.52501 D 0.999951 P 0.36222 0.544 B 0.27887 0.084 T 0.68398 -0.5419 10 0.87932 D 0 -11.3229 16.0186 0.80464 0.0:0.0:0.0:1.0 . 593 Q96MT3 PRIC1_HUMAN G 593 ENSP00000401060:E593G;ENSP00000398947:E593G;ENSP00000448359:E593G;ENSP00000345064:E593G;ENSP00000449819:E593G ENSP00000345064:E593G E - 2 0 PRICKLE1 41140596 1.000000 0.71417 0.989000 0.46669 0.996000 0.88848 4.756000 0.62205 2.244000 0.73946 0.528000 0.53228 GAG TCGA-IB-7646-01A-11D-2154-08 PRICKLE1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404069.1 1 0 1 170 692 0 91 1 9.745311e-01 8 18 0 91 2 1 1 208 474 0 434 2 1 1.000000 166 688 0 91 2 -20.000000 1 1 0 0 1 2 2 4 2.071951 0 0.320000 2.940000 0.431058 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 BEST3 144453 broad.mit.edu 37 12 70048804 70048804 + Missense_Mutation SNP G G C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr12:70048804G>C ENST00000330891.5 - 10 2116 c.1890C>G c.(1888-1890)atC>atG p.I630M BEST3_ENST00000331471.4_Intron|BEST3_ENST00000488961.1_Missense_Mutation_p.I417M|BEST3_ENST00000553096.1_Missense_Mutation_p.I524M NM_001282613.1|NM_032735.2 NP_001269542.1|NP_116124.2 Q8N1M1 BEST3_HUMAN bestrophin 3 12 Breast(13;2.31e-06)|Esophageal squamous(21;0.187) Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694) CCACAATGTTGATCCCACTGA 0.468000 0 SO:0001583 missense ENST00000330891.5 1 1 hg19 CCDS8992.2 . . . . . . . . . . G 10.87 1.473125 0.26423 . . ENSG00000127325 ENST00000488961;ENST00000330891;ENST00000553096 D;D;D 0.98090 -4.39;-4.71;-4.68 5.53 2.67 0.31697 . 0.874202 0.10059 N 0.721139 D 0.94006 0.8080 L 0.32530 0.975 0.09310 N 1 B;B 0.18461 0.022;0.028 B;B 0.19148 0.006;0.024 D 0.88148 0.2849 10 0.44086 T 0.13 -1.6889 5.3228 0.15891 0.2378:0.2019:0.5603:0.0 . 630;417 Q8N1M1;B5MDI8 BEST3_HUMAN;. M 417;630;524 ENSP00000433213:I417M;ENSP00000332413:I630M;ENSP00000449548:I524M ENSP00000332413:I630M I - 3 3 BEST3 68335071 0.078000 0.21339 0.076000 0.20297 0.118000 0.20060 0.955000 0.29188 1.323000 0.45263 0.563000 0.77884 ATC TCGA-IB-7646-01A-11D-2154-08 BEST3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313908.2 1 0 1 89 269 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 1.000000 89 267 0 42 2 -5.269355 1 1 0 0 1 2 2 4 2.084218 0 0.320000 2.940000 0.434088 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ING1 3621 broad.mit.edu 37 13 111368263 111368263 + Missense_Mutation SNP A A G TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr13:111368263A>G ENST00000375774.3 + 1 935 c.473A>G c.(472-474)gAc>gGc p.D158G ING1_ENST00000333219.7_Intron|ING1_ENST00000338450.7_Intron|CARS2_ENST00000535398.1_5'Flank|ING1_ENST00000375775.3_Intron|ING1_ENST00000464141.1_Intron NM_005537.4 NP_005528.3 Q9UK53 ING1_HUMAN inhibitor of growth family, member 1 12 all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148) BRCA - Breast invasive adenocarcinoma(86;0.188) TGCAGTTCGGACCGCCTCCCG 0.711000 0 SO:0001583 missense ENST00000375774.3 1 1 hg19 CCDS9517.1 . . . . . . . . . . A 0.643 -0.812678 0.02798 . . ENSG00000153487 ENST00000375774 T 0.55930 0.49 3.31 -2.11 0.07187 . . . . . T 0.24967 0.0606 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.13019 -1.0525 9 0.31617 T 0.26 . 3.314 0.07026 0.4814:0.0:0.3271:0.1915 . 158 Q9UK53 ING1_HUMAN G 158 ENSP00000364929:D158G ENSP00000364929:D158G D + 2 0 ING1 110166264 0.000000 0.05858 0.000000 0.03702 0.086000 0.17979 -3.845000 0.00352 -0.273000 0.09246 -0.252000 0.11476 GAC TCGA-IB-7646-01A-11D-2154-08 ING1-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000045770.2 1 0 0 62 144 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 1.000000 59 140 0 22 2 -20.000000 1 1 0 0 1 0 2 2 1.787785 1 0.320000 2.940000 0.320000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 MYH6 4624 broad.mit.edu 37 14 23869987 23869987 + Silent SNP G G C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr14:23869987G>C ENST00000356287.3 - 12 1370 c.1341C>G c.(1339-1341)acC>acG p.T447T MYH6_ENST00000405093.3_Silent_p.T447T P13533 MYH6_HUMAN myosin, heavy chain 6, cardiac muscle, alpha 119 all_cancers(95;2.54e-05) TGGTCTCCAGGGTGGCGTTGA 0.582000 0 SO:0001819 synonymous_variant ENST00000356287.3 1 1 hg19 CCDS9600.1 TCGA-IB-7646-01A-11D-2154-08 MYH6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071796.3 1 0 1 55 356 0 65 0 0 0 0 65 2 0 0 0 1 0 0 2 1 1.000000 54 353 0 65 2 -2.966728 1 1 0 0 1 1 2 3 2.050034 1 0.320000 2.940000 0.413793 0.960000 0.740000 1.000000 1.000000 0.940197 0.960000 1 8.500000e-01 1 LTB4R 1241 broad.mit.edu 37 14 24785420 24785420 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr14:24785420C>T ENST00000396789.4 + 2 2288 c.563C>T c.(562-564)aCg>aTg p.T188M LTB4R_ENST00000345363.3_Missense_Mutation_p.T188M|LTB4R_ENST00000396782.2_Missense_Mutation_p.T188M NM_181657.3 NP_858043.1 Q15722 LT4R1_HUMAN leukotriene B4 receptor 8 GAGGCTGTCACGGGCTTCCTG 0.667000 0 SO:0001583 missense ENST00000396789.4 1 1 hg19 CCDS9626.1 . . . . . . . . . . C 15.86 2.957500 0.53400 . . ENSG00000213903 ENST00000345363;ENST00000396789;ENST00000556141;ENST00000396782 T;T;T;T 0.37584 1.19;1.19;1.19;1.19 5.74 5.74 0.90152 GPCR, rhodopsin-like superfamily (1); 0.204720 0.41938 U 0.000790 T 0.37073 0.0990 N 0.25332 0.735 0.35269 D 0.780254 D 0.61697 0.99 P 0.55011 0.766 T 0.41716 -0.9493 10 0.35671 T 0.21 . 10.7916 0.46436 0.0:0.9141:0.0:0.0859 . 188 Q15722 LT4R1_HUMAN M 188;188;88;188 ENSP00000307445:T188M;ENSP00000380008:T188M;ENSP00000451929:T88M;ENSP00000380002:T188M ENSP00000307445:T188M T + 2 0 LTB4R 23855260 0.004000 0.15560 0.997000 0.53966 0.955000 0.61496 1.769000 0.38522 2.709000 0.92574 0.655000 0.94253 ACG TCGA-IB-7646-01A-11D-2154-08 LTB4R-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000073198.4 1 0 1 139 333 0 55 0 5.686495e-01 1 5 0 55 2 0 0 0 0 0 2 1 1.000000 138 329 0 53 2 -20.000000 1 1 0 0 1 1 2 3 2.050034 1 0.320000 2.940000 0.413793 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 LRFN5 145581 broad.mit.edu 37 14 42360832 42360832 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr14:42360832G>A ENST00000298119.4 + 4 2954 c.1765G>A c.(1765-1767)Gtg>Atg p.V589M LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron NM_152447.3 NP_689660.2 Q96NI6 LRFN5_HUMAN leucine rich repeat and fibronectin type III domain containing 5 120 LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728) GCCCCAGTCCGTGTCCAAACA 0.463000 HNSCC(30;0.082) 0 SO:0001583 missense ENST00000298119.4 1 1 hg19 CCDS9678.1 . . . . . . . . . . G 3.589 -0.084060 0.07097 . . ENSG00000165379 ENST00000298119 T 0.46819 0.86 5.95 -8.33 0.00992 . 0.719510 0.12218 N 0.488691 T 0.15435 0.0372 N 0.08118 0 0.33496 D 0.589311 P 0.37370 0.592 B 0.22880 0.042 T 0.20672 -1.0268 10 0.42905 T 0.14 . 7.3406 0.26635 0.2434:0.0993:0.5598:0.0975 . 589 Q96NI6 LRFN5_HUMAN M 589 ENSP00000298119:V589M ENSP00000298119:V589M V + 1 0 LRFN5 41430582 0.000000 0.05858 0.103000 0.21229 0.809000 0.45718 -0.726000 0.04936 -1.450000 0.01936 -0.157000 0.13467 GTG TCGA-IB-7646-01A-11D-2154-08 LRFN5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276786.1 1 0 1 79 251 0 53 0 0 0 1 0 53 2 0 0 0 0 0 2 1 1.000000 78 247 0 53 2 -20.000000 1 1 121412 1 30 1 2 2 4 2.084219 0 0.320000 2.940000 0.441524 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 KLHL28 54813 broad.mit.edu 37 14 45398354 45398354 + Silent SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr14:45398354G>A ENST00000396128.4 - 5 1712 c.1593C>T c.(1591-1593)gtC>gtT p.V531V KLHL28_ENST00000355081.2_Silent_p.V545V NM_017658.3 NP_060128.2 Q9NXS3 KLH28_HUMAN kelch-like family member 28 22 AGTGACCACCGACGACATAAA 0.423000 0 SO:0001819 synonymous_variant ENST00000396128.4 1 1 hg19 CCDS9680.1 TCGA-IB-7646-01A-11D-2154-08 KLHL28-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276790.3 1 0 1 88 516 0 91 0 8.817923e-01 1 23 0 91 2 0 0 0 0 0 2 1 1.000000 87 515 0 89 2 -3.222020 1 1 121410 2 35 1 2 2 4 2.084219 0 0.320000 2.940000 0.441524 0.990000 0.910000 1.000000 1.000000 0.993984 0.990000 1 9.900000e-01 1 CPSF2 53981 broad.mit.edu 37 14 92628035 92628035 + Nonsense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr14:92628035C>T ENST00000298875.4 + 16 2581 c.2296C>T c.(2296-2298)Caa>Taa p.Q766* NM_017437.2 NP_059133.1 Q9P2I0 CPSF2_HUMAN cleavage and polyadenylation specific factor 2, 100kDa 24 all_cancers(154;0.0766) CTGCCTTTGTCAAGATTTTTA 0.318000 Ovarian(78;28 1788 18702 44111) 0 SO:0001587 stop_gained ENST00000298875.4 0 1 hg19 CCDS9902.1 . . . . . . . . . . C 40 8.417780 0.98803 . . ENSG00000165934 ENST00000298875 . . . 5.7 5.7 0.88788 . 0.136439 0.56097 D 0.000038 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.29301 T 0.29 . 14.6844 0.69040 0.0:0.7349:0.265:0.0 . . . . X 766 . ENSP00000298875:Q766X Q + 1 0 CPSF2 91697788 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.426000 0.52778 2.683000 0.91414 0.655000 0.94253 CAA TCGA-IB-7646-01A-11D-2154-08 CPSF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412123.1 1 0 0 39 290 0 34 1 9.999885e-01 11 119 0 34 2 0 0 0 0 0 2 1 1.000000 38 289 0 34 2 -3.221908 1 1 0 0 1 0.320000 2.940000 0 0 TEKT5 146279 broad.mit.edu 37 16 10721628 10721628 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr16:10721628C>T ENST00000283025.2 - 7 1341 c.1270G>A c.(1270-1272)Gac>Aac p.D424N TEKT5_ENST00000574923.1_5'UTR NM_144674.1 NP_653275.1 Q96M29 TEKT5_HUMAN tektin 5 34 TGCAGGGTGTCGTCGATGGTG 0.542000 0 SO:0001583 missense ENST00000283025.2 0 1 hg19 CCDS10542.1 . . . . . . . . . . C 14.95 2.688739 0.48097 . . ENSG00000153060 ENST00000283025 T 0.02525 4.26 5.18 5.18 0.71444 . 0.000000 0.64402 D 0.000009 T 0.04724 0.0128 L 0.49513 1.565 0.58432 D 0.999996 B 0.25521 0.128 B 0.26517 0.07 T 0.43718 -0.9374 10 0.36615 T 0.2 -37.626 15.4575 0.75327 0.0:1.0:0.0:0.0 . 424 Q96M29 TEKT5_HUMAN N 424 ENSP00000283025:D424N ENSP00000283025:D424N D - 1 0 TEKT5 10629129 1.000000 0.71417 0.981000 0.43875 0.308000 0.27856 5.521000 0.67086 2.432000 0.82394 0.505000 0.49811 GAC TCGA-IB-7646-01A-11D-2154-08 TEKT5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251963.1 0 0 0 8 220 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.988761 8 215 0 29 2 -9.566960 1 1 121410 2 31 1 1 3 4 2.076180 1 0.320000 2.940000 0.426451 0.310000 0.130000 1.000000 0.260000 0.456251 0.310000 0 2.000000e-01 1 GTF3C1 2975 broad.mit.edu 37 16 27544625 27544625 + Missense_Mutation SNP A A C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr16:27544625A>C ENST00000356183.4 - 5 851 c.836T>G c.(835-837)cTg>cGg p.L279R GTF3C1_ENST00000561623.1_Missense_Mutation_p.L279R NM_001520.3 NP_001511.2 Q12789 TF3C1_HUMAN general transcription factor IIIC, polypeptide 1, alpha 220kDa 80 CTCTTCCCTCAGCTTTCCCAG 0.552000 0 SO:0001583 missense ENST00000356183.4 1 1 hg19 CCDS32414.1 . . . . . . . . . . A 23.8 4.454282 0.84209 . . ENSG00000077235 ENST00000356183;ENST00000388971 T 0.28069 1.63 5.96 5.96 0.96718 . 0.082944 0.49305 D 0.000153 T 0.45296 0.1335 L 0.29908 0.895 0.48632 D 0.999681 D;D 0.89917 1.0;0.999 D;D 0.77557 0.99;0.981 T 0.43956 -0.9359 10 0.87932 D 0 -3.0653 16.1077 0.81236 1.0:0.0:0.0:0.0 . 279;279 Q12789;Q12789-3 TF3C1_HUMAN;. R 279;277 ENSP00000348510:L279R ENSP00000348510:L279R L - 2 0 GTF3C1 27452126 1.000000 0.71417 1.000000 0.80357 0.788000 0.44548 7.664000 0.83830 2.285000 0.76669 0.528000 0.53228 CTG TCGA-IB-7646-01A-11D-2154-08 GTF3C1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433856.1 1 0 1 91 247 0 59 1 9.999644e-01 19 25 0 59 2 0 0 0 0 0 2 1 1.000000 91 243 0 58 2 -20.000000 1 1 0 0 1 1 3 4 2.095233 1 0.320000 2.940000 0.434088 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CYLD 1540 broad.mit.edu 37 16 50813757 50813757 + Silent SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr16:50813757G>A ENST00000427738.3 + 8 1525 c.1320G>A c.(1318-1320)ctG>ctA p.L440L CYLD_ENST00000398568.2_Silent_p.L437L|CYLD_ENST00000566206.1_Silent_p.L437L|CYLD_ENST00000568704.2_Intron|CYLD_ENST00000564326.1_Silent_p.L437L|CYLD_ENST00000540145.1_Silent_p.L440L|CYLD_ENST00000569418.1_Silent_p.L437L|CYLD_ENST00000311559.9_Silent_p.L440L Q9NQC7 CYLD_HUMAN cylindromatosis (turban tumor syndrome) 62 all_cancers(37;0.0156) CACTTTCTCTGTCAGCCCAGT 0.507000 Mis, N, F, S cylindroma cylindroma Multiple Trichoepithelioma, Familial;Familial Cylindromatosis yes Rec yes Familial cylindromatosis 16 16q12-q13 1540 familial cylindromatosis gene E 0 SO:0001819 synonymous_variant Familial Cancer Database ;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s. ENST00000427738.3 1 1 hg19 CCDS45482.1 TCGA-IB-7646-01A-11D-2154-08 CYLD-010 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000422998.2 1 0 1 83 492 0 108 1 9.930824e-01 14 33 0 108 2 0 0 0 0 0 2 1 1.000000 83 490 0 108 2 -20.000000 1 1 0 0 1 1 3 4 2.095233 1 0.320000 2.940000 0.434088 0.990000 0.880000 1.000000 1.000000 0.990632 0.990000 1 9.900000e-01 1 KRT38 8687 broad.mit.edu 37 17 39596736 39596736 + Silent SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr17:39596736G>A ENST00000246646.3 - 1 437 c.438C>T c.(436-438)acC>acT p.T146T NM_006771.3 NP_006762.3 O76015 KRT38_HUMAN keratin 38 29 Breast(137;0.000496) CGGGGCACACGGTGGACTCGT 0.612000 0 SO:0001819 synonymous_variant ENST00000246646.3 1 1 hg19 CCDS11392.1 TCGA-IB-7646-01A-11D-2154-08 KRT38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257307.2 1 0 1 132 441 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 1.000000 132 436 0 86 2 -4.109453 1 1 121412 1 30 1 2 2 4 2.339107 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 DHX40 79665 broad.mit.edu 37 17 57650476 57650476 + Splice_Site SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr17:57650476G>A ENST00000251241.4 + 4 573 c.e4-1 DHX40_ENST00000451169.2_Splice_Site|DHX40_ENST00000425628.3_Splice_Site NM_024612.4 NP_078888.4 Q8IX18 DHX40_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 40 20 all_neural(34;0.0878)|Medulloblastoma(34;0.0922) TTGAACATTAGGAGACAGCAA 0.368000 0 SO:0001630 splice_region_variant ENST00000251241.4 1 1 hg19 CCDS11617.1 . . . . . . . . . . G 24.1 4.491702 0.84962 . . ENSG00000108406 ENST00000251241;ENST00000538926;ENST00000425628;ENST00000451169 . . . 6.06 6.06 0.98353 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.6208 0.99490 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . DHX40 55005258 1.000000 0.71417 1.000000 0.80357 0.908000 0.53690 9.301000 0.96167 2.882000 0.98803 0.655000 0.94253 . TCGA-IB-7646-01A-11D-2154-08 DHX40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446095.1 1 0 0 185 622 0 82 1 4.169214e-01 6 0 0 82 2 0 0 0 0 0 2 1 1.000000 161 539 0 97 2 -4.495206 1 1 0 0 1 2 2 4 2.320145 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 QRICH2 84074 broad.mit.edu 37 17 74283929 74283929 + Missense_Mutation SNP C C G TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr17:74283929C>G ENST00000262765.5 - 6 3529 c.3350G>C c.(3349-3351)gGg>gCg p.G1117A NM_032134.1 NP_115510.1 Q9H0J4 QRIC2_HUMAN glutamine rich 2 62 CAGTTCCTTCCCTGCTTCTTG 0.562000 0 SO:0001583 missense ENST00000262765.5 1 1 hg19 CCDS32741.1 . . . . . . . . . . C 10.70 1.423478 0.25639 . . ENSG00000129646 ENST00000262765;ENST00000447564;ENST00000301613 T;T 0.61158 2.14;0.13 4.8 2.41 0.29592 . . . . . T 0.52901 0.1763 N 0.20986 0.625 0.09310 N 1 D;D 0.55605 0.972;0.972 P;P 0.58210 0.831;0.835 T 0.34477 -0.9827 9 0.33141 T 0.24 -11.7068 6.6966 0.23203 0.0:0.6871:0.0:0.3129 . 1117;1117 B5MD94;Q9H0J4 .;QRIC2_HUMAN A 1117;125;1117 ENSP00000262765:G1117A;ENSP00000394461:G125A ENSP00000262765:G1117A G - 2 0 QRICH2 71795524 0.004000 0.15560 0.622000 0.29159 0.024000 0.10985 0.401000 0.20948 1.001000 0.39076 0.462000 0.41574 GGG TCGA-IB-7646-01A-11D-2154-08 QRICH2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395140.1 0 0 0 20 451 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 0.999995 18 445 0 71 2 -2.780968 1 1 0 0 1 2 2 4 2.325129 1 0.320000 2.940000 0.484848 0.350000 0.210000 0.520000 0.360000 0.365462 0.350000 0 2.800000e-01 4.400000e-01 TP53 7157 broad.mit.edu 37 17 7577517 7577517 + Missense_Mutation SNP A A G TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 A G A A Valid Somatic Phase_I WXS targeted Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr17:7577517A>G ENST00000269305.4 - 7 953 c.764T>C c.(763-765)aTc>aCc p.I255T TP53_ENST00000445888.2_Missense_Mutation_p.I255T|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.I255T|TP53_ENST00000420246.2_Missense_Mutation_p.I255T|TP53_ENST00000359597.4_Missense_Mutation_p.I255T|TP53_ENST00000413465.2_Missense_Mutation_p.I255T NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.I255S(10)|p.0?(8)|p.I255T(7)|p.I255del(7)|p.I255N(7)|p.I255fs*8(1)|p.?(1)|p.I254fs*7(1)|p.I254_T256del(1)|p.R249_T256delRPILTIIT(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TTCCAGTGTGATGATGGTGAG 0.582000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 44 Substitution - Missense(24)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(2)|Unknown(1) SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . A 16.48 3.136463 0.56936 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D;D 0.99812 -6.88;-6.88;-6.88;-6.88;-6.88;-6.88;-6.88 4.62 4.62 0.57501 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.058771 0.64402 D 0.000004 D 0.99704 0.9887 M 0.82630 2.6 0.58432 D 0.999994 D;D;D;D;D 0.89917 0.999;0.981;0.998;0.999;1.0 D;P;D;D;D 0.87578 0.995;0.901;0.992;0.998;0.997 D 0.97329 0.9949 10 0.87932 D 0 -21.9257 12.3101 0.54924 1.0:0.0:0.0:0.0 . 255;255;255;255;255 P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7 .;.;P53_HUMAN;.;. T 255;255;255;255;255;255;244;123 ENSP00000410739:I255T;ENSP00000352610:I255T;ENSP00000269305:I255T;ENSP00000398846:I255T;ENSP00000391127:I255T;ENSP00000391478:I255T;ENSP00000425104:I123T ENSP00000269305:I255T I - 2 0 TP53 7518242 1.000000 0.71417 0.998000 0.56505 0.393000 0.30537 9.087000 0.94110 2.074000 0.62210 0.379000 0.24179 ATC TCGA-IB-7646-01A-11D-2154-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 59 161 0 49 1 1 67 38 0 49 2 1 1 341 526 0 708 2 1 1.000000 59 161 0 49 2 -20.000000 1 1 0 0 1 0 2 2 1.820247 1 0.320000 2.940000 0.320000 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 OSBPL1A 114876 broad.mit.edu 37 18 21745034 21745034 + Silent SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr18:21745034C>T ENST00000319481.3 - 27 2951 c.2745G>A c.(2743-2745)aaG>aaA p.K915K OSBPL1A_ENST00000357041.4_Silent_p.K533K|OSBPL1A_ENST00000399443.3_Silent_p.K402K|RP11-799B12.4_ENST00000583267.1_lincRNA NM_080597.3 NP_542164.2 Q9BXW6 OSBL1_HUMAN oxysterol binding protein-like 1A 36 all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17) CGCACCTCGTCTTCCAGTCCT 0.522000 0 SO:0001819 synonymous_variant ENST00000319481.3 1 0 hg19 CCDS11884.1 TCGA-IB-7646-01A-11D-2154-08 OSBPL1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254902.1 1 0 0 109 964 0 167 0 9.874380e-01 0 61 0 167 2 0 0 0 0 0 2 1 1.000000 115 948 0 165 2 -20.000000 1 0 0 0 1 1 2 3 2.061329 1 0.320000 2.940000 0.413793 0.730000 0.600000 0.870000 0.730000 0.740882 0.730000 0 6.600000e-01 8.100000e-01 OSBPL1A 114876 broad.mit.edu 37 18 21745037 21745037 + Missense_Mutation SNP C C A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr18:21745037C>A ENST00000319481.3 - 27 2948 c.2742G>T c.(2740-2742)tgG>tgT p.W914C OSBPL1A_ENST00000357041.4_Missense_Mutation_p.W532C|OSBPL1A_ENST00000399443.3_Missense_Mutation_p.W401C|RP11-799B12.4_ENST00000583267.1_lincRNA NM_080597.3 NP_542164.2 Q9BXW6 OSBL1_HUMAN oxysterol binding protein-like 1A 36 all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17) ACCTCGTCTTCCAGTCCTCTT 0.522000 0 SO:0001583 missense ENST00000319481.3 1 0 hg19 CCDS11884.1 . . . . . . . . . . C 22.4 4.290514 0.80914 . . ENSG00000141447 ENST00000319481;ENST00000399443;ENST00000357041 T;T;T 0.41758 0.99;0.99;0.99 5.62 5.62 0.85841 . 0.000000 0.85682 D 0.000000 T 0.78767 0.4335 H 0.97611 4.04 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.86277 0.1665 10 0.87932 D 0 -11.1594 19.6244 0.95672 0.0:1.0:0.0:0.0 . 914 Q9BXW6 OSBL1_HUMAN C 914;401;532 ENSP00000320291:W914C;ENSP00000382372:W401C;ENSP00000349545:W532C ENSP00000320291:W914C W - 3 0 OSBPL1A 19999035 1.000000 0.71417 1.000000 0.80357 0.904000 0.53231 7.783000 0.85696 2.631000 0.89168 0.491000 0.48974 TGG TCGA-IB-7646-01A-11D-2154-08 OSBPL1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254902.1 1 0 0 119 991 0 166 0 9.889558e-01 0 59 0 166 2 0 0 0 0 0 2 1 1.000000 118 971 0 163 2 -20.000000 1 0 0 0 1 1 2 3 2.061329 1 0.320000 2.940000 0.413793 0.770000 0.640000 0.910000 0.780000 0.781353 0.770000 0 7.000000e-01 8.500000e-01 TMEM200C 645369 broad.mit.edu 37 18 5892008 5892008 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr18:5892008G>A ENST00000581347.2 - 3 700 c.55C>T c.(55-57)Cgc>Tgc p.R19C RP11-945C19.4_ENST00000577694.1_RNA|TMEM200C_ENST00000383490.2_Missense_Mutation_p.R19C|RP11-945C19.4_ENST00000580845.1_RNA|RP11-945C19.4_ENST00000582939.1_RNA A6NKL6 T200C_HUMAN transmembrane protein 200C p.R19S(1) 12 CTTGGGGGGCGGAGTGGATCC 0.607000 1 Substitution - Missense(1) SO:0001583 missense ENST00000581347.2 0 1 hg19 CCDS45825.1 . . . . . . . . . . G 17.33 3.361603 0.61403 . . ENSG00000206432 ENST00000383490 . . . 4.3 4.3 0.51218 . 0.061497 0.64402 D 0.000004 T 0.74854 0.3771 M 0.65498 2.005 0.49130 D 0.99975 D 0.89917 1.0 D 0.70935 0.971 T 0.77629 -0.2516 9 0.87932 D 0 -9.4438 12.267 0.54684 0.0:0.0:0.6997:0.3003 . 19 A6NKL6 T200C_HUMAN C 19 . ENSP00000372982:R19C R - 1 0 TMEM200C 5882008 1.000000 0.71417 0.999000 0.59377 0.981000 0.71138 2.903000 0.48711 2.376000 0.81061 0.557000 0.71058 CGC TCGA-IB-7646-01A-11D-2154-08 TMEM200C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000441917.4 1 0 1 18 127 0 17 0 8.514661e-02 0 4 0 17 2 0 0 0 0 0 2 1 0.999986 18 126 0 17 2 -3.080264 1 1 0 0 1 1 2 3 2.061329 1 0.320000 2.940000 0.413793 0.900000 0.560000 1.000000 1.000000 0.878285 0.900000 1 7.200000e-01 1 TMEM38A 79041 broad.mit.edu 37 19 16797152 16797152 + Missense_Mutation SNP G G A rs78725797 TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr19:16797152G>A ENST00000187762.2 + 5 699 c.608G>A c.(607-609)cGc>cAc p.R203H NM_024074.1 NP_076979.1 Q9H6F2 TM38A_HUMAN transmembrane protein 38A 15 CAGCAGACCCGCTGGCTCCCA 0.562000 0 SO:0001583 missense ENST00000187762.2 0 1 hg19 CCDS12349.1 . . . . . . . . . . g 9.106 1.005306 0.19199 2.27E-4 0.0 ENSG00000072954 ENST00000187762 . . . 4.87 3.84 0.44239 . 0.110837 0.64402 D 0.000011 T 0.15349 0.0370 N 0.00869 -1.13 0.36185 D 0.849713 B 0.11235 0.004 B 0.08055 0.003 T 0.09907 -1.0653 9 0.33940 T 0.23 -42.5728 5.1808 0.15160 0.2785:0.0:0.7215:0.0 . 203 Q9H6F2 TM38A_HUMAN H 203 . ENSP00000187762:R203H R + 2 0 TMEM38A 16658152 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.170000 0.58229 2.257000 0.74773 0.655000 0.94253 CGC TCGA-IB-7646-01A-11D-2154-08 TMEM38A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462841.1 0 0 0 5 191 0 31 0 5.367631e-02 0 12 0 31 2 0 0 0 0 0 2 1 0.936663 5 189 0 31 2 -3.148671 1 1 121412 2 34 1 2 2 4 1.832396 0 0.320000 2.940000 0.357035 0.190000 0.060000 1.000000 0.170000 0.309946 0.190000 0 1.200000e-01 3.800000e-01 CKM 1158 broad.mit.edu 37 19 45818781 45818781 + Silent SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr19:45818781C>T ENST00000221476.3 - 4 597 c.423G>A c.(421-423)acG>acA p.T141T NM_001824.4 NP_001815.2 P06732 KCRM_HUMAN creatine kinase, muscle 17 Ovarian(192;0.0336)|all_neural(266;0.112) Creatine(DB00148) GTGGGGGCAACGTGTAGCCCT 0.682000 0 SO:0001819 synonymous_variant ENST00000221476.3 1 1 hg19 CCDS12659.1 TCGA-IB-7646-01A-11D-2154-08 CKM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457569.1 1 0 0 21 124 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 0.999999 21 123 0 18 2 -20.000000 1 1 121344 20 43 1 2 2 4 1.858363 1 0.320000 2.940000 0.364723 0.990000 0.640000 1.000000 1.000000 0.930601 0.990000 1 8.100000e-01 1 MYH14 79784 broad.mit.edu 37 19 50812427 50812427 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr19:50812427C>T ENST00000596571.1 + 39 5830 c.5830C>T c.(5830-5832)Cgg>Tgg p.R1944W MYH14_ENST00000440075.2_Missense_Mutation_p.R1985W|MYH14_ENST00000425460.1_Missense_Mutation_p.R1952W|MYH14_ENST00000601313.1_Missense_Mutation_p.R1985W|MYH14_ENST00000376970.2_Missense_Mutation_p.R1977W|MYH14_ENST00000262269.8_Missense_Mutation_p.R1985W|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000598205.1_Missense_Mutation_p.R1952W Q7Z406 MYH14_HUMAN myosin, heavy chain 14, non-muscle 46 all_neural(266;0.0571)|Ovarian(192;0.0728) ACTGAGGAACCGGCTTCGGTA 0.642000 0 SO:0001583 missense ENST00000596571.1 1 1 hg19 CCDS59411.1 . . . . . . . . . . C 15.51 2.854163 0.51270 0.0 1.18E-4 ENSG00000105357 ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 3.69 1.35 0.21983 Myosin tail (1); . . . . D 0.83482 0.5264 L 0.58510 1.815 0.30649 N 0.755608 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.76071 0.968;0.987;0.978 T 0.78743 -0.2085 9 0.87932 D 0 . 9.3434 0.38093 0.5854:0.4146:0.0:0.0 . 1985;1944;1952 Q7Z406-2;Q7Z406;Q7Z406-6 .;MYH14_HUMAN;. W 1985;1977;1952;1728;1985 ENSP00000406273:R1985W;ENSP00000366169:R1977W;ENSP00000407879:R1952W;ENSP00000262269:R1985W ENSP00000262269:R1985W R + 1 2 MYH14 55504239 0.000000 0.05858 1.000000 0.80357 0.770000 0.43624 -0.299000 0.08254 0.293000 0.22520 0.313000 0.20887 CGG TCGA-IB-7646-01A-11D-2154-08 MYH14-008 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000464710.2 1 0 1 48 322 0 79 1 7.762845e-01 11 10 0 79 2 0 0 0 0 0 2 1 1.000000 48 318 0 79 2 -2.807013 1 1 0 0 1 2 2 4 1.858363 1 0.320000 2.940000 0.364723 0.890000 0.660000 1.000000 1.000000 0.888921 0.890000 1 7.600000e-01 1 ADAMTS10 81794 broad.mit.edu 37 19 8666006 8666006 + Missense_Mutation SNP G G T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr19:8666006G>T ENST00000597188.1 - 6 886 c.616C>A c.(616-618)Cca>Aca p.P206T ADAMTS10_ENST00000270328.4_Missense_Mutation_p.P206T|ADAMTS10_ENST00000596709.1_5'UTR NM_030957.2 NP_112219.3 Q9H324 ATS10_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 10 53 AGCCACCATGGCCGCCCTTTC 0.627000 0 SO:0001583 missense ENST00000597188.1 1 1 hg19 CCDS12206.1 . . . . . . . . . . G 11.83 1.757132 0.31137 . . ENSG00000142303 ENST00000270328 T 0.59502 0.26 5.47 5.47 0.80525 . 0.254626 0.32401 N 0.006146 T 0.47210 0.1433 L 0.34521 1.04 0.28790 N 0.899372 B 0.06786 0.001 B 0.08055 0.003 T 0.24621 -1.0155 10 0.12766 T 0.61 . 18.3275 0.90259 0.0:0.0:1.0:0.0 . 206 Q9H324 ATS10_HUMAN T 206 ENSP00000270328:P206T ENSP00000270328:P206T P - 1 0 ADAMTS10 8572006 1.000000 0.71417 1.000000 0.80357 0.648000 0.38561 3.922000 0.56462 2.575000 0.86900 0.555000 0.69702 CCA TCGA-IB-7646-01A-11D-2154-08 ADAMTS10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000460085.3 1 0 1 33 179 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 1.000000 32 175 0 32 2 -20.000000 1 1 0 0 1 2 2 4 1.862622 1 0.320000 2.940000 0.366617 0.990000 0.750000 1.000000 1.000000 0.966347 0.990000 1 9.000000e-01 1 USH2A 7399 broad.mit.edu 37 1 216496975 216496975 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr1:216496975C>T ENST00000307340.3 - 8 1777 c.1391G>A c.(1390-1392)cGt>cAt p.R464H USH2A_ENST00000366943.2_Missense_Mutation_p.R464H|USH2A_ENST00000366942.3_Missense_Mutation_p.R464H NM_206933.2 NP_996816 O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 527 GTATCCAGGACGATAATTTGG 0.373000 HNSCC(13;0.011) 0 SO:0001583 missense ENST00000307340.3 1 1 hg19 CCDS31025.1 . . . . . . . . . . C 32 5.143821 0.94603 . . ENSG00000042781 ENST00000307340;ENST00000366943;ENST00000366942 T;T;T 0.25579 2.16;2.15;1.79 5.23 5.23 0.72850 Laminin, N-terminal (3); 0.000000 0.42420 D 0.000719 T 0.61986 0.2391 M 0.91920 3.255 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.987;1.0 T 0.72093 -0.4394 10 0.87932 D 0 . 18.8157 0.92076 0.0:1.0:0.0:0.0 . 464;464 O75445-2;O75445 .;USH2A_HUMAN H 464 ENSP00000305941:R464H;ENSP00000355910:R464H;ENSP00000355909:R464H ENSP00000305941:R464H R - 2 0 USH2A 214563598 1.000000 0.71417 0.994000 0.49952 0.975000 0.68041 5.485000 0.66850 2.424000 0.82194 0.655000 0.94253 CGT TCGA-IB-7646-01A-11D-2154-08 USH2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128138.1 1 0 1 179 648 0 82 0 0 0 0 82 2 0 0 0 0 0 2 1 1.000000 179 641 0 82 2 -20.000000 1 1 121410 3 41 1 3 3 6 2.355163 1 0.320000 2.940000 0.499411 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 OR1C1 26188 broad.mit.edu 37 1 247920822 247920822 + Missense_Mutation SNP T T C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr1:247920822T>C ENST00000408896.2 - 1 1160 c.887A>G c.(886-888)gAt>gGt p.D296G NM_012353.2 NP_036485.2 Q15619 OR1C1_HUMAN olfactory receptor, family 1, subfamily C, member 1 46 all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858) all_cancers(173;0.0247) OV - Ovarian serous cystadenocarcinoma(106;0.0168) CCTCTTCATATCCCTGTTCCT 0.428000 0 SO:0001583 missense ENST00000408896.2 1 1 hg19 CCDS41481.1 . . . . . . . . . . T 9.331 1.060439 0.19987 . . ENSG00000221888 ENST00000408896 T 0.39592 1.07 3.22 0.691 0.18045 . . . . . T 0.59500 0.2198 M 0.70903 2.155 0.09310 N 1 D 0.89917 1.0 D 0.76071 0.987 T 0.49854 -0.8895 9 0.87932 D 0 . 9.657 0.39932 0.0:0.0:0.3383:0.6617 . 296 Q15619 OR1C1_HUMAN G 296 ENSP00000386138:D296G ENSP00000386138:D296G D - 2 0 OR1C1 245987445 0.376000 0.25098 0.048000 0.18961 0.024000 0.10985 2.018000 0.40991 0.017000 0.15025 -1.419000 0.01111 GAT TCGA-IB-7646-01A-11D-2154-08 OR1C1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096855.1 1 0 1 143 560 0 82 0 0 0 0 82 2 0 0 0 0 0 2 1 1.000000 143 554 0 82 2 -20.000000 1 1 0 0 1 2 2 4 2.321657 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 MATN4 8785 broad.mit.edu 37 20 43933094 43933094 + Silent SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr20:43933094C>T ENST00000372754.1 - 2 425 c.417G>A c.(415-417)ccG>ccA p.P139P RBPJL_ENST00000343694.3_5'Flank|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000537548.1_Silent_p.P139P|MATN4_ENST00000353917.5_Silent_p.P139P|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000372756.1_Silent_p.P139P|MATN4_ENST00000342716.4_Silent_p.P139P|MATN4_ENST00000360607.6_Silent_p.P139P|RBPJL_ENST00000372741.3_5'Flank O95460 MATN4_HUMAN matrilin 4 27 Myeloproliferative disorder(115;0.0122) CAGCGACACGCGGCACGCGCT 0.701000 0 SO:0001819 synonymous_variant ENST00000372754.1 1 1 hg19 TCGA-IB-7646-01A-11D-2154-08 MATN4-002 KNOWN non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000080335.1 1 0 1 32 65 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 1.000000 31 65 0 12 2 -20.000000 1 1 119296 1 25 1 2 2 4 2.292060 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TSHZ2 128553 broad.mit.edu 37 20 51870106 51870106 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr20:51870106G>A ENST00000371497.5 + 2 996 c.109G>A c.(109-111)Ggt>Agt p.G37S TSHZ2_ENST00000603338.2_Missense_Mutation_p.G34S|TSHZ2_ENST00000329613.6_Missense_Mutation_p.G34S|RP4-678D15.1_ENST00000606932.1_RNA NM_001193421.1|NM_173485.5 NP_001180350.1|NP_775756.3 Q9NRE2 TSH2_HUMAN teashirt zinc finger homeobox 2 84 STAD - Stomach adenocarcinoma(23;0.1) ggaggaCAGCGGTTCAGTAGC 0.532000 0 SO:0001583 missense ENST00000371497.5 1 1 hg19 CCDS33490.1 . . . . . . . . . . G 5.295 0.239845 0.10023 0.0 1.16E-4 ENSG00000182463 ENST00000371497;ENST00000329613 T;T 0.14022 2.55;2.54 5.7 4.66 0.58398 . 0.302267 0.35615 N 0.003083 T 0.08670 0.0215 L 0.29908 0.895 0.30185 N 0.800061 B 0.19200 0.034 B 0.08055 0.003 T 0.04900 -1.0919 10 0.48119 T 0.1 -17.7222 3.7522 0.08570 0.3374:0.0:0.6626:0.0 . 37 Q9NRE2 TSH2_HUMAN S 37;34 ENSP00000360552:G37S;ENSP00000333114:G34S ENSP00000333114:G34S G + 1 0 TSHZ2 51303513 0.992000 0.36948 0.935000 0.37517 0.345000 0.29048 2.759000 0.47573 2.685000 0.91497 0.643000 0.83706 GGT TCGA-IB-7646-01A-11D-2154-08 TSHZ2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080398.6 1 0 1 46 162 0 23 0 5.607157e-01 1 7 0 23 2 0 0 0 0 0 2 1 1.000000 46 161 0 23 2 -20.000000 1 1 121412 5 38 1 2 2 4 2.292060 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 PHACTR3 116154 broad.mit.edu 37 20 58342409 58342409 + Missense_Mutation SNP C C T rs139799389 byFrequency TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr20:58342409C>T ENST00000371015.1 + 5 1177 c.710C>T c.(709-711)cCg>cTg p.P237L PHACTR3_ENST00000395639.4_Intron|PHACTR3_ENST00000355648.4_Missense_Mutation_p.P196L|PHACTR3_ENST00000361300.4_Intron|PHACTR3_ENST00000359926.3_Missense_Mutation_p.P234L|PHACTR3_ENST00000541461.1_Missense_Mutation_p.P196L|PHACTR3_ENST00000395636.2_Missense_Mutation_p.P196L NM_001281507.1|NM_080672.3 NP_001268436.1|NP_542403.1 Q96KR7 PHAR3_HUMAN phosphatase and actin regulator 3 59 all_lung(29;0.00344) BRCA - Breast invasive adenocarcinoma(7;2.76e-09) CTGCCCACTCCGCCACCCAAG 0.587000 0 SO:0001583 missense ENST00000371015.1 1 0 hg19 CCDS13480.1 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 C 14.73 2.621533 0.46736 2.27E-4 0.00186 ENSG00000087495 ENST00000359926;ENST00000371015;ENST00000541461;ENST00000355648;ENST00000395636 T;T;T;T;T 0.23147 1.92;1.93;1.93;1.93;1.93 4.7 4.7 0.59300 . 0.109577 0.64402 D 0.000006 T 0.24774 0.0601 M 0.63428 1.95 0.80722 D 1 P;B 0.38300 0.626;0.42 B;B 0.25506 0.059;0.061 T 0.11792 -1.0573 10 0.42905 T 0.14 -17.6812 16.6343 0.85042 0.0:1.0:0.0:0.0 . 237;234 Q96KR7;B1AKX0 PHAR3_HUMAN;. L 234;237;196;196;196 ENSP00000353002:P234L;ENSP00000360054:P237L;ENSP00000442483:P196L;ENSP00000347866:P196L;ENSP00000378998:P196L ENSP00000347866:P196L P + 2 0 PHACTR3 57775804 0.986000 0.35501 0.836000 0.33094 0.972000 0.66771 3.474000 0.53129 2.166000 0.68216 0.460000 0.39030 CCG TCGA-IB-7646-01A-11D-2154-08 PHACTR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079923.3 0 0 1 55 201 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 1.000000 55 200 0 28 2 -2.761986 1 1 121406 74 48 1 2 2 4 2.292060 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SLC5A3 6526 broad.mit.edu 37 21 35469256 35469256 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr21:35469256C>T ENST00000381151.3 + 2 2271 c.1759C>T c.(1759-1761)Ccc>Tcc p.P587S MRPS6_ENST00000399312.2_Intron|AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.P587S P53794 SC5A3_HUMAN solute carrier family 5 (sodium/myo-inositol cotransporter), member 3 20 CCACATCATTCCCAACGGGAA 0.473000 0 SO:0001583 missense ENST00000381151.3 1 0 hg19 CCDS33549.1 . . . . . . . . . . C 14.06 2.422391 0.43020 . . ENSG00000198743 ENST00000381151 D 0.85556 -2.0 6.06 6.06 0.98353 . 0.578471 0.16748 N 0.201173 T 0.76499 0.3996 L 0.34521 1.04 0.41674 D 0.989258 B 0.30326 0.276 B 0.21917 0.037 T 0.71199 -0.4663 10 0.14656 T 0.56 . 14.4021 0.67053 0.0:0.9291:0.0:0.0709 . 587 P53794 SC5A3_HUMAN S 587 ENSP00000370543:P587S ENSP00000370543:P587S P + 1 0 SLC5A3 34391126 0.999000 0.42202 0.985000 0.45067 0.966000 0.64601 1.925000 0.40074 2.885000 0.99019 0.643000 0.83706 CCC TCGA-IB-7646-01A-11D-2154-08 SLC5A3-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000141037.1 1 0 1 52 310 0 93 1 2.140893e-01 3 3 0 93 2 0 0 0 0 0 2 1 1.000000 57 308 0 92 2 -19.999420 1 0 0 0 1 0 1 1 1.551330 1 0.320000 2.940000 0.196597 0.750000 0.570000 0.940000 0.750000 0.760343 0.750000 0 6.600000e-01 8.500000e-01 FN1 2335 broad.mit.edu 37 2 216288871 216288871 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr2:216288871G>A ENST00000359671.1 - 8 1479 c.1214C>T c.(1213-1215)aCt>aTt p.T405I FN1_ENST00000357867.4_Missense_Mutation_p.T405I|FN1_ENST00000345488.5_Missense_Mutation_p.T405I|FN1_ENST00000336916.4_Missense_Mutation_p.T405I|FN1_ENST00000432072.2_Missense_Mutation_p.T405I|FN1_ENST00000446046.1_Missense_Mutation_p.T405I|FN1_ENST00000357009.2_Missense_Mutation_p.T405I|FN1_ENST00000346544.3_Missense_Mutation_p.T405I|FN1_ENST00000356005.4_Missense_Mutation_p.T405I|FN1_ENST00000323926.6_Missense_Mutation_p.T405I|FN1_ENST00000426059.1_Missense_Mutation_p.T405I|FN1_ENST00000421182.1_Missense_Mutation_p.T405I|FN1_ENST00000443816.1_Missense_Mutation_p.T405I|FN1_ENST00000354785.4_Missense_Mutation_p.T405I P02751 FINC_HUMAN fibronectin 1 FN1/ALK(2) 109 Renal(323;0.127) Ocriplasmin(DB08888) ACACTCACCAGTGTGGTCTGT 0.488000 0 SO:0001583 missense ENST00000359671.1 1 1 hg19 . . . . . . . . . . G 20.9 4.068483 0.76301 . . ENSG00000115414 ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.49432 0.78;2.14;2.32;0.86;2.38;2.02;2.36;2.02;2.31;2.06;1.55;0.85;1.45;1.47 5.97 5.97 0.96955 . 0.537042 0.19271 N 0.118405 T 0.51822 0.1697 L 0.29908 0.895 0.36489 D 0.868311 B;P;B;D;B;B;P;P;B;B;P 0.60575 0.073;0.839;0.198;0.988;0.265;0.173;0.511;0.843;0.265;0.265;0.715 B;P;B;P;B;B;B;B;B;B;B 0.60609 0.083;0.452;0.135;0.877;0.13;0.061;0.239;0.128;0.13;0.13;0.39 T 0.59156 -0.7507 10 0.66056 D 0.02 . 10.327 0.43798 0.0:0.1207:0.6964:0.1828 . 405;405;405;405;405;405;405;405;405;405;405 E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15 .;.;.;.;.;.;.;.;.;.;. I 405 ENSP00000394423:T405I;ENSP00000323534:T405I;ENSP00000338200:T405I;ENSP00000350534:T405I;ENSP00000346839:T405I;ENSP00000352696:T405I;ENSP00000265312:T405I;ENSP00000273049:T405I;ENSP00000349509:T405I;ENSP00000410422:T405I;ENSP00000415018:T405I;ENSP00000399538:T405I;ENSP00000348285:T405I;ENSP00000398907:T405I ENSP00000265313:T405I T - 2 0 FN1 215997116 0.995000 0.38212 0.985000 0.45067 0.985000 0.73830 2.437000 0.44828 2.836000 0.97738 0.655000 0.94253 ACT TCGA-IB-7646-01A-11D-2154-08 FN1-204 KNOWN basic protein_coding protein_coding 1 0 1 134 545 0 75 0 1 0 6381 0 75 2 0 0 0 0 0 2 1 1.000000 133 536 0 75 2 -20.000000 1 1 0 0 1 2 2 4 2.161681 1 0.320000 2.940000 0.454429 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ARHGAP31 57514 broad.mit.edu 37 3 119121128 119121128 + Missense_Mutation SNP G G C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr3:119121128G>C ENST00000264245.4 + 10 2061 c.1529G>C c.(1528-1530)aGa>aCa p.R510T NM_020754.2 NP_065805.2 Q2M1Z3 RHG31_HUMAN Rho GTPase activating protein 31 67 ACGCCGTGCAGAACACCCCCG 0.592000 Pancreas(7;176 297 5394 51128 51241) 0 SO:0001583 missense ENST00000264245.4 1 1 hg19 CCDS43135.1 . . . . . . . . . . G 28.3 4.904142 0.92035 . . ENSG00000031081 ENST00000264245;ENST00000543280 T 0.18657 2.2 5.33 5.33 0.75918 . 0.000000 0.64402 D 0.000002 T 0.45538 0.1347 M 0.66939 2.045 0.80722 D 1 D 0.76494 0.999 D 0.70716 0.97 T 0.16512 -1.0400 10 0.42905 T 0.14 . 18.1871 0.89796 0.0:0.0:1.0:0.0 . 510 Q2M1Z3 RHG31_HUMAN T 510 ENSP00000264245:R510T ENSP00000264245:R510T R + 2 0 ARHGAP31 120603818 1.000000 0.71417 0.874000 0.34290 0.996000 0.88848 9.263000 0.95617 2.774000 0.95407 0.655000 0.94253 AGA TCGA-IB-7646-01A-11D-2154-08 ARHGAP31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354942.2 0 0 0 12 408 0 86 0 7.855959e-02 1 14 0 86 2 0 0 0 0 0 2 1 0.999117 12 406 0 86 2 -11.358160 1 1 0 0 1 2 2 4 2.335509 1 0.320000 2.940000 0.484848 0.240000 0.120000 0.390000 0.240000 0.253511 0.240000 0 1.700000e-01 3.200000e-01 TRIM42 287015 broad.mit.edu 37 3 140397360 140397360 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr3:140397360C>T ENST00000286349.3 + 1 480 c.289C>T c.(289-291)Cgc>Tgc p.R97C NM_152616.4 NP_689829.3 Q8IWZ5 TRI42_HUMAN tripartite motif containing 42 69 CCGCTGCTGCCGCAATACCAT 0.542000 0 SO:0001583 missense ENST00000286349.3 1 1 hg19 CCDS3113.1 . . . . . . . . . . C 15.22 2.768237 0.49680 . . ENSG00000155890 ENST00000286349 T 0.18810 2.19 5.15 2.12 0.27331 . 0.000000 0.48767 D 0.000162 T 0.16981 0.0408 N 0.14661 0.345 0.42892 D 0.994201 D 0.76494 0.999 P 0.54924 0.764 T 0.04053 -1.0981 10 0.66056 D 0.02 -23.7362 5.0235 0.14372 0.3777:0.5241:0.0:0.0982 . 97 Q8IWZ5 TRI42_HUMAN C 97 ENSP00000286349:R97C ENSP00000286349:R97C R + 1 0 TRIM42 141880050 1.000000 0.71417 1.000000 0.80357 0.666000 0.39218 1.466000 0.35310 1.262000 0.44165 0.655000 0.94253 CGC TCGA-IB-7646-01A-11D-2154-08 TRIM42-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359531.2 1 0 1 63 248 0 31 0 0 0 0 31 2 1 1 425 1413 1 1288 7 1 1.000000 63 244 0 30 2 -3.439551 1 1 121342 5 35 1 2 2 4 2.335509 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 PTPN23 25930 broad.mit.edu 37 3 47453870 47453870 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr3:47453870C>T ENST00000265562.4 + 23 4353 c.4276C>T c.(4276-4278)Cgg>Tgg p.R1426W PTPN23_ENST00000431726.1_Missense_Mutation_p.R1300W NM_015466.2 NP_056281.1 Q9H3S7 PTN23_HUMAN protein tyrosine phosphatase, non-receptor type 23 p.R1426W(1) 23 TCAGCTGGTGCGGCGCATGCG 0.647000 1 Substitution - Missense(1) SO:0001583 missense ENST00000265562.4 0 1 hg19 CCDS2754.1 . . . . . . . . . . C 14.52 2.559102 0.45590 . . ENSG00000076201 ENST00000265562 D 0.84146 -1.81 3.99 3.08 0.35506 Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1); 0.315773 0.26304 N 0.025156 D 0.86377 0.5918 L 0.49571 1.57 0.32817 D 0.502271 D 0.76494 0.999 P 0.57846 0.828 D 0.87764 0.2600 10 0.56958 D 0.05 -21.5748 9.5586 0.39355 0.5458:0.4541:0.0:0.0 . 1426 Q9H3S7 PTN23_HUMAN W 1426 ENSP00000265562:R1426W ENSP00000265562:R1426W R + 1 2 PTPN23 47428874 1.000000 0.71417 1.000000 0.80357 0.570000 0.35934 1.491000 0.35583 0.813000 0.34350 0.563000 0.77884 CGG TCGA-IB-7646-01A-11D-2154-08 PTPN23-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257492.2 0 0 0 5 198 0 46 0 6.713330e-01 0 86 0 46 2 0 0 0 0 0 2 1 0.936688 5 196 0 46 2 -3.447885 1 1 121390 1 27 1 0 2 2 1.781462 1 0.320000 2.940000 0.320000 0.160000 0.060000 0.330000 0.160000 0.181005 0.160000 0 1.000000e-01 2.500000e-01 APPL1 26060 broad.mit.edu 37 3 57282266 57282266 + Silent SNP A A C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr3:57282266A>C ENST00000288266.3 + 10 897 c.750A>C c.(748-750)acA>acC p.T250T NM_012096.2 NP_036228.1 Q9UKG1 DP13A_HUMAN adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1 27 TGCAACAGACAATAGAGGATT 0.428000 0 SO:0001819 synonymous_variant ENST00000288266.3 1 1 hg19 CCDS2882.1 TCGA-IB-7646-01A-11D-2154-08 APPL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258196.2 1 0 1 154 463 0 55 1 9.999991e-01 20 42 0 55 2 0 0 0 0 0 2 1 1.000000 154 459 0 54 2 -20.000000 1 1 0 0 1 2 2 4 2.335423 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 RAPGEF2 9693 broad.mit.edu 37 4 160260455 160260455 + Missense_Mutation SNP G G T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr4:160260455G>T ENST00000264431.4 + 13 2419 c.2000G>T c.(1999-2001)aGa>aTa p.R667I NM_014247.2 NP_055062.1 Q9Y4G8 RPGF2_HUMAN Rap guanine nucleotide exchange factor (GEF) 2 70 all_hematologic(180;0.24) AAACAAAGAAGACTTCCAGAT 0.438000 0 SO:0001583 missense ENST00000264431.4 1 1 hg19 CCDS43277.1 . . . . . . . . . . G 26.7 4.766898 0.90020 . . ENSG00000109756 ENST00000264431 T 0.30182 1.54 5.18 5.18 0.71444 Ras-association (3);Ras guanine nucleotide exchange factor, domain (1); 0.000000 0.85682 D 0.000000 T 0.60573 0.2279 M 0.80982 2.52 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.65705 -0.6103 10 0.87932 D 0 . 19.0561 0.93066 0.0:0.0:1.0:0.0 . 667 Q9Y4G8 RPGF2_HUMAN I 667 ENSP00000264431:R667I ENSP00000264431:R667I R + 2 0 RAPGEF2 160479905 1.000000 0.71417 0.020000 0.16555 0.929000 0.56500 9.726000 0.98782 2.571000 0.86741 0.591000 0.81541 AGA TCGA-IB-7646-01A-11D-2154-08 RAPGEF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000364980.2 1 0 1 48 664 0 114 1 4.256963e-01 8 13 0 114 2 0 0 0 0 0 2 1 1.000000 48 660 0 113 2 -10.116810 1 1 0 0 1 1 2 3 1.979019 0 0.320000 2.940000 0.395448 0.490000 0.350000 1.000000 0.470000 0.566109 0.490000 0 4.100000e-01 1 CPE 1363 broad.mit.edu 37 4 166418730 166418730 + Missense_Mutation SNP T T C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 T C T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr4:166418730T>C ENST00000402744.4 + 9 1679 c.1399T>C c.(1399-1401)Tgg>Cgg p.W467R NM_001873.2 NP_001864.1 P16870 CBPE_HUMAN carboxypeptidase E 26 all_hematologic(180;0.221) Prostate(90;0.0962)|Melanoma(52;0.18) """Insulin(DB00071)|Insulin Regular(DB00030)" GATGGAATGGTGGAAAATGAT 0.289000 0 SO:0001583 missense ENST00000402744.4 1 1 hg19 CCDS3810.1 . . . . . . . . . . T 17.01 3.280597 0.59758 . . ENSG00000109472 ENST00000402744 T 0.12774 2.65 6.08 6.08 0.98989 Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1); 0.000000 0.85682 D 0.000000 T 0.33876 0.0878 L 0.51422 1.61 0.80722 D 1 D 0.76494 0.999 D 0.83275 0.996 T 0.01829 -1.1265 10 0.87932 D 0 -11.282 16.643 0.85134 0.0:0.0:0.0:1.0 . 467 P16870 CBPE_HUMAN R 467 ENSP00000386104:W467R ENSP00000386104:W467R W + 1 0 CPE 166638180 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.085000 0.76875 2.330000 0.79161 0.533000 0.62120 TGG TCGA-IB-7646-01A-11D-2154-08 CPE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317094.2 1 0 0 13 286 0 51 0 9.989164e-01 0 260 0 51 2 0 0 0 0 0 2 1 0.999553 13 285 0 51 2 -4.371902 1 1 0 0 1 1 2 3 1.911743 0 0.320000 2.940000 0.364723 0.330000 0.170000 1.000000 0.290000 0.474326 0.330000 0 2.300000e-01 1 CCKAR 886 broad.mit.edu 37 4 26491074 26491074 + Missense_Mutation SNP A A C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr4:26491074A>C ENST00000295589.3 - 2 339 c.145T>G c.(145-147)Tcc>Gcc p.S49A NM_000730.2 NP_000721.1 P32238 CCKAR_HUMAN cholecystokinin A receptor 29 Breast(46;0.0503) Ceruletide(DB00403) AATATCAAGGAGTACAAGAGA 0.547000 0 SO:0001583 missense ENST00000295589.3 1 1 hg19 CCDS3438.1 . . . . . . . . . . A 9.049 0.991544 0.18966 . . ENSG00000163394 ENST00000295589 T 0.37752 1.18 5.24 4.03 0.46877 . 0.310205 0.34986 N 0.003532 T 0.17831 0.0428 N 0.12502 0.225 0.32321 N 0.562438 B 0.16166 0.016 B 0.20184 0.028 T 0.25813 -1.0121 10 0.02654 T 1 . 11.3334 0.49490 0.8638:0.0:0.0:0.1362 . 49 P32238 CCKAR_HUMAN A 49 ENSP00000295589:S49A ENSP00000295589:S49A S - 1 0 CCKAR 26100172 1.000000 0.71417 0.996000 0.52242 0.985000 0.73830 3.999000 0.57031 0.796000 0.33947 0.459000 0.35465 TCC TCGA-IB-7646-01A-11D-2154-08 CCKAR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250418.2 1 0 0 44 401 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 43 398 0 53 2 -20.000000 1 1 0 0 1 1 2 3 1.977537 0 0.320000 2.940000 0.397163 0.720000 0.520000 1.000000 0.700000 0.751564 0.720000 0 6.100000e-01 9.600000e-01 GABRB1 2560 broad.mit.edu 37 4 47322169 47322169 + Missense_Mutation SNP A A T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr4:47322169A>T ENST00000295454.3 + 5 779 c.487A>T c.(487-489)Atg>Ttg p.M163L GABRB1_ENST00000538619.1_Missense_Mutation_p.M93L NM_000812.3 NP_000803.2 P18505 GBRB1_HUMAN gamma-aminobutyric acid (GABA) A receptor, beta 1 44 Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) TGCATGTATGATGGATCTTCG 0.423000 0 SO:0001583 missense ENST00000295454.3 1 1 hg19 CCDS3474.1 . . . . . . . . . . A 31 5.067721 0.93950 . . ENSG00000163288 ENST00000295454;ENST00000538619 T;T 0.78707 -1.2;-1.2 5.19 5.19 0.71726 Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1); 0.196139 0.44285 D 0.000466 T 0.81394 0.4813 L 0.43554 1.36 0.58432 D 0.999998 D;P 0.57257 0.979;0.699 P;P 0.60345 0.873;0.833 T 0.82839 -0.0259 10 0.62326 D 0.03 -26.9689 13.0442 0.58916 1.0:0.0:0.0:0.0 . 93;163 F5GXV5;P18505 .;GBRB1_HUMAN L 163;93 ENSP00000295454:M163L;ENSP00000440330:M93L ENSP00000295454:M163L M + 1 0 GABRB1 47016926 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 8.665000 0.91144 2.178000 0.69098 0.477000 0.44152 ATG TCGA-IB-7646-01A-11D-2154-08 GABRB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216896.1 1 0 0 18 275 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 0.999984 18 274 0 58 2 -5.929462 1 1 0 0 1 1 2 3 1.977537 0 0.320000 2.940000 0.397163 0.460000 0.270000 1.000000 0.430000 0.534842 0.460000 0 3.500000e-01 7.200000e-01 IGJ 3512 broad.mit.edu 37 4 71522118 71522118 + Silent SNP G G T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr4:71522118G>T ENST00000254801.4 - 4 577 c.408C>A c.(406-408)gtC>gtA p.V136V IGJ_ENST00000543780.1_Silent_p.V152V|ENAM_ENST00000472903.1_Intron NM_144646.3 NP_653247.1 P01591 IGJ_HUMAN immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides 7 Lung(101;0.235) ATACGAGTGGGACCACAGCTG 0.453000 0 SO:0001819 synonymous_variant ENST00000254801.4 1 1 hg19 CCDS3545.1 TCGA-IB-7646-01A-11D-2154-08 IGJ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252160.1 1 0 1 74 224 0 51 0 9.999450e-01 0 47 0 51 2 0 0 0 0 0 2 1 1.000000 73 224 0 51 2 -20.000000 1 1 0 0 1 1 2 3 1.979019 0 0.320000 2.940000 0.395448 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 GABRA6 2559 broad.mit.edu 37 5 161115979 161115979 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr5:161115979C>T ENST00000274545.5 + 4 683 c.250C>T c.(250-252)Cgc>Tgc p.R84C RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000522269.1_3'UTR|GABRA6_ENST00000523217.1_Intron Q16445 GBRA6_HUMAN gamma-aminobutyric acid (GABA) A receptor, alpha 6 57 Renal(175;0.00259) Medulloblastoma(196;0.0208)|all_neural(177;0.0672) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897) TGTTTTTTTCCGCCAGACCTG 0.408000 TCGA Ovarian(5;0.080) 0 SO:0001583 missense ENST00000274545.5 1 1 hg19 CCDS4356.1 . . . . . . . . . . C 28.4 4.915608 0.92178 . . ENSG00000145863 ENST00000274545;ENST00000517823 T;T 0.80566 -1.39;-1.39 5.65 5.65 0.86999 Neurotransmitter-gated ion-channel ligand-binding (3); 0.000000 0.85682 D 0.000000 D 0.93103 0.7804 H 0.94886 3.595 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.94213 0.7460 10 0.87932 D 0 . 20.0965 0.97849 0.0:1.0:0.0:0.0 . 84 Q16445 GBRA6_HUMAN C 84;31 ENSP00000274545:R84C;ENSP00000430212:R31C ENSP00000274545:R84C R + 1 0 GABRA6 161048557 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 5.843000 0.69424 2.824000 0.97209 0.655000 0.94253 CGC TCGA-IB-7646-01A-11D-2154-08 GABRA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252707.2 0 0 1 128 444 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1.000000 127 441 0 66 2 -3.685264 1 1 121412 4 39 1 1 2 3 2.067916 1 0.320000 2.940000 0.413793 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 BVES 11149 broad.mit.edu 37 6 105563588 105563588 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr6:105563588G>A ENST00000314641.5 - 7 1147 c.931C>T c.(931-933)Cgg>Tgg p.R311W BVES_ENST00000446408.2_Missense_Mutation_p.R311W|BVES_ENST00000336775.5_Missense_Mutation_p.R311W NM_001199563.1 NP_001186492.1 Q8NE79 POPD1_HUMAN blood vessel epicardial substance p.R311W(1) 21 all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238) GAGGTACCCCGAAGAAACTGG 0.478000 1 Substitution - Missense(1) SO:0001583 missense ENST00000314641.5 1 1 hg19 CCDS5051.1 . . . . . . . . . . G 19.75 3.884860 0.72410 0.0 1.16E-4 ENSG00000112276 ENST00000314641;ENST00000336775;ENST00000446408 T;T;T 0.29397 1.57;1.57;1.57 5.95 5.95 0.96441 . 0.000000 0.85682 D 0.000000 T 0.43853 0.1266 L 0.55990 1.75 0.58432 D 0.999994 D 0.89917 1.0 D 0.91635 0.999 T 0.29822 -0.9999 10 0.72032 D 0.01 -21.4302 15.137 0.72576 0.0:0.0:0.8587:0.1413 . 311 Q8NE79 POPD1_HUMAN W 311 ENSP00000313172:R311W;ENSP00000337259:R311W;ENSP00000397310:R311W ENSP00000313172:R311W R - 1 2 BVES 105670281 1.000000 0.71417 0.997000 0.53966 0.708000 0.40852 3.314000 0.51943 2.822000 0.97130 0.563000 0.77884 CGG TCGA-IB-7646-01A-11D-2154-08 BVES-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406075.1 1 0 1 70 390 0 83 0 1.723761e-01 0 5 0 83 2 0 0 0 0 0 2 1 1.000000 69 386 0 82 2 -3.077796 1 1 121412 2 42 1 1 2 3 1.781456 0 0.320000 2.940000 0.329653 0.970000 0.760000 1.000000 1.000000 0.945027 0.970000 1 8.600000e-01 1 IL20RA 53832 broad.mit.edu 37 6 137323435 137323435 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr6:137323435C>T ENST00000316649.5 - 7 1157 c.922G>A c.(922-924)Gtg>Atg p.V308M RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000541547.1_Missense_Mutation_p.V259M|IL20RA_ENST00000468393.1_5'Flank|IL20RA_ENST00000367748.1_Missense_Mutation_p.V197M NM_001278722.1|NM_014432.2 NP_001265651.1|NP_055247 Q9UHF4 I20RA_HUMAN interleukin 20 receptor, alpha 27 Colorectal(23;0.24) AAGTTAATCACGATTTTTTCA 0.318000 0 SO:0001583 missense ENST00000316649.5 1 1 hg19 CCDS5181.1 . . . . . . . . . . C 10.87 1.473496 0.26423 . . ENSG00000016402 ENST00000316649;ENST00000367748;ENST00000541547 T;T;T 0.62364 0.29;1.74;0.03 5.79 -1.79 0.07932 . 0.528864 0.18758 N 0.131980 T 0.26122 0.0637 L 0.56769 1.78 0.09310 N 1 P;P 0.40230 0.708;0.669 B;B 0.28305 0.088;0.046 T 0.15292 -1.0442 10 0.46703 T 0.11 -2.8981 6.3867 0.21563 0.0:0.478:0.1229:0.3991 . 197;308 Q9UHF4-2;Q9UHF4 .;I20RA_HUMAN M 308;197;259 ENSP00000314976:V308M;ENSP00000356722:V197M;ENSP00000437843:V259M ENSP00000314976:V308M V - 1 0 IL20RA 137365128 0.845000 0.29573 0.013000 0.15412 0.940000 0.58332 0.935000 0.28924 -0.331000 0.08501 -0.777000 0.03380 GTG TCGA-IB-7646-01A-11D-2154-08 IL20RA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042393.1 1 0 1 40 210 0 40 1 3.191575e-01 3 4 0 40 2 0 0 0 0 0 2 1 1.000000 40 209 0 40 2 -20.000000 1 1 0 0 1 1 2 3 1.778247 0 0.320000 2.940000 0.329653 0.990000 0.750000 1.000000 1.000000 0.956409 0.990000 1 8.700000e-01 1 PXT1 222659 broad.mit.edu 37 6 36368236 36368236 + Nonsense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr6:36368236G>A ENST00000454782.2 - 4 778 c.295C>T c.(295-297)Cga>Tga p.R99* NM_152990.3 NP_694535.2 Q8NFP0 PXT1_HUMAN peroxisomal, testis specific 1 CTCACCTCTCGAACCATCCTA 0.493000 0 SO:0001587 stop_gained ENST00000454782.2 0 1 hg19 CCDS4820.2 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 G 39 7.886637 0.98542 . . ENSG00000179165 ENST00000454782;ENST00000538109 . . . 4.9 4.01 0.46588 . 0.919982 0.08824 N 0.888375 . . . . . . 0.49915 D 0.999834 . . . . . . . . . . 0.02654 T 1 -1.0883 10.898 0.47034 0.0:0.1901:0.8099:0.0 . . . . X 99;16 . ENSP00000419944:R99X R - 1 2 PXT1 36476214 0.069000 0.21087 0.259000 0.24435 0.603000 0.37013 1.193000 0.32162 1.250000 0.43966 0.555000 0.69702 CGA TCGA-IB-7646-01A-11D-2154-08 PXT1-001 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000357516.2 1 0 1 75 353 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 74 348 0 69 2 -3.367243 1 1 121412 11 44 1 1 2 3 1.787259 0 0.320000 2.940000 0.330709 0.990000 0.890000 1.000000 1.000000 0.991920 0.990000 1 9.900000e-01 1 TMEM30A 55754 broad.mit.edu 37 6 75965841 75965841 + Missense_Mutation SNP T T C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr6:75965841T>C ENST00000230461.6 - 7 1392 c.1063A>G c.(1063-1065)Aat>Gat p.N355D TMEM30A_ENST00000475111.2_Missense_Mutation_p.N319D|TMEM30A_ENST00000370050.5_Missense_Mutation_p.N236D NM_018247.3 NP_060717.1 Q9NV96 CC50A_HUMAN transmembrane protein 30A 21 TCAGCTGTATTACTACTGTTT 0.358000 0 SO:0001583 missense ENST00000230461.6 1 1 hg19 CCDS4983.1 . . . . . . . . . . T 17.99 3.523412 0.64747 . . ENSG00000112697 ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111 . . . 5.77 5.77 0.91146 . 0.082960 0.85682 D 0.000000 T 0.34135 0.0887 L 0.45228 1.405 0.50171 D 0.999851 B;B 0.09022 0.002;0.002 B;B 0.17433 0.006;0.018 T 0.36578 -0.9742 9 0.05525 T 0.97 . 16.0847 0.81038 0.0:0.0:0.0:1.0 . 319;355 Q9NV96-2;Q9NV96 .;CC50A_HUMAN D 355;339;236;319 . ENSP00000230461:N355D N - 1 0 TMEM30A 76022561 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.698000 0.84413 2.202000 0.70862 0.528000 0.53228 AAT TCGA-IB-7646-01A-11D-2154-08 TMEM30A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041248.2 1 0 1 30 165 0 24 1 1 104 231 0 24 2 0 0 0 0 0 2 1 1.000000 30 164 0 24 2 -20.000000 1 1 0 0 1 1 2 3 1.781456 0 0.320000 2.940000 0.329653 0.990000 0.680000 1.000000 1.000000 0.933726 0.990000 1 8.200000e-01 1 DPP6 1804 broad.mit.edu 37 7 154596629 154596629 + Missense_Mutation SNP A A G TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr7:154596629A>G ENST00000377770.3 + 15 1643 c.1502A>G c.(1501-1503)tAc>tGc p.Y501C DPP6_ENST00000427557.1_Missense_Mutation_p.Y394C|DPP6_ENST00000332007.3_Missense_Mutation_p.Y439C|DPP6_ENST00000404039.1_Missense_Mutation_p.Y437C P42658 DPP6_HUMAN dipeptidyl-peptidase 6 71 all_neural(206;0.181) all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204) OV - Ovarian serous cystadenocarcinoma(82;0.0562) CTTTGCAGCTACTTCCTGAGC 0.577000 NSCLC(125;1384 1783 2490 7422 34254) 0 SO:0001583 missense ENST00000377770.3 1 1 hg19 . . . . . . . . . . A 21.1 4.092541 0.76756 . . ENSG00000130226 ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557 T;T;T;T 0.42900 0.96;0.96;0.96;0.96 5.04 5.04 0.67666 Peptidase S9B, dipeptidylpeptidase IV N-terminal (1); 0.056551 0.64402 D 0.000001 T 0.73560 0.3602 H 0.95780 3.72 0.58432 D 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.87578 0.998;0.998;0.998;0.998 T 0.81904 -0.0719 10 0.87932 D 0 -22.1949 13.0759 0.59087 1.0:0.0:0.0:0.0 . 394;439;501;437 E9PDL2;P42658-2;P42658;E9PF59 .;.;DPP6_HUMAN;. C 437;501;439;394 ENSP00000385578:Y437C;ENSP00000367001:Y501C;ENSP00000328226:Y439C;ENSP00000397303:Y394C ENSP00000328226:Y439C Y + 2 0 DPP6 154227562 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 6.947000 0.75959 2.018000 0.59344 0.529000 0.55759 TAC TCGA-IB-7646-01A-11D-2154-08 DPP6-003 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000322932.1 1 0 1 11 34 0 12 0 1.679331e-01 0 3 0 12 2 0 0 0 0 0 2 1 0.999034 11 34 0 12 2 -19.998920 1 1 0 0 1 0 2 2 1.768284 1 0.320000 2.940000 0.320000 0.990000 0.830000 1.000000 1.000000 0.990012 0.990000 1 9.900000e-01 1 INHBA 3624 broad.mit.edu 37 7 41729807 41729807 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr7:41729807C>T ENST00000242208.4 - 3 968 c.722G>A c.(721-723)cGg>cAg p.R241Q INHBA_ENST00000442711.1_Missense_Mutation_p.R241Q|AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR NM_002192.2 NP_002183.1 P08476 INHBA_HUMAN inhibin, beta A 55 ACAGGCAATCCGAACGTCCAG 0.572000 TSP Lung(11;0.080) 0 SO:0001583 missense ENST00000242208.4 1 1 hg19 CCDS5464.1 . . . . . . . . . . . 36 5.853696 0.97030 . . ENSG00000122641 ENST00000242208;ENST00000442711 T;T 0.62788 0.0;0.0 6.06 6.06 0.98353 Transforming growth factor-beta, N-terminal (1); 0.431115 0.26859 N 0.022126 T 0.73118 0.3546 L 0.40543 1.245 0.80722 D 1 D 0.71674 0.998 D 0.68353 0.957 T 0.67352 -0.5692 10 0.33141 T 0.24 -20.8404 20.6208 0.99490 0.0:1.0:0.0:0.0 . 241 P08476 INHBA_HUMAN Q 241 ENSP00000242208:R241Q;ENSP00000397197:R241Q ENSP00000242208:R241Q R - 2 0 INHBA 41696332 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 4.915000 0.63355 2.882000 0.98803 0.655000 0.94253 CGG TCGA-IB-7646-01A-11D-2154-08 INHBA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250793.1 1 0 1 43 196 0 37 0 1 0 441 0 37 2 0 0 0 0 0 2 1 1.000000 43 192 0 37 2 -3.083655 1 1 121412 1 31 1 2 2 4 2.290144 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 0.999811 0.990000 1 9.900000e-01 1 GLI3 2737 broad.mit.edu 37 7 42079807 42079807 + Silent SNP G G T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr7:42079807G>T ENST00000395925.3 - 7 942 c.858C>A c.(856-858)gcC>gcA p.A286A GLI3_ENST00000479210.1_5'UTR NM_000168.5 NP_000159.3 P10071 GLI3_HUMAN GLI family zinc finger 3 112 GGCTCGGCCTGGCTGACAGCC 0.468000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 0 SO:0001819 synonymous_variant Familial Cancer Database ; ENST00000395925.3 1 1 hg19 CCDS5465.1 TCGA-IB-7646-01A-11D-2154-08 GLI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250806.3 1 0 1 50 433 0 63 0 1.255287e-01 0 6 0 63 2 0 0 0 0 0 2 1 1.000000 50 430 0 63 2 -16.432610 1 1 0 0 1 2 2 4 2.290144 1 0.320000 2.940000 0.484848 0.850000 0.640000 1.000000 1.000000 0.857625 0.850000 1 7.400000e-01 9.800000e-01 POM121L12 285877 broad.mit.edu 37 7 53104077 53104077 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr7:53104077C>T ENST00000408890.4 + 1 729 c.713C>T c.(712-714)cCg>cTg p.P238L NM_182595.3 NP_872401.3 Q8N7R1 P1L12_HUMAN POM121 transmembrane nucleoporin-like 12 61 CCTCTGAAGCCGAGCCTCGGC 0.652000 0 SO:0001583 missense ENST00000408890.4 1 1 hg19 CCDS43584.1 . . . . . . . . . . C 3.553 -0.091246 0.07053 2.55E-4 0.0 ENSG00000221900 ENST00000408890 T 0.10860 2.83 1.84 -3.67 0.04476 . . . . . T 0.05502 0.0145 N 0.08118 0 0.09310 N 1 P 0.49635 0.926 P 0.45037 0.467 T 0.19353 -1.0308 9 0.51188 T 0.08 . 5.1209 0.14860 0.4429:0.2886:0.2685:0.0 . 238 Q8N7R1 P1L12_HUMAN L 238 ENSP00000386133:P238L ENSP00000386133:P238L P + 2 0 POM121L12 53071571 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -1.714000 0.01881 -2.499000 0.00511 -1.083000 0.02208 CCG TCGA-IB-7646-01A-11D-2154-08 POM121L12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342656.1 1 0 0 93 301 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 93 299 0 43 2 -20.000000 1 1 0 0 1 2 2 4 2.290144 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 USP42 84132 broad.mit.edu 37 7 6189801 6189801 + Silent SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr7:6189801C>T ENST00000306177.5 + 13 2132 c.1974C>T c.(1972-1974)aaC>aaT p.N658N NM_032172.2 NP_115548.1 Q9H9J4 UBP42_HUMAN ubiquitin specific peptidase 42 35 Ovarian(82;0.0423) TGACCCTAAACGGTGCTAATA 0.567000 0 SO:0001819 synonymous_variant ENST00000306177.5 1 1 hg19 CCDS47535.1 TCGA-IB-7646-01A-11D-2154-08 USP42-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324262.3 1 0 1 34 135 0 24 1 8.317724e-01 9 6 0 24 2 0 0 0 0 0 2 1 1.000000 34 134 0 23 2 -20.000000 1 1 0 0 1 2 2 4 2.309781 1 0.320000 2.940000 0.484848 0.990000 0.990000 1.000000 1.000000 0.999930 0.990000 1 9.900000e-01 1 SLC30A8 169026 broad.mit.edu 37 8 118165302 118165302 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr8:118165302C>T ENST00000456015.2 + 3 391 c.391C>T c.(391-393)Cgg>Tgg p.R131W SLC30A8_ENST00000427715.2_Missense_Mutation_p.R82W|SLC30A8_ENST00000519688.1_Missense_Mutation_p.R82W|SLC30A8_ENST00000521243.1_Missense_Mutation_p.R82W NM_173851.2 NP_776250.2 Q8IWU4 ZNT8_HUMAN solute carrier family 30 (zinc transporter), member 8 41 all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173) STAD - Stomach adenocarcinoma(47;0.203) TCCCTCTAAGCGGCTGACATT 0.507000 Ovarian(162;1202 1922 6011 16223 52092) 0 SO:0001583 missense ENST00000456015.2 1 1 hg19 CCDS6322.1 . . . . . . . . . . C 16.09 3.024966 0.54683 . . ENSG00000164756 ENST00000521243;ENST00000524274;ENST00000427715;ENST00000519688;ENST00000456015 T;T;T;T;T 0.66280 -0.2;-0.2;-0.2;-0.2;-0.2 5.37 0.822 0.18806 . 0.812377 0.11451 N 0.562795 T 0.78104 0.4231 M 0.82923 2.615 0.09310 N 0.999999 D 0.65815 0.995 P 0.61722 0.893 T 0.70912 -0.4743 10 0.72032 D 0.01 -1.0271 15.0224 0.71640 0.69:0.31:0.0:0.0 . 131 Q8IWU4 ZNT8_HUMAN W 82;82;82;82;131 ENSP00000428545:R82W;ENSP00000427760:R82W;ENSP00000407505:R82W;ENSP00000431069:R82W;ENSP00000415011:R131W ENSP00000407505:R82W R + 1 2 SLC30A8 118234483 0.046000 0.20272 0.094000 0.20943 0.336000 0.28762 0.600000 0.24104 0.243000 0.21327 0.655000 0.94253 CGG TCGA-IB-7646-01A-11D-2154-08 SLC30A8-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381205.1 1 0 1 37 141 0 27 0 0 0 0 27 2 0 0 0 0 0 2 1 1.000000 37 139 0 26 2 -19.999780 1 1 121410 1 28 1 2 2 4 2.139731 1 0.320000 2.940000 0.448768 0.990000 0.990000 1.000000 1.000000 0.999932 0.990000 1 9.900000e-01 1 ARHGEF10 9639 broad.mit.edu 37 8 1882002 1882002 + Missense_Mutation SNP A A G TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr8:1882002A>G ENST00000398564.1 + 26 3191 c.3191A>G c.(3190-3192)aAg>aGg p.K1064R ARHGEF10_ENST00000520359.1_Missense_Mutation_p.K1001R|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.K1063R|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.K1039R|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.K1035R O15013 ARHGA_HUMAN Rho guanine nucleotide exchange factor (GEF) 10 35 Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834) AAAGTGATCAAGTTAGGCGTC 0.433000 0 SO:0001583 missense ENST00000398564.1 1 1 hg19 . . . . . . . . . . A 5.753 0.323425 0.10900 . . ENSG00000104728 ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435 T;T;T;T;T;T 0.34072 1.38;1.38;1.38;1.38;1.38;1.38 5.11 2.74 0.32292 . 0.095581 0.64402 N 0.000001 T 0.27241 0.0668 L 0.41079 1.255 0.38419 D 0.946126 B;B 0.21520 0.057;0.004 B;B 0.25405 0.06;0.013 T 0.08371 -1.0725 10 0.23891 T 0.37 -32.4453 9.2439 0.37513 0.8544:0.0:0.1456:0.0 . 1001;1039 O15013-7;O15013-5 .;. R 1039;1001;1063;1064;1035;683 ENSP00000340297:K1039R;ENSP00000427909:K1001R;ENSP00000431012:K1063R;ENSP00000381571:K1064R;ENSP00000262112:K1035R;ENSP00000427768:K683R ENSP00000262112:K1035R K + 2 0 ARHGEF10 1869409 0.983000 0.35010 0.000000 0.03702 0.003000 0.03518 4.878000 0.63093 0.369000 0.24510 0.533000 0.62120 AAG TCGA-IB-7646-01A-11D-2154-08 ARHGEF10-203 KNOWN basic protein_coding protein_coding 1 0 1 177 502 0 69 1 9.666073e-01 6 12 0 69 2 0 0 0 0 0 2 1 1.000000 176 498 0 69 2 -20.000000 1 1 121412 2 36 1 1 2 3 2.097200 1 0.320000 2.940000 0.413793 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ESCO2 157570 broad.mit.edu 37 8 27634027 27634027 + Silent SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr8:27634027C>T ENST00000305188.8 + 3 440 c.202C>T c.(202-204)Ctg>Ttg p.L68L ESCO2_ENST00000523910.1_3'UTR|ESCO2_ENST00000397418.2_5'UTR|RNU6-1276P_ENST00000365372.1_RNA NM_001017420.2 NP_001017420.1 Q56NI9 ESCO2_HUMAN establishment of sister chromatid cohesion N-acetyltransferase 2 18 Ovarian(32;0.000953) AATAAATAGACTGCCATCAGC 0.368000 SC Phocomelia syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database SC-Pseudothalidomide s., incl.: Roberts s. ENST00000305188.8 1 1 hg19 CCDS34872.1 TCGA-IB-7646-01A-11D-2154-08 ESCO2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376276.1 1 0 1 69 182 0 40 1 6.917410e-01 5 3 0 40 2 0 0 0 0 0 2 1 1.000000 68 179 0 40 2 -20.000000 1 1 0 0 1 2 2 4 2.180446 1 0.320000 2.940000 0.459975 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 UNC5D 137970 broad.mit.edu 37 8 35647893 35647893 + Missense_Mutation SNP G G A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chr8:35647893G>A ENST00000404895.2 + 17 3002 c.2674G>A c.(2674-2676)Gct>Act p.A892T UNC5D_ENST00000287272.2_Missense_Mutation_p.A823T|UNC5D_ENST00000449677.1_Missense_Mutation_p.A468T|UNC5D_ENST00000453357.2_Missense_Mutation_p.A887T|UNC5D_ENST00000416672.1_Missense_Mutation_p.A897T|AC012215.1_ENST00000437887.1_5'Flank|UNC5D_ENST00000420357.1_Missense_Mutation_p.A825T NM_080872.2 NP_543148.2 Q6UXZ4 UNC5D_HUMAN unc-5 homolog D (C. elegans) 112 ATCTTATTTCGCTACACAAAG 0.393000 0 SO:0001583 missense ENST00000404895.2 1 1 hg19 CCDS6093.2 . . . . . . . . . . G 23.9 4.470526 0.84533 0.0 1.16E-4 ENSG00000156687 ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677 D;D;D;D;D;D 0.85258 -1.96;-1.96;-1.96;-1.96;-1.96;-1.96 5.72 5.72 0.89469 Death (2);DEATH-like (2); 0.049286 0.85682 D 0.000000 D 0.86694 0.5994 L 0.52011 1.625 0.58432 D 0.999999 P;P;P 0.52692 0.955;0.944;0.955 P;B;B 0.48598 0.583;0.177;0.271 D 0.87244 0.2268 10 0.59425 D 0.04 -14.2436 19.873 0.96856 0.0:0.0:1.0:0.0 . 468;887;892 E9PDS8;Q6UXZ4-2;Q6UXZ4 .;.;UNC5D_HUMAN T 892;825;823;897;887;468 ENSP00000385143:A892T;ENSP00000392739:A825T;ENSP00000287272:A823T;ENSP00000412652:A897T;ENSP00000394303:A887T;ENSP00000397211:A468T ENSP00000287272:A823T A + 1 0 UNC5D 35767435 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 7.497000 0.81536 2.705000 0.92388 0.557000 0.71058 GCT TCGA-IB-7646-01A-11D-2154-08 UNC5D-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000347586.2 1 0 1 114 392 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 114 390 0 47 2 -4.349722 1 1 121408 4 40 1 2 4 6 2.211130 1 0.320000 2.940000 0.466750 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 IRS4 8471 broad.mit.edu 37 X 107977753 107977753 + Nonsense_Mutation SNP T T A TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chrX:107977753T>A ENST00000372129.2 - 1 1898 c.1822A>T c.(1822-1824)Aaa>Taa p.K608* RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank NM_003604.2 NP_003595.1 O14654 IRS4_HUMAN insulin receptor substrate 4 78 TTCAGAGATTTTCCACGTTCA 0.542000 0 SO:0001587 stop_gained ENST00000372129.2 0 1 hg19 CCDS14544.1 . . . . . . . . . . T 38 6.696633 0.97772 . . ENSG00000133124 ENST00000372129 . . . 4.77 4.77 0.60923 . 0.116050 0.53938 D 0.000052 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -17.1376 13.1593 0.59535 0.0:0.0:0.0:1.0 . . . . X 608 . ENSP00000361202:K608X K - 1 0 IRS4 107864409 1.000000 0.71417 0.998000 0.56505 0.957000 0.61999 3.745000 0.55119 1.757000 0.51966 0.417000 0.27973 AAA TCGA-IB-7646-01A-11D-2154-08 IRS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057879.1 1 0 1 439 491 0 126 0 0 0 0 126 2 0 0 0 0 0 2 1 1.000000 435 482 0 125 2 -20.000000 1 1 0 0 1 0 1 1 0.320000 2.940000 0.320000 0.990000 0.970000 1.000000 1.000000 0.997513 0.990000 1 9.800000e-01 1 POLA1 5422 broad.mit.edu 37 X 24839663 24839663 + Missense_Mutation SNP T T C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chrX:24839663T>C ENST00000379059.3 + 31 3521 c.3506T>C c.(3505-3507)gTg>gCg p.V1169A POLA1_ENST00000379068.3_Missense_Mutation_p.V1175A NM_016937.3 NP_058633.2 P09884 DPOLA_HUMAN polymerase (DNA directed), alpha 1, catalytic subunit 11 Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280) GGCAGAAAGGTGAAAGCTGGA 0.393000 0 SO:0001583 missense ENST00000379059.3 1 1 hg19 CCDS14214.1 . . . . . . . . . . T 16.66 3.184335 0.57800 . . ENSG00000101868 ENST00000379068;ENST00000379059 T;T 0.17528 2.27;2.27 4.9 4.9 0.64082 DNA-directed DNA polymerase, family B, multifunctional domain (1); 0.246861 0.40302 N 0.001126 T 0.26268 0.0641 M 0.69823 2.125 0.58432 D 0.999998 P 0.37207 0.587 B 0.43754 0.43 T 0.03240 -1.1057 10 0.21540 T 0.41 -0.1434 13.7335 0.62804 0.0:0.0:0.0:1.0 . 1169 P09884 DPOLA_HUMAN A 1175;1169 ENSP00000368358:V1175A;ENSP00000368349:V1169A ENSP00000368349:V1169A V + 2 0 POLA1 24749584 1.000000 0.71417 0.984000 0.44739 0.989000 0.77384 7.463000 0.80869 1.816000 0.52996 0.441000 0.28932 GTG TCGA-IB-7646-01A-11D-2154-08 POLA1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000056111.1 0 0 1 81 80 0 19 1 1 24 9 0 19 2 0 0 0 0 0 2 1 1.000000 81 79 0 19 2 -20.000000 1 1 0 0 1 0 1 1 0.320000 2.940000 0.320000 0.980000 0.920000 1.000000 0.990000 0.982590 0.980000 1 9.500000e-01 1 PAGE1 8712 broad.mit.edu 37 X 49459355 49459355 + Missense_Mutation SNP A A C TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chrX:49459355A>C ENST00000376150.3 - 2 151 c.19T>G c.(19-21)Tta>Gta p.L7V NM_003785.3 NP_003776.2 O75459 PAGE1_HUMAN P antigen family, member 1 (prostate associated) 7 Ovarian(276;0.236) CGATAGATTAATCTTCTTAGA 0.373000 0 SO:0001583 missense ENST00000376150.3 0 1 hg19 CCDS14327.1 . . . . . . . . . . A 6.763 0.509661 0.12883 . . ENSG00000068985 ENST00000376150 T 0.10005 2.92 1.57 1.57 0.23409 . . . . . T 0.11067 0.0270 L 0.50333 1.59 0.09310 N 1 D 0.56521 0.976 P 0.46389 0.515 T 0.21211 -1.0252 9 0.24483 T 0.36 . 4.6903 0.12778 1.0:0.0:0.0:0.0 . 7 O75459 GAGB1_HUMAN V 7 ENSP00000365320:L7V ENSP00000365320:L7V L - 1 2 PAGE1 49346066 0.001000 0.12720 0.000000 0.03702 0.002000 0.02628 0.800000 0.27042 0.857000 0.35407 0.314000 0.21332 TTA TCGA-IB-7646-01A-11D-2154-08 PAGE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000081210.1 1 0 1 45 61 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 1.000000 45 60 0 13 2 -20.000000 1 1 0 0 1 0 1 1 0.320000 2.940000 0.320000 0.960000 0.840000 1.000000 0.990000 0.956454 0.960000 1 9.100000e-01 9.900000e-01 ALAS2 212 broad.mit.edu 37 X 55047614 55047614 + Missense_Mutation SNP C C T TCGA-IB-7646-01A-11D-2154-08 TCGA-IB-7646-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx e26b2473-9399-4eb8-9574-5b934b560740 5218f2a6-5b5d-4e1a-aaf1-a0cd5e536571 g.chrX:55047614C>T ENST00000330807.5 - 5 646 c.509G>A c.(508-510)cGc>cAc p.R170H ALAS2_ENST00000396198.3_Missense_Mutation_p.R157H|ALAS2_ENST00000335854.4_Missense_Mutation_p.R133H|ALAS2_ENST00000498636.1_5'Flank NM_000032.4 NP_000023.2 P22557 HEM0_HUMAN aminolevulinate, delta-, synthase 2 17 Glycine(DB00145) ATCAGCCCAGCGGTTCACAGT 0.483000 0 GRCh37 CM983851|CM983852 ALAS2 M SO:0001583 missense ENST00000330807.5 1 1 hg19 CCDS14366.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 32|32 5.145686|5.145686 0.94603|0.94603 .|. .|. ENSG00000158578|ENSG00000158578 ENST00000455688|ENST00000330807;ENST00000396198;ENST00000335854 .|D;D;D .|0.95554 .|-3.74;-3.74;-3.74 4.92|4.92 4.92|4.92 0.64577|0.64577 .|Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major domain (1); .|0.000000 .|0.85682 .|D .|0.000000 D|D 0.97971|0.97971 0.9332|0.9332 M|M 0.88310|0.88310 2.945|2.945 0.80722|0.80722 D|D 1|1 .|D;D;D .|0.89917 .|1.0;1.0;1.0 .|D;D;D .|0.87578 .|0.998;0.996;0.998 D|D 0.99123|0.99123 1.0850|1.0850 5|10 .|0.87932 .|D .|0 -17.4214|-17.4214 16.2829|16.2829 0.82707|0.82707 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|133;157;170 .|A8K6C4;Q5JZF5;P22557 .|.;.;HEM0_HUMAN T|H 122|170;157;133 .|ENSP00000332369:R170H;ENSP00000379501:R157H;ENSP00000337131:R133H .|ENSP00000332369:R170H A|R -|- 1|2 0|0 ALAS2|ALAS2 55064339|55064339 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.996000|0.996000 0.88848|0.88848 7.818000|7.818000 0.86416|0.86416 2.185000|2.185000 0.69588|0.69588 0.529000|0.529000 0.55759|0.55759 GCT|CGC TCGA-IB-7646-01A-11D-2154-08 ALAS2-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056843.3 1 0 1 109 113 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 1.000000 109 113 0 33 2 -20.000000 1 1 0 0 1 0 1 1 0.320000 2.940000 0.320000 0.980000 0.930000 1.000000 0.990000 0.986981 0.980000 1 9.600000e-01 1