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 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 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-2J-AAB9-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 0 0 8 204 0 59 0 1.764996e-02 0 5 0 59 2 1 9.978920e-01 11 289 0 297 2 1 0.989367 8 202 0 57 2 -4.033993 1 1 121404 2 44 1 1 2 3 2.100239 0 0.100000 2.020000 0.127907 0.900000 0.400000 1.000000 1.000000 0.835757 0.900000 1 0.600000 1.000000 CINP 51550 broad.mit.edu 37 14 102815068 102815068 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr14:102815068C>T ENST00000216756.6 - 5 505 c.465G>A c.(463-465)atG>atA p.M155I CINP_ENST00000560326.1_5'Flank|CINP_ENST00000536961.2_Missense_Mutation_p.M170I|CINP_ENST00000541568.2_Missense_Mutation_p.C112Y NM_032630.2 NP_116019.1 Q9BW66 CINP_HUMAN cyclin-dependent kinase 2 interacting protein 4 CCTTCCTGTACATCTCCAAGA 0.527000 0 SO:0001583 missense ENST00000216756.6 0 1 hg19 CCDS9972.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 17.80|17.80 3.477860|3.477860 0.63849|0.63849 .|. .|. ENSG00000100865|ENSG00000100865 ENST00000541568|ENST00000216756;ENST00000536961 .|T;T .|0.51817 .|0.72;0.69 6.07|6.07 5.17|5.17 0.71159|0.71159 .|. .|0.256618 .|0.46442 .|D .|0.000283 T|T 0.55909|0.55909 0.1950|0.1950 M|M 0.73598|0.73598 2.24|2.24 0.31559|0.31559 N|N 0.657829|0.657829 .|P .|0.49559 .|0.925 .|P .|0.46758 .|0.526 T|T 0.69026|0.69026 -0.5254|-0.5254 6|10 0.52906|0.66056 T|D 0.07|0.02 .|. 14.4832|14.4832 0.67597|0.67597 0.0:0.9291:0.0:0.0709|0.0:0.9291:0.0:0.0709 .|. .|155 .|Q9BW66 .|CINP_HUMAN Y|I 112|155;170 .|ENSP00000216756:M155I;ENSP00000442057:M170I ENSP00000442377:C112Y|ENSP00000216756:M155I C|M -|- 2|3 0|0 CINP|CINP 101884821|101884821 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.436000|0.436000 0.31835|0.31835 1.313000|1.313000 0.33585|0.33585 1.549000|1.549000 0.49425|0.49425 0.655000|0.655000 0.94253|0.94253 TGT|ATG TCGA-2J-AAB9-01A-11D-A40W-08 CINP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415055.1 0 0 1 4 84 0 25 1 6.588245e-01 9 36 0 25 2 0 0 0 0 0 2 1 0.886537 4 82 0 25 2 -7.715463 1 1 0 0 1 1 2 3 2.002445 0 0.100000 2.020000 0.106700 0.990000 0.340000 1.000000 1.000000 0.856403 0.990000 1 0.610000 1.000000 TEPP 374739 broad.mit.edu 37 16 58018681 58018681 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr16:58018681G>A ENST00000441824.2 + 4 629 c.592G>A c.(592-594)Ggg>Agg p.G198R TEPP_ENST00000290871.5_Missense_Mutation_p.G198R|TEPP_ENST00000569996.1_3'UTR NM_199456.2 NP_955535.2 Q6URK8 TEPP_HUMAN testis, prostate and placenta expressed 8 GTCCTCGGCCGGGGAGTTCAA 0.682000 0 SO:0001583 missense ENST00000441824.2 0 1 hg19 CCDS45496.1 . . . . . . . . . . G 16.03 3.006870 0.54361 . . ENSG00000159648 ENST00000290871;ENST00000441824 T;T 0.59772 0.24;0.26 5.29 4.34 0.51931 . 0.285249 0.29948 N 0.010788 T 0.59715 0.2214 M 0.81682 2.555 0.09310 N 1 D;D 0.56287 0.975;0.975 B;B 0.43386 0.418;0.418 T 0.60042 -0.7340 10 0.59425 D 0.04 8.7723 10.1043 0.42524 0.0933:0.0:0.9067:0.0 . 198;198 Q6URK8;Q6URK8-2 TEPP_HUMAN;. R 198 ENSP00000290871:G198R;ENSP00000401917:G198R ENSP00000290871:G198R G + 1 0 TEPP 56576182 0.766000 0.28496 0.091000 0.20842 0.959000 0.62525 1.217000 0.32455 1.229000 0.43630 -0.149000 0.13747 GGG TCGA-2J-AAB9-01A-11D-A40W-08 TEPP-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000431966.1 1 0 0 4 72 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 0.889105 4 71 0 10 2 -3.179890 1 1 121310 1 19 1 1 2 3 1.999303 0 0.100000 2.020000 0.105812 0.990000 0.390000 1.000000 1.000000 0.892126 0.990000 1 0.690000 1.000000 CNTNAP4 85445 broad.mit.edu 37 16 76486445 76486445 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr16:76486445C>T ENST00000476707.1 + 7 1260 c.1121C>T c.(1120-1122)cCc>cTc p.P374L CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.P298L|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.P322L|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.P370L Q9C0A0 CNTP4_HUMAN contactin associated protein-like 4 64 CAATCTATGCCCGTGACTTTT 0.393000 0 SO:0001583 missense ENST00000476707.1 1 1 hg19 . . . . . . . . . . C 21.5 4.161570 0.78226 . . ENSG00000152910 ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707 T;T;T;T 0.79247 -1.25;-1.25;-1.25;-1.25 5.52 5.52 0.82312 Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1); 0.000000 0.41294 D 0.000901 D 0.89192 0.6645 . . . 0.80722 D 1 D;D;P;D 0.89917 0.996;0.984;0.937;1.0 D;D;P;D 0.97110 0.977;0.909;0.533;1.0 D 0.89667 0.3881 9 0.87932 D 0 . 19.6434 0.95767 0.0:1.0:0.0:0.0 . 298;374;346;371 E9PFZ6;E9PDN6;Q96M80;Q9C0A0 .;.;.;CNTP4_HUMAN L 370;322;298;374 ENSP00000306893:P370L;ENSP00000439733:P322L;ENSP00000418741:P298L;ENSP00000417628:P374L ENSP00000306893:P370L P + 2 0 CNTNAP4 75043946 1.000000 0.71417 1.000000 0.80357 0.817000 0.46193 5.376000 0.66178 2.880000 0.98712 0.655000 0.94253 CCC TCGA-2J-AAB9-01A-11D-A40W-08 CNTNAP4-005 PUTATIVE basic protein_coding protein_coding OTTHUMT00000348216.1 1 0 0 20 358 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 0.999995 20 354 0 78 2 -5.005502 1 1 0 0 1 1 2 3 1.999303 0 0.100000 2.020000 0.105812 0.990000 0.680000 1.000000 1.000000 0.953544 0.990000 1 0.870000 1.000000 EVI2A 2123 broad.mit.edu 37 17 29645681 29645681 + Silent SNP A A G TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr17:29645681A>G ENST00000462804.2 - 2 750 c.351T>C c.(349-351)caT>caC p.H117H EVI2A_ENST00000461237.1_Silent_p.H117H|NF1_ENST00000581113.2_Intron|NF1_ENST00000358273.4_Intron|EVI2A_ENST00000247270.3_Silent_p.H140H|NF1_ENST00000356175.3_Intron|CTD-2370N5.3_ENST00000578584.1_Missense_Mutation_p.W57R NM_014210.3 NP_055025.2 P22794 EVI2A_HUMAN ecotropic viral integration site 2A p.0?(8)|p.?(3) 14 all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094) AAATTTCACCATGACTTTTGC 0.358000 11 Whole gene deletion(8)|Unknown(3) SO:0001819 synonymous_variant ENST00000462804.2 1 0 hg19 CCDS42293.1 TCGA-2J-AAB9-01A-11D-A40W-08 EVI2A-001 KNOWN alternative_5_UTR|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000354491.3 1 0 0 33 501 0 123 0 4.930097e-01 0 26 0 123 2 0 0 0 0 0 2 1 1.000000 32 496 0 122 2 -7.648710 1 1 121412 1 30 1 1 2 3 2.076903 0 0.100000 2.020000 0.122807 0.990000 0.910000 1.000000 1.000000 0.995055 0.990000 1 0.990000 1.000000 KRT13 3860 broad.mit.edu 37 17 39658808 39658808 + Silent SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr17:39658808G>A ENST00000246635.3 - 6 1108 c.1062C>T c.(1060-1062)tgC>tgT p.C354C AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Silent_p.C354C|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000587544.1_Silent_p.C354C NM_153490.2 NP_705694 P13646 K1C13_HUMAN keratin 13 33 Breast(137;0.000286) GGGCATAGCGGCACTCCGTCT 0.607000 0 SO:0001819 synonymous_variant ENST00000246635.3 0 1 hg19 CCDS11396.1 TCGA-2J-AAB9-01A-11D-A40W-08 KRT13-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000257297.1 0 0 0 6 573 1 98 0 6.599619e-03 0 1221 1 98 36 0 0 0 0 0 2 1 0.963981 6 567 0 95 2 -2.617260 1 1 0 0 1 1 2 3 2.076903 0 0.100000 2.020000 0.122807 0.260000 0.090000 1.000000 0.210000 0.427164 0.260000 0 0.160000 1.000000 TP53 7157 broad.mit.edu 37 17 7579377 7579377 + Nonsense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr17:7579377G>A ENST00000269305.4 - 4 499 c.310C>T c.(310-312)Cag>Tag p.Q104* TP53_ENST00000445888.2_Nonsense_Mutation_p.Q104*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q104*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q104*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q104*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q104* 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.Q104*(12)|p.0?(8)|p.Q100fs*37(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.Y103_Q104>**(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(1)|p.Y103fs*15(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TAGCTGCCCTGGTAGGTTTTC 0.632000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 34 Substitution - Nonsense(12)|Deletion - Frameshift(11)|Whole gene deletion(8)|Complex - deletion inframe(2)|Complex - compound substitution(1) SO:0001587 stop_gained Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . G 17.73 3.460479 0.63401 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591 . . . 4.75 4.75 0.60458 . 0.378699 0.29424 N 0.012186 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.66056 D 0.02 2.2505 11.3383 0.49518 0.0:0.1837:0.8163:0.0 . . . . X 104 . ENSP00000269305:Q104X Q - 1 0 TP53 7520102 1.000000 0.71417 0.643000 0.29450 0.384000 0.30261 1.618000 0.36954 2.630000 0.89119 0.655000 0.94253 CAG TCGA-2J-AAB9-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 23 314 0 76 0 5.288786e-01 1 24 0 76 2 1 9.997745e-01 9 174 0 181 2 1 0.999999 23 308 0 75 2 -6.975264 1 1 0 0 1 0 1 1 1.940295 0 0.100000 2.020000 0.064449 0.990000 0.780000 1.000000 1.000000 0.975665 0.990000 1 0.940000 1.000000 FHOD3 80206 broad.mit.edu 37 18 34205579 34205579 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr18:34205579C>T ENST00000359247.4 + 10 1063 c.1063C>T c.(1063-1065)Cgg>Tgg p.R355W FHOD3_ENST00000591635.1_Silent_p.T29T|FHOD3_ENST00000590592.1_Missense_Mutation_p.R355W|FHOD3_ENST00000445677.1_Missense_Mutation_p.R355W|FHOD3_ENST00000257209.4_Missense_Mutation_p.R355W NM_001281739.1 NP_001268668.1 Q2V2M9 FHOD3_HUMAN formin homology 2 domain containing 3 p.R355W(1) 90 all_epithelial(2;0.0181)|Colorectal(2;0.0195) AGGCGAGCACCGGGGCCTGGA 0.697000 1 Substitution - Missense(1) SO:0001583 missense ENST00000359247.4 1 1 hg19 . . . . . . . . . . C 20.8 4.056169 0.76074 . . ENSG00000134775 ENST00000257209;ENST00000359247;ENST00000445677 T;T;T 0.35236 1.33;1.33;1.32 5.28 5.28 0.74379 GTPase-binding/formin homology 3 (1);Armadillo-type fold (1); 0.269957 0.36167 N 0.002746 T 0.44891 0.1315 L 0.58101 1.795 0.32709 N 0.51179 D;D;D;D 0.71674 0.986;0.994;0.994;0.998 P;P;P;P 0.51657 0.471;0.614;0.502;0.676 T 0.61554 -0.7039 10 0.87932 D 0 . 11.5603 0.50772 0.1781:0.8219:0.0:0.0 . 355;355;355;355 Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0 .;FHOD3_HUMAN;.;. W 355 ENSP00000257209:R355W;ENSP00000352186:R355W;ENSP00000411430:R355W ENSP00000257209:R355W R + 1 2 FHOD3 32459577 1.000000 0.71417 0.114000 0.21550 0.842000 0.47809 3.935000 0.56560 2.469000 0.83416 0.655000 0.94253 CGG TCGA-2J-AAB9-01A-11D-A40W-08 FHOD3-001 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460884.1 1 0 0 11 279 0 57 0 4.220521e-02 0 8 0 57 2 0 0 0 0 0 2 1 0.998189 11 272 0 56 2 -3.398903 1 1 0 0 1 0 0 0 1.935203 0 0.100000 2.020000 0.064449 0.720000 0.380000 1.000000 1.000000 0.730714 0.720000 0 0.530000 0.940000 KLK15 55554 broad.mit.edu 37 19 51330383 51330383 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr19:51330383G>A ENST00000598239.1 - 3 262 c.232C>T c.(232-234)Cgc>Tgc p.R78C KLK15_ENST00000596931.1_Missense_Mutation_p.R77C|KLK15_ENST00000416184.1_Missense_Mutation_p.R78C|KLK15_ENST00000326856.4_Missense_Mutation_p.R77C|KLK15_ENST00000301421.2_Missense_Mutation_p.R78C NM_017509.2 NP_059979.2 Q9H2R5 KLK15_HUMAN kallikrein-related peptidase 15 24 all_neural(266;0.057) TCGCGCTTGCGCAGGTTGTGC 0.632000 Pancreas(140;10 2513 7143 9246) 0 SO:0001583 missense ENST00000598239.1 0 1 hg19 CCDS12805.1 . . . . . . . . . . G 17.20 3.329160 0.60743 . . ENSG00000174562 ENST00000326856;ENST00000416184;ENST00000301421;ENST00000544946 D;D 0.89415 -2.51;-2.51 4.51 4.51 0.55191 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.000000 0.46442 D 0.000293 D 0.91778 0.7399 L 0.61218 1.895 0.09310 N 1 D;D;D;D 0.89917 1.0;0.999;0.999;0.999 P;P;D;P 0.65987 0.892;0.892;0.94;0.892 D 0.84525 0.0630 10 0.56958 D 0.05 . 10.1981 0.43067 0.0:0.0:0.8015:0.1985 . 78;77;78;78 Q6UBM2;Q6ISI0;Q9H2R5-4;Q9H2R5 .;.;.;KLK15_HUMAN C 78 ENSP00000415136:R78C;ENSP00000301421:R78C ENSP00000301421:R78C R - 1 0 KLK15 56022195 0.000000 0.05858 0.999000 0.59377 0.951000 0.60555 0.118000 0.15605 2.519000 0.84933 0.561000 0.74099 CGC TCGA-2J-AAB9-01A-11D-A40W-08 KLK15-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465160.1 0 0 0 8 479 0 106 0 0 0 0 106 2 0 0 0 0 0 2 1 0.988842 9 471 0 102 2 -6.712205 1 1 0 0 1 1 2 3 2.008441 0 0.100000 2.020000 0.108028 0.370000 0.160000 1.000000 0.320000 0.453419 0.370000 0 0.250000 0.640000 ACTL9 284382 broad.mit.edu 37 19 8808452 8808452 + Silent SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr19:8808452G>A ENST00000324436.3 - 1 720 c.600C>T c.(598-600)caC>caT p.H200H NM_178525.3 NP_848620.3 Q8TC94 ACTL9_HUMAN actin-like 9 36 AGGTGACCCCGTGTCCCGTGT 0.672000 0 SO:0001819 synonymous_variant ENST00000324436.3 1 1 hg19 CCDS12207.1 TCGA-2J-AAB9-01A-11D-A40W-08 ACTL9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459953.1 1 0 0 19 275 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 0.999991 19 270 0 43 2 -19.998160 1 1 0 0 1 1 2 3 1.999602 0 0.100000 2.020000 0.105812 0.990000 0.820000 1.000000 1.000000 0.987903 0.990000 1 0.990000 1.000000 ATP8B2 57198 broad.mit.edu 37 1 154306722 154306722 + Silent SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr1:154306722C>T ENST00000368489.3 + 10 828 c.828C>T c.(826-828)ttC>ttT p.F276F ATP8B2_ENST00000368487.3_Silent_p.F243F|ATP8B2_ENST00000341822.2_Silent_p.F262F|ATP8B2_ENST00000426445.1_3'UTR NM_020452.3 NP_065185.1 P98198 AT8B2_HUMAN ATPase, aminophospholipid transporter, class I, type 8B, member 2 IL6R/ATP8B2(2) 51 all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877) LUSC - Lung squamous cell carcinoma(543;0.185) AGTGGTGCTTCGGGCTGGTCA 0.542000 0 SO:0001819 synonymous_variant ENST00000368489.3 1 1 hg19 CCDS1066.1 TCGA-2J-AAB9-01A-11D-A40W-08 ATP8B2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087658.2 1 0 0 36 773 0 181 0 6.185315e-03 0 3 0 181 2 0 0 0 0 0 2 1 1.000000 36 763 0 179 2 -4.293961 1 1 0 0 1 1 2 3 1.999988 0 0.100000 2.020000 0.106256 0.920000 0.640000 1.000000 1.000000 0.897092 0.920000 1 0.770000 1.000000 PAQR6 79957 broad.mit.edu 37 1 156215369 156215369 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr1:156215369C>T ENST00000292291.5 - 5 627 c.469G>A c.(469-471)Gca>Aca p.A157T PAQR6_ENST00000368270.1_Missense_Mutation_p.A133T|PAQR6_ENST00000492619.1_5'UTR|PAQR6_ENST00000335852.1_Missense_Mutation_p.A51T|PAQR6_ENST00000356983.2_Missense_Mutation_p.A51T|PAQR6_ENST00000540423.1_Missense_Mutation_p.A154T NM_001272104.1|NM_001272105.1|NM_198406.2 NP_001259033.1|NP_001259034.1|NP_940798.1 Q6TCH4 PAQR6_HUMAN progestin and adipoQ receptor family member VI 5 Hepatocellular(266;0.158) GAGTTGAGTGCGGCGGCAGGC 0.687000 GBM(16;219 398 12385 32425 38531) 0 SO:0001583 missense ENST00000292291.5 0 1 hg19 CCDS1136.1 . . . . . . . . . . C 14.76 2.630223 0.46944 . . ENSG00000160781 ENST00000292291;ENST00000360733;ENST00000335852;ENST00000356983;ENST00000368270;ENST00000540423 T;T;T;T;T;T 0.35605 1.3;1.3;1.3;1.3;1.3;1.3 4.2 3.26 0.37387 . . . . . T 0.21801 0.0525 L 0.61036 1.89 0.30241 N 0.795024 P;P;P 0.42584 0.784;0.744;0.784 B;B;B 0.41332 0.121;0.354;0.121 T 0.02942 -1.1091 9 0.33141 T 0.24 . 11.2653 0.49106 0.0:0.9047:0.0:0.0953 . 154;51;157 B7Z9R9;Q6TCH4-2;Q6TCH4 .;.;PAQR6_HUMAN T 157;51;51;51;133;154 ENSP00000292291:A157T;ENSP00000353961:A51T;ENSP00000338330:A51T;ENSP00000349474:A51T;ENSP00000357253:A133T;ENSP00000443167:A154T ENSP00000292291:A157T A - 1 0 PAQR6 154481993 0.456000 0.25744 0.999000 0.59377 0.785000 0.44390 1.863000 0.39459 2.146000 0.66826 0.462000 0.41574 GCA TCGA-2J-AAB9-01A-11D-A40W-08 PAQR6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000046297.2 0 0 0 5 237 0 43 0 7.025761e-04 0 2 0 43 2 0 0 0 0 0 2 1 0.936819 5 235 0 41 2 -2.807899 1 1 0 0 1 1 2 3 1.999988 0 0.100000 2.020000 0.106256 0.470000 0.170000 1.000000 0.410000 0.535104 0.470000 0 0.290000 0.820000 USP24 23358 broad.mit.edu 37 1 55562215 55562215 + Missense_Mutation SNP T T G TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr1:55562215T>G ENST00000294383.6 - 50 6016 c.6017A>C c.(6016-6018)tAt>tCt p.Y2006S USP24_ENST00000407756.1_Missense_Mutation_p.Y1846S NM_015306.2 NP_056121.2 Q9UPU5 UBP24_HUMAN ubiquitin specific peptidase 24 60 AAAGCATTCATACTCCAGGGT 0.323000 0 SO:0001583 missense ENST00000294383.6 1 1 hg19 CCDS44154.2 . . . . . . . . . . T 8.490 0.861857 0.17178 . . ENSG00000162402 ENST00000294383;ENST00000407756 T;T 0.04454 3.62;3.62 6.06 4.87 0.63330 . 0.000000 0.85682 D 0.000000 T 0.02230 0.0069 N 0.05124 -0.11 0.58432 D 0.999995 B 0.27013 0.166 B 0.21151 0.033 T 0.37526 -0.9702 10 0.02654 T 1 . 12.2795 0.54755 0.127:0.0:0.0:0.873 . 1846 B7WPF4 . S 2006;1846 ENSP00000294383:Y2006S;ENSP00000385700:Y1846S ENSP00000294383:Y2006S Y - 2 0 USP24 55334803 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.868000 0.69605 2.324000 0.78689 0.533000 0.62120 TAT TCGA-2J-AAB9-01A-11D-A40W-08 USP24-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000022275.2 1 0 0 7 209 0 32 0 2.002875e-02 0 6 0 32 2 0 0 0 0 0 2 1 0.979458 7 204 0 32 2 -9.711997 1 1 0 0 1 0 0 0 1.936615 0 0.100000 2.020000 0.065421 0.620000 0.280000 1.000000 1.000000 0.645975 0.620000 0 0.430000 0.860000 ASXL1 171023 broad.mit.edu 37 20 31023733 31023733 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr20:31023733G>A ENST00000375687.4 + 13 3642 c.3218G>A c.(3217-3219)cGc>cAc p.R1073H ASXL1_ENST00000306058.5_Missense_Mutation_p.R1068H NM_015338.5 NP_056153 Q8IXJ9 ASXL1_HUMAN additional sex combs like transcriptional regulator 1 722 TGTGCGGTCCGCCAAAAGATC 0.572000 F, N, Mis MDS, CMML Rec yes 20 20q11.1 171023 additional sex combs like 1 L 0 SO:0001583 missense ENST00000375687.4 0 1 hg19 CCDS13201.1 . . . . . . . . . . G 14.42 2.530985 0.45073 . . ENSG00000171456 ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058 T;T 0.32515 1.45;1.45 4.17 3.22 0.36961 . 0.398033 0.27696 N 0.018224 T 0.14356 0.0347 N 0.14661 0.345 0.27406 N 0.954705 P;P 0.46327 0.733;0.876 B;B 0.28638 0.092;0.082 T 0.11203 -1.0597 10 0.66056 D 0.02 -8.1008 13.3344 0.60509 0.0:0.8381:0.1619:0.0 . 1068;1073 A6NIZ6;Q8IXJ9 .;ASXL1_HUMAN H 1073;1073;1073;994;1068 ENSP00000364839:R1073H;ENSP00000305119:R1068H ENSP00000305119:R1068H R + 2 0 ASXL1 30487394 0.043000 0.20138 0.202000 0.23494 0.973000 0.67179 1.798000 0.38814 1.347000 0.45714 -0.270000 0.10280 CGC TCGA-2J-AAB9-01A-11D-A40W-08 ASXL1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000078624.2 0 0 0 9 432 0 81 0 2.056837e-01 0 37 0 81 2 0 0 0 0 0 2 1 0.993826 11 422 0 80 2 -2.130350 0 1 0 0 1 1 2 3 2.015589 0 0.100000 2.020000 0.109352 0.460000 0.210000 1.000000 0.400000 0.534748 0.460000 0 0.310000 0.930000 CSE1L 1434 broad.mit.edu 37 20 47704596 47704596 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr20:47704596C>T ENST00000262982.2 + 17 1897 c.1774C>T c.(1774-1776)Cct>Tct p.P592S CSE1L_ENST00000542325.1_Missense_Mutation_p.P375S|CSE1L_ENST00000396192.3_Missense_Mutation_p.P536S NM_001256135.1|NM_001316.3 NP_001243064.1|NP_001307.2 P55060 XPO2_HUMAN CSE1 chromosome segregation 1-like (yeast) 35 BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198) CCCCTACATCCCTACTCTCAT 0.358000 0 SO:0001583 missense ENST00000262982.2 1 1 hg19 CCDS13412.1 . . . . . . . . . . C 12.85 2.061197 0.36373 . . ENSG00000124207 ENST00000417408;ENST00000262982;ENST00000542325;ENST00000396192 T;T;T 0.66280 -0.2;-0.2;-0.2 5.57 4.62 0.57501 Armadillo-like helical (1);Armadillo-type fold (1);CAS/CSE, C-terminal (1); 0.047464 0.85682 D 0.000000 T 0.53997 0.1831 L 0.41632 1.29 0.80722 D 1 P;P;B;B;P 0.41345 0.57;0.746;0.017;0.032;0.746 B;B;B;B;B 0.41988 0.255;0.372;0.105;0.064;0.372 T 0.50541 -0.8816 10 0.08599 T 0.76 -9.7713 16.5517 0.84474 0.0:0.8694:0.1306:0.0 . 281;375;536;536;592 F5GX54;B4DUC5;A3RLL6;F8W904;P55060 .;.;.;.;XPO2_HUMAN S 190;592;375;536 ENSP00000262982:P592S;ENSP00000446477:P375S;ENSP00000379495:P536S ENSP00000262982:P592S P + 1 0 CSE1L 47138003 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 5.689000 0.68234 1.336000 0.45506 -0.172000 0.13284 CCT TCGA-2J-AAB9-01A-11D-A40W-08 CSE1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080345.2 0 0 1 18 273 1 69 1 2.113186e-01 9 27 1 69 4 0 0 0 0 0 2 1 0.750202 18 270 1 69 15 -2.642480 1 1 0 0 1 1 2 3 2.015589 0 0.100000 2.020000 0.109352 0.990000 0.790000 1.000000 1.000000 0.983564 0.990000 1 0.990000 1.000000 MGAT3 4248 broad.mit.edu 37 22 39884148 39884148 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr22:39884148C>T ENST00000341184.6 + 2 1011 c.796C>T c.(796-798)Cgc>Tgc p.R266C NM_001098270.1|NM_002409.4 NP_001091740.1|NP_002400.3 Q09327 MGAT3_HUMAN mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase 24 Melanoma(58;0.04) CGAGTACATCCGCCACAAGGT 0.637000 0 SO:0001583 missense ENST00000341184.6 0 1 hg19 CCDS13994.2 . . . . . . . . . . C 23.2 4.388329 0.82902 . . ENSG00000128268 ENST00000341184 . . . 5.43 5.43 0.79202 . 0.065075 0.64402 D 0.000012 T 0.65873 0.2733 L 0.43152 1.355 0.58432 D 0.999995 D 0.76494 0.999 P 0.60609 0.877 T 0.68070 -0.5506 9 0.72032 D 0.01 . 14.1179 0.65167 0.1502:0.8498:0.0:0.0 . 266 Q09327 MGAT3_HUMAN C 266 . ENSP00000345270:R266C R + 1 0 MGAT3 38214094 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.306000 0.59117 2.571000 0.86741 0.561000 0.74099 CGC TCGA-2J-AAB9-01A-11D-A40W-08 MGAT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075039.2 0 0 0 7 440 0 83 0 0 0 1 0 83 2 0 0 0 0 0 2 1 0.978641 7 427 0 83 2 -2.491321 0 1 0 0 1 1 2 3 2.000803 0 0.100000 2.020000 0.106256 0.350000 0.150000 1.000000 0.300000 0.424407 0.350000 0 0.230000 0.570000 PHF21B 112885 broad.mit.edu 37 22 45312324 45312324 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr22:45312324C>T ENST00000313237.5 - 4 550 c.400G>A c.(400-402)Gcc>Acc p.A134T PHF21B_ENST00000396103.3_Missense_Mutation_p.A134T|PHF21B_ENST00000447824.3_Missense_Mutation_p.A122T|PHF21B_ENST00000403565.1_5'UTR|PHF21B_ENST00000404079.2_Missense_Mutation_p.A122T NM_138415.4 NP_612424.1 Q96EK2 PF21B_HUMAN PHD finger protein 21B 25 all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731) GCGGGCTCGGCGAGGGCCTGG 0.726000 0 SO:0001583 missense ENST00000313237.5 0 1 hg19 CCDS14061.1 . . . . . . . . . . C 6.580 0.475266 0.12521 0.0 2.34E-4 ENSG00000056487 ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000420689 D;T;T;T;T 0.82167 -1.58;-1.49;-1.49;1.51;0.84 4.68 0.208 0.15221 . 0.598227 0.16002 N 0.234261 T 0.66607 0.2806 L 0.29908 0.895 0.20074 N 0.999932 B;B;B;B 0.12013 0.003;0.004;0.002;0.005 B;B;B;B 0.09377 0.004;0.002;0.002;0.004 T 0.46830 -0.9163 10 0.11182 T 0.66 -4.4072 6.0924 0.20001 0.0:0.5743:0.1259:0.2999 . 122;134;122;134 B7Z657;Q96EK2-3;B7Z4F8;Q96EK2 .;.;.;PF21B_HUMAN T 134;134;122;122;122 ENSP00000324403:A134T;ENSP00000379410:A134T;ENSP00000385105:A122T;ENSP00000388619:A122T;ENSP00000401294:A122T ENSP00000324403:A134T A - 1 0 PHF21B 43690988 0.001000 0.12720 0.237000 0.24090 0.423000 0.31445 -0.245000 0.08890 -0.031000 0.13781 -0.136000 0.14681 GCC TCGA-2J-AAB9-01A-11D-A40W-08 PHF21B-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000321731.2 1 0 0 10 131 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.996524 10 125 0 23 2 -14.480290 1 1 120466 5 35 1 1 2 3 2.000803 0 0.100000 2.020000 0.106256 0.990000 0.750000 1.000000 1.000000 0.982075 0.990000 1 0.990000 1.000000 EPB41L5 57669 broad.mit.edu 37 2 120776837 120776837 + Silent SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr2:120776837G>A ENST00000263713.5 + 2 391 c.177G>A c.(175-177)ttG>ttA p.L59L EPB41L5_ENST00000443124.1_Silent_p.L59L|EPB41L5_ENST00000452780.1_Silent_p.L59L|EPB41L5_ENST00000443902.2_Silent_p.L59L|EPB41L5_ENST00000331393.4_Silent_p.L59L NM_020909.3 NP_065960.2 Q9HCM4 E41L5_HUMAN erythrocyte membrane protein band 4.1 like 5 26 GTGTGGACTTGCCAGTAAGTA 0.443000 0 SO:0001819 synonymous_variant ENST00000263713.5 1 1 hg19 CCDS2130.1 TCGA-2J-AAB9-01A-11D-A40W-08 EPB41L5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000254230.2 1 0 0 52 676 0 125 1 2.156136e-01 4 8 0 125 2 0 0 0 0 0 2 1 1.000000 52 671 0 125 2 -10.771600 1 1 0 0 1 1 2 3 2.041853 0 0.100000 2.020000 0.115044 0.990000 0.990000 1.000000 1.000000 0.999847 0.990000 1 0.990000 1.000000 PARD3B 117583 broad.mit.edu 37 2 205983664 205983664 + Nonsense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr2:205983664C>T ENST00000406610.2 + 7 907 c.700C>T c.(700-702)Cga>Tga p.R234* PARD3B_ENST00000349953.3_Nonsense_Mutation_p.R234*|PARD3B_ENST00000462231.1_Nonsense_Mutation_p.R234*|PARD3B_ENST00000351153.1_Nonsense_Mutation_p.R234*|PARD3B_ENST00000358768.2_Nonsense_Mutation_p.R234* NM_057177.6|NM_152526.5|NM_205863.3 NP_476518.4|NP_689739.4|NP_995585.2 Q8TEW8 PAR3L_HUMAN par-3 family cell polarity regulator beta 65 all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06) ACTCTTCATCCGAGGCATTGA 0.338000 0 SO:0001587 stop_gained ENST00000406610.2 0 1 hg19 . . . . . . . . . . C 35 5.441097 0.96187 . . ENSG00000116117 ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953 . . . 5.64 4.75 0.60458 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.06236 T 0.91 . 15.9455 0.79789 0.1361:0.8639:0.0:0.0 . . . . X 234 . ENSP00000340280:R234X R + 1 2 PARD3B 205691909 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 3.696000 0.54757 1.361000 0.45981 -0.188000 0.12872 CGA TCGA-2J-AAB9-01A-11D-A40W-08 PARD3B-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000335992.1 0 0 0 6 290 0 47 0 0 0 1 0 47 2 0 0 0 0 0 2 1 0.964661 6 288 0 47 2 -2.644345 1 1 0 0 1 1 2 3 2.037688 0 0.100000 2.020000 0.114173 0.490000 0.190000 1.000000 0.410000 0.576634 0.490000 0 0.310000 1.000000 FARSB 10056 broad.mit.edu 37 2 223489170 223489170 + Silent SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr2:223489170G>A ENST00000281828.6 - 12 1254 c.991C>T c.(991-993)Ctg>Ttg p.L331L FARSB_ENST00000536361.1_Silent_p.L232L NM_005687.3 NP_005678.3 Q9NSD9 SYFB_HUMAN phenylalanyl-tRNA synthetase, beta subunit 24 Renal(207;0.0183) L-Phenylalanine(DB00120) ATCCTGGTCAGAAGTTTGGCA 0.338000 0 SO:0001819 synonymous_variant ENST00000281828.6 1 1 hg19 CCDS2454.1 TCGA-2J-AAB9-01A-11D-A40W-08 FARSB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256855.2 1 0 0 12 204 0 54 1 5.728947e-01 7 26 0 54 2 0 0 0 0 0 2 1 0.999173 12 203 0 54 2 -15.097390 1 1 0 0 1 1 2 3 2.037688 0 0.100000 2.020000 0.114173 0.990000 0.650000 1.000000 1.000000 0.958661 0.990000 1 0.890000 1.000000 MYLK 4638 broad.mit.edu 37 3 123345771 123345771 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:123345771G>A ENST00000475616.1 - 28 5131 c.5132C>T c.(5131-5133)aCg>aTg p.T1711M MYLK_ENST00000354792.5_Missense_Mutation_p.T511M|MYLK_ENST00000360772.3_Missense_Mutation_p.T1660M|MYLK_ENST00000359169.1_Missense_Mutation_p.T1660M|MYLK_ENST00000418370.2_5'Flank|MYLK-AS1_ENST00000463408.1_RNA|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000346322.5_Missense_Mutation_p.T1642M|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000360304.3_Missense_Mutation_p.T1711M Q15746 MYLK_HUMAN myosin light chain kinase 113 Lung NSC(201;0.0496) AAGGCACTGCGTGCAGTCCAG 0.502000 0 SO:0001583 missense ENST00000475616.1 1 1 hg19 CCDS46896.1 . . . . . . . . . . G 21.1 4.096308 0.76870 . . ENSG00000065534 ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000354792;ENST00000475616 T;T;T;T;T;T 0.66099 1.04;-0.19;1.04;-0.19;-0.19;-0.19 5.22 5.22 0.72569 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); . . . . T 0.71160 0.3307 L 0.31752 0.955 0.42283 D 0.992105 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.78314 0.978;0.978;0.978;0.978;0.991 T 0.73764 -0.3880 9 0.62326 D 0.03 . 18.9654 0.92694 0.0:0.0:1.0:0.0 . 1711;1591;1660;1642;1711 Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746 .;.;.;.;MYLK_HUMAN M 1660;1711;1660;1642;511;1711 ENSP00000354004:T1660M;ENSP00000353452:T1711M;ENSP00000352088:T1660M;ENSP00000320622:T1642M;ENSP00000346846:T511M;ENSP00000418335:T1711M ENSP00000320622:T1642M T - 2 0 MYLK 124828461 1.000000 0.71417 1.000000 0.80357 0.915000 0.54546 5.036000 0.64164 2.732000 0.93576 0.591000 0.81541 ACG TCGA-2J-AAB9-01A-11D-A40W-08 MYLK-004 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356464.1 1 0 1 19 166 0 37 0 8.246527e-01 0 30 0 37 2 0 0 0 0 0 2 1 0.999992 19 164 0 37 2 -9.308555 1 1 121412 1 39 1 0 1 1 1.995938 0 0.100000 2.020000 0.093656 0.990000 0.990000 1.000000 1.000000 0.999602 0.990000 1 0.990000 1.000000 MSL2 55167 broad.mit.edu 37 3 135913815 135913815 + Splice_Site SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:135913815G>A ENST00000309993.2 - 1 873 c.141C>T c.(139-141)tgC>tgT p.C47C MSL2_ENST00000434835.2_5'Flank NM_018133.3 NP_060603.2 Q9HCI7 MSL2_HUMAN male-specific lethal 2 homolog (Drosophila) 18 GCGTCTCACCGCAAACACAGC 0.507000 0 SO:0001630 splice_region_variant ENST00000309993.2 0 1 hg19 CCDS33861.1 TCGA-2J-AAB9-01A-11D-A40W-08 MSL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357347.1 0 0 0 7 742 0 150 0 9.026759e-03 0 13 0 150 2 0 0 0 0 0 2 1 0.980280 7 738 0 148 2 -1.879099 0 1 121412 1 33 1 0 1 1 1.995938 0 0.100000 2.020000 0.093656 0.190000 0.080000 0.360000 0.180000 0.208829 0.190000 0 0.130000 0.280000 GRIP2 80852 broad.mit.edu 37 3 14552768 14552768 + RNA SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:14552768C>T ENST00000273083.3 - 0 1902 Q9C0E4 GRIP2_HUMAN glutamate receptor interacting protein 2 25 GTTGTCCAGGCGGATATTGTC 0.612000 0 ENST00000273083.3 1 1 hg19 TCGA-2J-AAB9-01A-11D-A40W-08 GRIP2-001 KNOWN basic processed_transcript processed_transcript OTTHUMT00000340582.2 0 0 0 16 159 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.999939 16 156 0 34 2 -7.802773 1 1 121072 10 38 1 0 1 1 1.919377 0 0.100000 2.020000 0.058577 0.990000 0.750000 1.000000 1.000000 0.963068 0.990000 1 0.900000 1.000000 MED12L 116931 broad.mit.edu 37 3 151107890 151107890 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:151107890G>A ENST00000474524.1 + 36 5508 c.5470G>A c.(5470-5472)Ggc>Agc p.G1824S MED12L_ENST00000273432.4_Missense_Mutation_p.G1684S NM_053002.4 NP_443728.3 Q86YW9 MD12L_HUMAN mediator complex subunit 12-like 128 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) CCAGCAGCCCGGCTTTTTCCT 0.502000 0 SO:0001583 missense ENST00000474524.1 1 1 hg19 CCDS33876.1 . . . . . . . . . . G 15.08 2.727184 0.48833 . . ENSG00000144893 ENST00000474524;ENST00000273432 T;T 0.59906 0.37;0.23 5.75 -0.308 0.12773 Mediator complex, subunit Med12, catenin-binding (1); 0.320200 0.34110 N 0.004251 T 0.40886 0.1135 L 0.35723 1.085 0.23449 N 0.997655 B;B 0.32409 0.37;0.033 B;B 0.27380 0.079;0.038 T 0.22382 -1.0218 10 0.52906 T 0.07 -5.806 9.6232 0.39734 0.4167:0.0:0.5833:0.0 . 1684;1824 F8WAE6;Q86YW9 .;MD12L_HUMAN S 1824;1684 ENSP00000417235:G1824S;ENSP00000273432:G1684S ENSP00000273432:G1684S G + 1 0 MED12L 152590580 0.860000 0.29831 0.190000 0.23270 0.991000 0.79684 0.622000 0.24433 -0.386000 0.07821 0.655000 0.94253 GGC TCGA-2J-AAB9-01A-11D-A40W-08 MED12L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357707.2 1 0 0 34 694 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 1.000000 33 672 0 123 2 -4.357162 1 1 0 0 1 0 1 1 1.995938 0 0.100000 2.020000 0.093656 0.920000 0.650000 1.000000 1.000000 0.902447 0.920000 1 0.780000 1.000000 ABCF3 55324 broad.mit.edu 37 3 183904017 183904017 + Silent SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:183904017C>T ENST00000429586.2 + 1 207 c.22C>T c.(22-24)Ctg>Ttg p.L8L ABCF3_ENST00000292808.5_Silent_p.L8L|EIF2B5_ENST00000444495.1_Intron NM_018358.2 NP_060828.2 Q9NUQ8 ABCF3_HUMAN ATP-binding cassette, sub-family F (GCN20), member 3 39 all_cancers(143;1.12e-10)|Ovarian(172;0.0339) Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22) CGCCGAAATCCTGCGGAGCGA 0.652000 0 SO:0001819 synonymous_variant ENST00000429586.2 1 1 hg19 CCDS3254.1 TCGA-2J-AAB9-01A-11D-A40W-08 ABCF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346047.1 1 0 0 16 309 0 55 1 2.409718e-01 3 15 0 55 2 0 0 0 0 0 2 1 0.999932 17 304 0 55 2 -2.921758 1 1 121410 2 34 1 0 1 1 1.995938 0 0.100000 2.020000 0.093656 0.970000 0.580000 1.000000 1.000000 0.907662 0.970000 1 0.760000 1.000000 FETUB 26998 broad.mit.edu 37 3 186370361 186370361 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:186370361C>T ENST00000265029.3 + 7 1191 c.1090C>T c.(1090-1092)Cgc>Tgc p.R364C FETUB_ENST00000539949.1_Missense_Mutation_p.R216C|FETUB_ENST00000450521.1_Missense_Mutation_p.R364C|RP11-134F2.2_ENST00000428501.1_RNA|RP11-134F2.2_ENST00000455926.1_RNA|FETUB_ENST00000382134.3_Missense_Mutation_p.R299C|FETUB_ENST00000382136.3_Missense_Mutation_p.R327C NM_014375.2 NP_055190.2 Q9UGM5 FETUB_HUMAN fetuin B p.R364C(1) 20 all_cancers(143;6.64e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;5.73e-20) AGAAAAAGCACGCACTGCTGA 0.562000 1 Substitution - Missense(1) SO:0001583 missense ENST00000265029.3 0 1 hg19 CCDS3279.1 . . . . . . . . . . C 14.97 2.694262 0.48202 . . ENSG00000090512 ENST00000450521;ENST00000539949;ENST00000265029;ENST00000382134;ENST00000382136 T;T;T;T;T 0.62788 -0.0;-0.0;-0.0;-0.0;-0.0 4.27 2.33 0.28932 . 0.527286 0.17286 N 0.179826 T 0.70979 0.3286 M 0.69823 2.125 0.09310 N 0.999991 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.66602 0.92;0.945;0.91 T 0.58707 -0.7589 10 0.87932 D 0 -7.428 4.7449 0.13033 0.2128:0.6758:0.0:0.1115 . 327;299;364 E9PG06;E9PG08;Q9UGM5 .;.;FETUB_HUMAN C 364;216;364;299;327 ENSP00000404288:R364C;ENSP00000443704:R216C;ENSP00000265029:R364C;ENSP00000371569:R299C;ENSP00000371571:R327C ENSP00000265029:R364C R + 1 0 FETUB 187853055 0.000000 0.05858 0.170000 0.22879 0.001000 0.01503 0.050000 0.14120 1.169000 0.42739 -0.140000 0.14226 CGC TCGA-2J-AAB9-01A-11D-A40W-08 FETUB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344679.1 0 0 0 7 343 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 0.979855 6 339 0 48 2 -3.303856 1 1 121412 8 40 1 0 1 1 1.995938 0 0.100000 2.020000 0.093656 0.410000 0.180000 0.750000 0.390000 0.438764 0.410000 0 0.280000 0.580000 CCDC50 152137 broad.mit.edu 37 3 191098488 191098488 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr3:191098488G>A ENST00000392455.3 + 7 1175 c.577G>A c.(577-579)Gac>Aac p.D193N CCDC50_ENST00000392456.3_Missense_Mutation_p.D369N NM_174908.3 NP_777568.1 Q8IVM0 CCD50_HUMAN coiled-coil domain containing 50 23 all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221) LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06) TACCCAGGTGGACATGAGAGC 0.348000 0 SO:0001583 missense ENST00000392455.3 1 1 hg19 CCDS33913.1 . . . . . . . . . . G 25.4 4.634726 0.87660 . . ENSG00000152492 ENST00000392455;ENST00000392456 T;T 0.55413 0.88;0.52 5.49 5.49 0.81192 . 0.109300 0.64402 D 0.000008 T 0.72930 0.3522 M 0.79258 2.445 0.38906 D 0.957439 D;D 0.89917 0.999;1.0 D;D 0.87578 0.951;0.998 T 0.77768 -0.2464 10 0.87932 D 0 . 14.8753 0.70491 0.0:0.0:1.0:0.0 . 193;369 Q8IVM0;Q8IVM0-2 CCD50_HUMAN;. N 193;369 ENSP00000376249:D193N;ENSP00000376250:D369N ENSP00000376249:D193N D + 1 0 CCDC50 192581182 1.000000 0.71417 0.994000 0.49952 0.975000 0.68041 5.382000 0.66213 2.576000 0.86940 0.591000 0.81541 GAC TCGA-2J-AAB9-01A-11D-A40W-08 CCDC50-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000343315.1 1 0 0 7 139 0 36 1 9.024162e-01 14 71 0 36 2 0 0 0 0 0 2 1 0.979474 7 135 0 36 2 -10.124270 1 1 0 0 1 0 1 1 1.995938 0 0.100000 2.020000 0.093656 0.950000 0.430000 1.000000 1.000000 0.866096 0.950000 1 0.660000 1.000000 C1QTNF7 114905 broad.mit.edu 37 4 15444115 15444115 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr4:15444115G>A ENST00000444304.2 + 3 888 c.562G>A c.(562-564)Gct>Act p.A188T C1QTNF7_ENST00000295297.4_Missense_Mutation_p.A195T|C1QTNF7_ENST00000429690.1_Missense_Mutation_p.A188T Q9BXJ2 C1QT7_HUMAN C1q and tumor necrosis factor related protein 7 16 GTTCATCTGTGCTTTCCCAGG 0.438000 0 SO:0001583 missense ENST00000444304.2 1 1 hg19 CCDS3414.1 . . . . . . . . . . G 18.59 3.656712 0.67586 . . ENSG00000163145 ENST00000295297;ENST00000429690;ENST00000444304 T;T;T 0.74842 -0.88;-0.88;-0.88 5.8 5.8 0.92144 Tumour necrosis factor-like (2);Complement C1q protein (4); 0.052703 0.85682 D 0.000000 T 0.72669 0.3489 N 0.21617 0.685 0.80722 D 1 P 0.51240 0.943 P 0.51516 0.672 T 0.69665 -0.5084 9 . . . . 20.0545 0.97645 0.0:0.0:1.0:0.0 . 188 Q9BXJ2 C1QT7_HUMAN T 195;188;188 ENSP00000295297:A195T;ENSP00000410722:A188T;ENSP00000388914:A188T . A + 1 0 C1QTNF7 15053213 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.830000 0.99415 2.748000 0.94277 0.655000 0.94253 GCT TCGA-2J-AAB9-01A-11D-A40W-08 C1QTNF7-002 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000250891.2 1 0 0 49 845 0 194 0 0 0 1 0 194 2 0 0 0 0 0 2 1 1.000000 48 831 0 191 2 -7.395627 1 1 0 0 1 0 0 0 1.955828 0 0.100000 2.020000 0.075026 0.990000 0.790000 1.000000 1.000000 0.971265 0.990000 1 0.910000 1.000000 WDR36 134430 broad.mit.edu 37 5 110459563 110459563 + Missense_Mutation SNP A A G TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr5:110459563A>G ENST00000513710.2 + 20 2381 c.2377A>G c.(2377-2379)Aca>Gca p.T793A WDR36_ENST00000506538.2_Missense_Mutation_p.T793A Q8NI36 WDR36_HUMAN WD repeat domain 36 45 all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244) TTTCATTCCAACAATTCCTGG 0.353000 0 SO:0001583 missense ENST00000513710.2 1 1 hg19 CCDS4102.1 . . . . . . . . . . A 23.5 4.419359 0.83559 . . ENSG00000134987 ENST00000506538;ENST00000513710 T;T 0.80824 -1.42;-1.42 5.65 5.65 0.86999 Small-subunit processome, Utp21 (1); 0.000000 0.85682 D 0.000000 D 0.89529 0.6741 M 0.76838 2.35 0.80722 D 1 D 0.76494 0.999 D 0.72338 0.977 D 0.90801 0.4694 10 0.87932 D 0 -21.8617 16.1611 0.81712 1.0:0.0:0.0:0.0 . 793 Q8NI36 WDR36_HUMAN A 793 ENSP00000423067:T793A;ENSP00000424628:T793A ENSP00000423067:T793A T + 1 0 WDR36 110487462 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.965000 0.87945 2.272000 0.75746 0.460000 0.39030 ACA TCGA-2J-AAB9-01A-11D-A40W-08 WDR36-008 NOVEL not_organism_supported|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000373504.3 1 0 0 18 318 0 93 0 1.458305e-01 1 11 0 93 2 0 0 0 0 0 2 1 0.999984 18 318 0 91 2 -19.799980 1 1 121410 1 36 1 0 0 0 1.975219 0 0.100000 2.020000 0.083503 0.990000 0.640000 1.000000 1.000000 0.937443 0.990000 1 0.820000 1.000000 EPB41L4A 64097 broad.mit.edu 37 5 111616005 111616005 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr5:111616005C>T ENST00000261486.5 - 3 496 c.220G>A c.(220-222)Gca>Aca p.A74T NM_022140.3 NP_071423 Q9HCS5 E41LA_HUMAN erythrocyte membrane protein band 4.1 like 4A 34 all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135) AGGGTTTTTGCAGGATCCAGC 0.338000 0 SO:0001583 missense ENST00000261486.5 0 1 hg19 CCDS43350.1 . . . . . . . . . . C 9.117 1.008081 0.19199 . . ENSG00000129595 ENST00000261486 T 0.76709 -1.04 5.95 4.08 0.47627 FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);FERM conserved site (1); 0.284025 0.35262 N 0.003333 T 0.55337 0.1914 N 0.11000 0.08 0.29488 N 0.855849 B 0.18461 0.028 B 0.17722 0.019 T 0.47209 -0.9135 10 0.27082 T 0.32 . 6.3895 0.21579 0.149:0.6989:0.0:0.1521 . 74 Q9HCS5 E41LA_HUMAN T 74 ENSP00000261486:A74T ENSP00000261486:A74T A - 1 0 EPB41L4A 111643904 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 1.000000 0.29770 1.524000 0.49035 0.655000 0.94253 GCA TCGA-2J-AAB9-01A-11D-A40W-08 EPB41L4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370969.1 0 0 0 7 784 1 200 0 6.729738e-04 0 4 1 200 2 0 0 0 0 0 2 0 0.063656 7 780 1 196 15 -1.817398 0 1 0 0 1 0 0 0 1.975219 0 0.100000 2.020000 0.083503 0.180000 0.070000 0.340000 0.170000 0.195387 0.180000 0 0.120000 0.260000 PCDHA3 56145 broad.mit.edu 37 5 140183013 140183013 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr5:140183013C>T ENST00000522353.2 + 1 2231 c.2231C>T c.(2230-2232)gCg>gTg p.A744V PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.A744V|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron NM_018906.2 NP_061729.1 Q9Y5H8 PCDA3_HUMAN protocadherin alpha 3 95 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGCTCCAGCGCGGTGGGGAGC 0.637000 0 SO:0001583 missense ENST00000522353.2 1 1 hg19 CCDS54915.1 . . . . . . . . . . c 20.5 3.999339 0.74818 . . ENSG00000255408 ENST00000522353;ENST00000532566 T;T 0.76709 -1.04;-1.04 4.16 3.22 0.36961 . 0.177603 0.26187 U 0.025825 D 0.85974 0.5822 M 0.93550 3.43 0.21020 N 0.999808 D;P 0.62365 0.991;0.714 P;B 0.56216 0.794;0.285 T 0.77048 -0.2732 10 0.34782 T 0.22 . 7.9252 0.29870 0.2451:0.6621:0.0:0.0928 . 744;744 Q9Y5H8-2;Q9Y5H8 .;PCDA3_HUMAN V 744 ENSP00000429808:A744V;ENSP00000434086:A744V ENSP00000429808:A744V A + 2 0 PCDHA3 140163197 0.005000 0.15991 1.000000 0.80357 0.975000 0.68041 0.359000 0.20233 2.039000 0.60335 0.467000 0.42956 GCG TCGA-2J-AAB9-01A-11D-A40W-08 PCDHA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372848.2 1 0 0 23 476 0 104 0 2.385667e-03 0 2 0 104 2 0 0 0 0 0 2 1 0.999999 23 464 0 102 2 -4.890256 1 1 0 0 1 0 0 0 1.975219 0 0.100000 2.020000 0.083503 0.900000 0.590000 1.000000 1.000000 0.878971 0.900000 1 0.730000 1.000000 TXLNB 167838 broad.mit.edu 37 6 139563774 139563774 + Silent SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr6:139563774G>A ENST00000358430.3 - 10 2176 c.1944C>T c.(1942-1944)tgC>tgT p.C648C RP1-225E12.3_ENST00000585874.1_RNA NM_153235.3 NP_694967.3 Q8N3L3 TXLNB_HUMAN taxilin beta 37 TACTGGGCTCGCATGCAGGCA 0.652000 0 SO:0001819 synonymous_variant ENST00000358430.3 1 1 hg19 CCDS34545.1 TCGA-2J-AAB9-01A-11D-A40W-08 TXLNB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042458.1 0 0 0 16 658 1 99 0 0 0 1 99 2 0 0 0 0 0 2 0 0.180870 16 640 1 93 22 -2.696289 1 1 0 0 1 1 9 10 2.842403 1 0.100000 2.020000 0.357143 0.680000 0.390000 1.000000 1.000000 0.697189 0.680000 0 0.520000 0.870000 SYNJ2 8871 broad.mit.edu 37 6 158484842 158484842 + Missense_Mutation SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr6:158484842C>T ENST00000355585.4 + 9 1222 c.1147C>T c.(1147-1149)Cgg>Tgg p.R383W SYNJ2_ENST00000367122.2_Missense_Mutation_p.R383W|SYNJ2_ENST00000449859.2_Missense_Mutation_p.R311W|SYNJ2_ENST00000367121.3_Missense_Mutation_p.R383W NM_001178088.1|NM_003898.3 NP_001171559.1|NP_003889.1 O15056 SYNJ2_HUMAN synaptojanin 2 46 AGGCACTTTGCGGATGAACTG 0.502000 0 SO:0001583 missense ENST00000355585.4 0 1 hg19 CCDS5254.1 . . . . . . . . . . C 21.7 4.188294 0.78789 . . ENSG00000078269 ENST00000367122;ENST00000367121;ENST00000355585;ENST00000449859 T;T;T;T 0.25579 1.79;1.79;1.79;1.79 4.98 4.98 0.66077 Synaptojanin, N-terminal (1); 0.000000 0.56097 D 0.000035 T 0.68805 0.3041 H 0.99668 4.69 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.997;1.0;0.999;0.999 D 0.85064 0.0936 10 0.87932 D 0 . 18.3154 0.90218 0.0:1.0:0.0:0.0 . 311;383;383;383 B4DJU8;E7ER60;O15056;O15056-3 .;.;SYNJ2_HUMAN;. W 383;383;383;311 ENSP00000356089:R383W;ENSP00000356088:R383W;ENSP00000347792:R383W;ENSP00000388371:R311W ENSP00000347792:R383W R + 1 2 SYNJ2 158404830 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 3.324000 0.52022 2.327000 0.79052 0.456000 0.33151 CGG TCGA-2J-AAB9-01A-11D-A40W-08 SYNJ2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042858.2 0 0 0 6 526 0 113 0 1.153527e-02 0 12 0 113 2 0 0 0 0 0 2 1 0.963261 7 516 0 111 2 -1.967216 0 1 121412 3 40 1 0 1 1 1.921593 0 0.100000 2.020000 0.064935 0.220000 0.090000 0.440000 0.210000 0.245516 0.220000 0 0.150000 0.330000 HIST1H2BE 8344 broad.mit.edu 37 6 26184241 26184241 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr6:26184241G>A ENST00000356530.3 + 1 284 c.218G>A c.(217-219)cGc>cAc p.R73H NM_003523.2 NP_003514.2 P62807 H2B1C_HUMAN histone cluster 1, H2be 4 ATCTTCGAGCGCATCGCCGGC 0.597000 0 SO:0001583 missense ENST00000356530.3 0 1 hg19 CCDS4588.1 . . . . . . . . . . . 14.91 2.676040 0.47886 . . ENSG00000197697 ENST00000356530 T 0.69561 -0.41 4.96 4.96 0.65561 . 0.000000 0.34555 U 0.003862 T 0.73560 0.3602 . . . 0.52501 D 0.999953 . . . . . . T 0.74734 -0.3565 7 0.49607 T 0.09 . 17.6163 0.88068 0.0:0.0:1.0:0.0 . . . . H 73 ENSP00000348924:R73H ENSP00000348924:R73H R + 2 0 HIST1H2BE 26292220 1.000000 0.71417 1.000000 0.80357 0.091000 0.18340 7.562000 0.82300 2.479000 0.83701 0.537000 0.68136 CGC TCGA-2J-AAB9-01A-11D-A40W-08 HIST1H2BE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040090.1 0 0 0 7 758 0 128 0 0 0 1 0 128 2 0 0 0 0 0 2 1 0.978422 7 735 0 127 2 -1.790174 0 1 0 0 1 0 1 1 1.959608 0 0.100000 2.020000 0.081633 0.180000 0.080000 0.350000 0.180000 0.201434 0.180000 0 0.120000 0.270000 TRIP6 7205 broad.mit.edu 37 7 100466383 100466383 + Silent SNP G G T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr7:100466383G>T ENST00000200457.4 + 4 990 c.630G>T c.(628-630)ggG>ggT p.G210G NM_003302.2 NP_003293.2 Q15654 TRIP6_HUMAN thyroid hormone receptor interactor 6 14 Lung NSC(181;0.041)|all_lung(186;0.0581) AAGTCTGGGGGCCTGGCTATA 0.701000 0 SO:0001819 synonymous_variant ENST00000200457.4 1 1 hg19 CCDS5708.1 TCGA-2J-AAB9-01A-11D-A40W-08 TRIP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347151.2 1 0 1 8 98 0 30 1 9.805972e-01 26 63 0 30 2 0 0 0 0 0 2 1 0.989896 8 97 0 28 2 -13.072860 1 1 120162 1 29 1 1 2 3 2.025660 0 0.100000 2.020000 0.111550 0.990000 0.750000 1.000000 1.000000 0.983687 0.990000 1 0.990000 1.000000 SSPO 23145 broad.mit.edu 37 7 149477126 149477126 + RNA SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr7:149477126C>T ENST00000378016.2 + 0 1303 A2VEC9 SSPO_HUMAN SCO-spondin Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) GCAAGAGGGGCGGCAGCAGGC 0.637000 0 ENST00000378016.2 0 1 hg19 TCGA-2J-AAB9-01A-11D-A40W-08 SSPO-202 KNOWN basic processed_transcript processed_transcript 0 0 0 5 74 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 0.937555 5 73 0 13 2 -9.539402 1 1 120664 13 39 1 1 2 3 2.040487 0 0.100000 2.020000 0.115044 0.990000 0.540000 1.000000 1.000000 0.951540 0.990000 1 0.900000 1.000000 ABCB1 5243 broad.mit.edu 37 7 87190672 87190672 + Missense_Mutation SNP A A G TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr7:87190672A>G ENST00000265724.3 - 9 1151 c.734T>C c.(733-735)tTa>tCa p.L245S ABCB1_ENST00000543898.1_Missense_Mutation_p.L181S NM_000927.4 NP_000918.2 P08183 MDR1_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 1 111 Esophageal squamous(14;0.00164) Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495) TGCATACGCTAAGAGTTCTTT 0.318000 0 SO:0001583 missense ENST00000265724.3 1 1 hg19 CCDS5608.1 . . . . . . . . . . A 1.804 -0.476462 0.04414 . . ENSG00000085563 ENST00000543174;ENST00000265724;ENST00000543898 D;D 0.88896 -2.44;-2.44 5.74 -1.39 0.08997 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 1.288110 0.05571 N 0.571119 T 0.68879 0.3049 N 0.02368 -0.58 0.09310 N 1 B;B 0.09022 0.002;0.002 B;B 0.13407 0.0;0.009 T 0.60265 -0.7297 10 0.09338 T 0.73 0.2998 4.5323 0.12011 0.2258:0.0:0.2567:0.5174 . 181;245 B5AK60;P08183 .;MDR1_HUMAN S 26;245;181 ENSP00000265724:L245S;ENSP00000444095:L181S ENSP00000265724:L245S L - 2 0 ABCB1 87028608 0.000000 0.05858 0.034000 0.17996 0.760000 0.43138 0.871000 0.28023 -0.139000 0.11414 -0.336000 0.08194 TTA TCGA-2J-AAB9-01A-11D-A40W-08 ABCB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335444.2 1 0 0 10 185 0 41 0 1.858242e-02 0 4 0 41 2 0 0 0 0 0 2 1 0.996953 10 183 0 39 2 -13.362400 1 1 0 0 1 1 2 3 2.025660 0 0.100000 2.020000 0.111550 0.990000 0.560000 1.000000 1.000000 0.931651 0.990000 1 0.800000 1.000000 VPS13B 157680 broad.mit.edu 37 8 100729436 100729436 + Silent SNP C C T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr8:100729436C>T ENST00000358544.2 + 37 6678 c.6567C>T c.(6565-6567)aaC>aaT p.N2189N VPS13B_ENST00000357162.2_Silent_p.N2164N|VPS13B_ENST00000395996.1_3'UTR NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TCAGTATAAACGATTTTCTCC 0.353000 Colon(161;2205 2542 7338 31318) 0 SO:0001819 synonymous_variant ENST00000358544.2 1 1 hg19 CCDS6280.1 TCGA-2J-AAB9-01A-11D-A40W-08 VPS13B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000277138.1 1 0 0 15 209 0 45 1 1.506866e-02 2 1 0 45 2 0 0 0 0 0 2 1 0.999885 15 208 0 42 2 -6.173016 1 1 121404 2 25 1 0 1 1 1.996969 0 0.100000 2.020000 0.094112 0.990000 0.770000 1.000000 1.000000 0.982189 0.990000 1 0.990000 1.000000 KCNS2 3788 broad.mit.edu 37 8 99440470 99440470 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chr8:99440470G>A ENST00000287042.4 + 2 613 c.263G>A c.(262-264)gGc>gAc p.G88D KCNS2_ENST00000521839.1_Missense_Mutation_p.G88D NM_020697.2 NP_065748.1 Q9ULS6 KCNS2_HUMAN potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2 p.G88D(1) 31 Breast(36;2.4e-06) OV - Ovarian serous cystadenocarcinoma(57;0.0448) TATCACACCGGCAAGCTTCAC 0.542000 Pancreas(138;844 2489 9202 24627) 1 Substitution - Missense(1) SO:0001583 missense ENST00000287042.4 0 1 hg19 CCDS6279.1 . . . . . . . . . . G 23.1 4.376631 0.82682 . . ENSG00000156486 ENST00000287042;ENST00000521839 T;T 0.55930 0.49;0.49 5.41 5.41 0.78517 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); 0.055844 0.64402 D 0.000001 T 0.80864 0.4705 M 0.93638 3.44 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.85918 0.1444 10 0.87932 D 0 . 19.1973 0.93695 0.0:0.0:1.0:0.0 . 88 Q9ULS6 KCNS2_HUMAN D 88 ENSP00000287042:G88D;ENSP00000430712:G88D ENSP00000287042:G88D G + 2 0 KCNS2 99509646 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.869000 0.99810 2.527000 0.85204 0.563000 0.77884 GGC TCGA-2J-AAB9-01A-11D-A40W-08 KCNS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000103134.1 0 0 0 6 453 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 0.963996 6 448 0 89 2 -2.133737 0 1 0 0 1 0 1 1 1.996969 0 0.100000 2.020000 0.094112 0.270000 0.110000 0.520000 0.250000 0.295399 0.270000 0 0.180000 0.400000 L1CAM 3897 broad.mit.edu 37 X 153130847 153130847 + Missense_Mutation SNP G G A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chrX:153130847G>A ENST00000370060.1 - 21 2845 c.2656C>T c.(2656-2658)Cgg>Tgg p.R886W L1CAM_ENST00000361981.3_Missense_Mutation_p.R881W|L1CAM_ENST00000361699.4_Missense_Mutation_p.R886W|L1CAM_ENST00000538883.1_Missense_Mutation_p.R888W|L1CAM_ENST00000370055.1_Missense_Mutation_p.R881W|L1CAM_ENST00000370057.3_Missense_Mutation_p.R886W|L1CAM_ENST00000543994.1_Missense_Mutation_p.R888W NM_001278116.1 NP_001265045.1 P32004 L1CAM_HUMAN L1 cell adhesion molecule p.R886W(1) 81 all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CTATAGGGCCGCAAGCCACTG 0.612000 1 Substitution - Missense(1) SO:0001583 missense ENST00000370060.1 0 1 hg19 CCDS14733.1 . . . . . . . . . . G 11.63 1.695980 0.30052 . . ENSG00000198910 ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699 T;T;T;T;T;T;T 0.59502 0.26;0.26;0.26;0.26;0.26;0.26;0.26 5.33 1.51 0.23008 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.290733 0.23770 N 0.044730 T 0.49575 0.1565 M 0.68952 2.095 0.39443 D 0.967286 B;B;B 0.26195 0.065;0.144;0.048 B;B;B 0.25405 0.025;0.06;0.043 T 0.43491 -0.9388 10 0.54805 T 0.06 . 5.1621 0.15066 0.1693:0.0:0.2808:0.5499 . 881;886;886 G3XAF4;P32004-2;P32004 .;.;L1CAM_HUMAN W 886;888;886;888;881;881;886 ENSP00000359077:R886W;ENSP00000438430:R888W;ENSP00000359074:R886W;ENSP00000439645:R888W;ENSP00000354712:R881W;ENSP00000359072:R881W;ENSP00000355380:R886W ENSP00000355380:R886W R - 1 2 L1CAM 152784041 0.135000 0.22499 0.333000 0.25482 0.410000 0.31052 1.255000 0.32909 0.105000 0.17753 0.529000 0.55759 CGG TCGA-2J-AAB9-01A-11D-A40W-08 L1CAM-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000061094.2 0 0 0 6 618 0 116 0 4.239339e-04 0 3 0 116 2 0 9.331763e-01 0 499 0 488 2 1 0.962188 6 602 0 111 2 -1.565663 0 1 121410 5 41 1 0 1 1 0.100000 2.020000 0.100000 0.200000 0.080000 0.390000 0.190000 0.220406 0.200000 0 0.130000 0.300000 DMD 1756 broad.mit.edu 37 X 31525402 31525402 + Missense_Mutation SNP T T A TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chrX:31525402T>A ENST00000357033.4 - 56 8592 c.8386A>T c.(8386-8388)Att>Ttt p.I2796F DMD_ENST00000474231.1_Missense_Mutation_p.I336F|DMD_ENST00000445312.1_5'UTR|DMD_ENST00000378707.3_Missense_Mutation_p.I336F|DMD_ENST00000541735.1_Missense_Mutation_p.I336F|DMD_ENST00000343523.2_Missense_Mutation_p.I336F|DMD_ENST00000378677.2_Missense_Mutation_p.I2792F|DMD_ENST00000359836.1_Missense_Mutation_p.I336F NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2 NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1 P11532 DMD_HUMAN dystrophin 77 all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203) TCCTACCTAATGTTGAGAGAC 0.408000 0 SO:0001583 missense ENST00000357033.4 1 1 hg19 CCDS14233.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 19.85|19.85 3.903073|3.903073 0.72754|0.72754 .|. .|. ENSG00000198947|ENSG00000198947 ENST00000465285|ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231 .|T;T;T;T;T;T;T;T .|0.49720 .|0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77 5.75|5.75 5.75|5.75 0.90469|0.90469 .|. .|0.000000 .|0.37304 .|U .|0.002147 T|T 0.69287|0.69287 0.3094|0.3094 M|M 0.78049|0.78049 2.395|2.395 0.58432|0.58432 D|D 0.999999|0.999999 .|D;D;D;D;D;D;D;D;D;D;D .|0.89917 .|0.994;0.994;0.993;0.994;0.994;0.989;0.996;0.996;0.997;0.993;1.0 .|P;D;D;D;D;D;D;D;D;P;D .|0.76575 .|0.791;0.917;0.912;0.917;0.917;0.949;0.978;0.978;0.917;0.865;0.988 T|T 0.72491|0.72491 -0.4277|-0.4277 5|10 .|0.54805 .|T .|0.06 .|. 14.9992|14.9992 0.71459|0.71459 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. .|2788;2796;2792;1455;1452;336;336;336;336;336;2673 .|P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3 .|.;DMD_HUMAN;.;.;.;.;.;.;.;.;. L|F 524|2788;1455;1452;492;2792;2796;336;336;2796;2673;336;336;336 .|ENSP00000350765:I492F;ENSP00000367948:I2792F;ENSP00000354923:I2796F;ENSP00000352894:I336F;ENSP00000340057:I336F;ENSP00000367979:I336F;ENSP00000444119:I336F;ENSP00000417123:I336F .|ENSP00000340057:I336F H|I -|- 2|1 0|0 DMD|DMD 31435323|31435323 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.988000|0.988000 0.76386|0.76386 5.220000|5.220000 0.65267|0.65267 1.924000|1.924000 0.55735|0.55735 0.481000|0.481000 0.45027|0.45027 CAT|ATT TCGA-2J-AAB9-01A-11D-A40W-08 DMD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056182.2 1 0 0 17 283 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 0.999964 17 278 0 81 2 -19.727000 1 1 0 0 1 0 1 1 0.100000 2.020000 0.100000 0.990000 0.690000 1.000000 1.000000 0.959545 0.990000 1 0.890000 1.000000 KDM6A 7403 broad.mit.edu 37 X 44928823 44928823 + Splice_Site SNP G G T TCGA-2J-AAB9-01A-11D-A40W-08 TCGA-2J-AAB9-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx e8075728-2dc4-4d9b-8343-57b2da7bde0d ac03264a-a295-4e60-bf15-03a7e921c667 g.chrX:44928823G>T ENST00000377967.4 + 17 1964 c.e17-1 KDM6A_ENST00000536777.1_Splice_Site|KDM6A_ENST00000382899.4_Splice_Site|KDM6A_ENST00000543216.1_Splice_Site NM_021140.2 NP_066963.2 O15550 KDM6A_HUMAN lysine (K)-specific demethylase 6A p.0?(6) 170 TTTCTTTTTAGGGGCTTCACA 0.378000 D, N, F, S renal, oesophageal SCC, MM Colon(129;1273 1667 15230 27352 52914) Rec yes X Xp11.2 7403 lysine (K)-specific demethylase 6A, UTX E, L 6 Whole gene deletion(6) SO:0001630 splice_region_variant ENST00000377967.4 1 1 hg19 CCDS14265.1 . . . . . . . . . . G 17.32 3.360767 0.61403 . . ENSG00000147050 ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000414389;ENST00000433797 . . . 5.08 5.08 0.68730 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.9308 0.88996 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . KDM6A 44813767 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 9.114000 0.94329 2.255000 0.74692 0.600000 0.82982 . TCGA-2J-AAB9-01A-11D-A40W-08 KDM6A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056324.1 1 0 0 8 149 0 38 0 0 0 0 38 2 1 9.998065e-01 46 641 1 731 6 1 0.989685 8 148 0 37 2 -2.934003 1 1 0 0 1 0 1 1 0.100000 2.020000 0.100000 0.990000 0.490000 1.000000 1.000000 0.898247 0.990000 1 0.720000 1.000000