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 TP53 7157 broad.mit.edu 37 17 7579320 7579321 + Frame_Shift_Ins INS - - C TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 - C - - Valid Somatic Phase_I WXS targeted Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr17:7579320_7579321insC ENST00000269305.4 - 4 555_556 c.366_367insG c.(364-369)gtgactfs p.T123fs TP53_ENST00000445888.2_Frame_Shift_Ins_p.T123fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Ins_p.T123fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.T123fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.T123fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.T123fs 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.0?(8)|p.V122fs*26(5)|p.G59fs*23(3)|p.V73fs*9(1)|p.T123fs*24(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.P13fs*18(1)|p.S33fs*23(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ACCGTGCAAGTCACAGACTTGG 0.550000 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 24 Deletion - Frameshift(14)|Whole gene deletion(8)|Deletion - In frame(2) SO:0001589 frameshift_variant 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 TCGA-IB-AAUU-01A-11D-A377-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 48 280 0 74 0 8.504663e-01 0 22 0 74 2 1 9.994585e-01 18 50 0 55 2 1 1 49 276 0 76 2 0 0 0 0 0 0 -3.145735 1 1 0 0 1 0 1 1 1.363146 1 0.370000 3.300000 0.226994 0.630000 4.800000e-01 0.810000 0.640000 0.647331 0.630000 0 0.550000 0.730000 ZNF566 84924 broad.mit.edu 37 19 36940853 36940853 + Frame_Shift_Del DEL A A - TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr19:36940853delA ENST00000434377.2 - 5 364 c.283delT c.(283-285)tatfs p.Y95fs ZNF566_ENST00000454319.1_Frame_Shift_Del_p.Y96fs|ZNF566_ENST00000493391.1_5'UTR|ZNF566_ENST00000424129.2_Frame_Shift_Del_p.Y95fs|ZNF566_ENST00000392170.2_Frame_Shift_Del_p.Y96fs NM_032838.4 NP_116227.1 Q969W8 ZN566_HUMAN zinc finger protein 566 24 Esophageal squamous(110;0.162) TCTATTTCATAAATTTCTTTC 0.348000 0 SO:0001589 frameshift_variant ENST00000434377.2 1 0 hg19 CCDS12494.1 TCGA-IB-AAUU-01A-11D-A377-08 ZNF566-201 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000341054.1 1 0 0 94 892 0 191 0 1.072795e-01 1 5 0 191 2 0 0 0 0 1 9.932648e-01 132 880 9 189 67 0 0 0 0 0 0 -20.000000 1 1 0 0 1 2 4 6 2.429890 1 0.370000 3.300000 0.578821 0.790000 6.300000e-01 1.000000 0.760000 0.824389 0.790000 0 0.700000 1.000000 HIST1H1B 3009 broad.mit.edu 37 6 27834834 27834845 + In_Frame_Del DEL CTTCTTCGGAGT CTTCTTCGGAGT - rs143393068 byFrequency TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr6:27834834_27834845delCTTCTTCGGAGT ENST00000331442.3 - 1 514_525 c.463_474delACTCCGAAGAAG c.(463-474)actccgaagaagdel p.TPKK155del NM_005322.2 NP_005313.1 P16401 H15_HUMAN histone cluster 1, H1b 24 GCTTCTTCGCCTTCTTCGGAGTCTTCTTCACT 0.599000 0 SO:0001651 inframe_deletion ENST00000331442.3 1 1 hg19 CCDS4635.1 TCGA-IB-AAUU-01A-11D-A377-08 HIST1H1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043371.1 1 0 0 70 1034 0 197 0 0 0 197 0 0 0 0 1 5.591003e-03 169 1124 16 210 119 0 0 0 0 0 0 -11.622140 1 1 0 0 1 1 2 3 1.637296 0 0.370000 3.300000 0.376916 0.340000 2.600000e-01 1.000000 0.350000 0.380840 0.340000 0 0.300000 0.400000 PDCD11 22984 broad.mit.edu 37 10 105182763 105182763 + Missense_Mutation SNP C C T rs142899352 TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr10:105182763C>T ENST00000369797.3 + 18 2610 c.2516C>T c.(2515-2517)aCg>aTg p.T839M NM_014976.1 NP_055791.1 Q14690 RRP5_HUMAN programmed cell death 11 p.T839M(1) 64 Colorectal(252;0.0747)|Breast(234;0.128) TTGATCCAGACGCTGGCCGAG 0.527000 1 Substitution - Missense(1) SO:0001583 missense ENST00000369797.3 1 1 hg19 CCDS31276.1 . . . . . . . . . . C 14.89 2.669172 0.47677 2.27E-4 0.0 ENSG00000148843 ENST00000369797;ENST00000543503 T 0.10288 2.89 5.95 5.04 0.67666 . 0.388932 0.31092 N 0.008272 T 0.12646 0.0307 L 0.51422 1.61 0.35143 D 0.769016 D 0.67145 0.996 B 0.44163 0.443 T 0.07616 -1.0763 10 0.45353 T 0.12 -14.7673 11.5381 0.50651 0.0:0.9178:0.0:0.0822 . 839 Q14690 RRP5_HUMAN M 839 ENSP00000358812:T839M ENSP00000358812:T839M T + 2 0 PDCD11 105172753 0.029000 0.19370 0.968000 0.41197 0.402000 0.30811 0.122000 0.15687 2.826000 0.97356 0.491000 0.48974 ACG TCGA-IB-AAUU-01A-11D-A377-08 PDCD11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050151.1 1 0 1 41 270 0 48 1 8.839784e-01 5 22 0 48 2 0 0 0 0 0 2 1 1 40 267 0 48 2 0 0 0 0 48 2 -18.301170 1 1 121374 4 39 1 2 2 4 2.262088 1 0.370000 3.300000 0.540146 0.970000 7.200000e-01 1.000000 1.000000 0.938249 0.970000 1 0.840000 1.000000 FAM160B1 57700 broad.mit.edu 37 10 116608431 116608431 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr10:116608431G>A ENST00000369248.4 + 13 2073 c.1738G>A c.(1738-1740)Gca>Aca p.A580T FAM160B1_ENST00000369250.3_Missense_Mutation_p.A580T NM_020940.3 NP_065991.3 Q5W0V3 F16B1_HUMAN family with sequence similarity 160, member B1 25 ACCGGATGACGCAAAATCCTC 0.403000 0 SO:0001583 missense ENST00000369248.4 0 1 hg19 CCDS31290.1 . . . . . . . . . . G 25.2 4.609124 0.87258 . . ENSG00000151553 ENST00000369248;ENST00000369250 T;T 0.16457 2.36;2.34 5.58 5.58 0.84498 . 0.000000 0.85682 D 0.000000 T 0.29321 0.0730 L 0.49126 1.545 0.80722 D 1 D;P 0.56287 0.975;0.598 P;B 0.54100 0.742;0.06 T 0.00849 -1.1541 10 0.15952 T 0.53 -23.8406 19.9439 0.97175 0.0:0.0:1.0:0.0 . 580;580 Q5W0V3-2;Q5W0V3 .;F16B1_HUMAN T 580 ENSP00000358251:A580T;ENSP00000358253:A580T ENSP00000358251:A580T A + 1 0 FAM160B1 116598421 1.000000 0.71417 1.000000 0.80357 0.932000 0.56968 9.477000 0.97925 2.797000 0.96272 0.561000 0.74099 GCA TCGA-IB-AAUU-01A-11D-A377-08 FAM160B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050499.1 0 0 0 4 259 0 43 0 4.961700e-02 0 18 0 43 2 0 0 0 0 0 2 1 8.874457e-01 4 255 0 42 2 0 0 0 0 43 2 -2.936984 1 1 0 0 1 2 2 4 2.262088 1 0.370000 3.300000 0.540146 0.120000 3.000000e-02 0.270000 0.120000 0.139136 0.120000 0 0.070000 0.200000 SLC18A3 6572 broad.mit.edu 37 10 50819803 50819803 + Silent SNP G G T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr10:50819803G>T ENST00000374115.3 + 1 1457 c.1017G>T c.(1015-1017)gtG>gtT p.V339V CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000455728.2_5'Flank|CHAT_ENST00000395559.2_5'Flank|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000339797.1_Intron|CHAT_ENST00000351556.3_5'Flank NM_003055.2 NP_003046.2 Q16572 VACHT_HUMAN solute carrier family 18 (vesicular acetylcholine transporter), member 3 43 TGCCTCATGTGCTGGGCGTCT 0.667000 0 SO:0001819 synonymous_variant ENST00000374115.3 1 1 hg19 CCDS7231.1 TCGA-IB-AAUU-01A-11D-A377-08 SLC18A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047995.1 1 0 1 72 538 0 88 0 1.439934e-02 0 2 0 88 2 0 0 0 0 0 2 1 1 69 529 0 87 2 0 0 0 0 88 2 -20.000000 1 1 0 0 1 2 2 4 2.262088 1 0.370000 3.300000 0.540146 0.870000 6.900000e-01 1.000000 1.000000 0.875944 0.870000 1 0.770000 0.980000 CTNNA3 29119 broad.mit.edu 37 10 68940134 68940134 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr10:68940134C>T ENST00000433211.2 - 7 1162 c.988G>A c.(988-990)Gca>Aca p.A330T CTNNA3_ENST00000545309.1_Missense_Mutation_p.A330T|CTNNA3_ENST00000373744.4_Missense_Mutation_p.A330T NM_013266.2 NP_037398.2 catenin (cadherin-associated protein), alpha 3 95 TTGCATTCTGCGATAATCCGC 0.527000 0 SO:0001583 missense ENST00000433211.2 1 1 hg19 CCDS7269.1 . . . . . . . . . . C 17.65 3.441070 0.63067 . . ENSG00000183230 ENST00000433211;ENST00000373744;ENST00000545309 T;T;T 0.44083 1.38;1.38;0.93 5.83 3.75 0.43078 . 0.123947 0.35349 N 0.003278 T 0.45558 0.1348 M 0.86178 2.8 0.44234 D 0.997079 B;B;B;B 0.21821 0.013;0.033;0.061;0.031 B;B;B;B 0.25759 0.018;0.03;0.063;0.012 T 0.50541 -0.8816 10 0.54805 T 0.06 -7.2666 7.2252 0.26012 0.0:0.7176:0.0:0.2824 . 330;330;330;330 A8K141;F2Z2R0;Q9UI47-2;Q9UI47 .;.;.;CTNA3_HUMAN T 330 ENSP00000389714:A330T;ENSP00000362849:A330T;ENSP00000441444:A330T ENSP00000362849:A330T A - 1 0 CTNNA3 68610140 0.971000 0.33674 0.957000 0.39632 0.910000 0.53928 2.199000 0.42715 1.458000 0.47871 0.585000 0.79938 GCA TCGA-IB-AAUU-01A-11D-A377-08 CTNNA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048282.2 0 0 0 11 331 0 58 0 3.097623e-02 0 8 0 58 2 0 0 0 0 0 2 1 9.982917e-01 11 327 0 55 2 0 0 0 0 58 2 -2.878262 1 1 121404 5 40 1 2 2 4 2.262088 1 0.370000 3.300000 0.540146 0.240000 1.200000e-01 0.410000 0.240000 0.257692 0.240000 0 0.170000 0.330000 MARCH5 54708 broad.mit.edu 37 10 94110927 94110927 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr10:94110927G>A ENST00000358935.2 + 6 1132 c.800G>A c.(799-801)cGc>cAc p.R267H NM_017824.4 NP_060294.1 Q9NX47 MARH5_HUMAN membrane-associated ring finger (C3HC4) 5 9 CAGGCACACCGCAAAATTCTG 0.353000 0 SO:0001583 missense ENST00000358935.2 0 1 hg19 CCDS7420.1 . . . . . . . . . . G 25.3 4.627017 0.87560 . . ENSG00000198060 ENST00000358935 T 0.70986 -0.53 5.62 5.62 0.85841 . 0.000000 0.85682 D 0.000000 D 0.87067 0.6085 M 0.87827 2.91 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 D 0.88657 0.3186 10 0.87932 D 0 -4.1613 19.6604 0.95864 0.0:0.0:1.0:0.0 . 267 Q9NX47 MARH5_HUMAN H 267 ENSP00000351813:R267H ENSP00000351813:R267H R + 2 0 MARCH5 94100907 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.378000 0.97191 2.648000 0.89879 0.655000 0.94253 CGC TCGA-IB-AAUU-01A-11D-A377-08 MARCH5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049388.1 0 0 0 6 726 0 129 0 2.840820e-01 0 111 0 129 2 0 0 0 0 0 2 1 9.627546e-01 7 710 0 128 2 0 0 0 0 129 2 -2.111543 0 1 0 0 1 2 2 4 2.262088 1 0.370000 3.300000 0.540146 0.060000 0 0.130000 0.080000 0.069162 0.060000 0 0.030000 0.100000 POU2AF1 5450 broad.mit.edu 37 11 111225288 111225288 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr11:111225288C>T ENST00000393067.3 - 5 983 c.469G>A c.(469-471)Gcc>Acc p.A157T NM_006235.2 NP_006226.2 Q16633 OBF1_HUMAN POU class 2 associating factor 1 5 all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389) GCGGGCGTGGCGGAGCTTCTT 0.642000 T BCL6 NHL Dom yes 11 11q23.1 5450 POU domain, class 2, associating factor 1 (OBF1) L 0 SO:0001583 missense ENST00000393067.3 0 1 hg19 CCDS31675.1 . . . . . . . . . . C 18.23 3.578757 0.65878 . . ENSG00000110777 ENST00000393067 T 0.30448 1.53 4.87 1.8 0.24995 . 0.529845 0.18793 N 0.131018 T 0.26085 0.0636 L 0.56769 1.78 0.09310 N 1 B 0.09022 0.002 B 0.11329 0.006 T 0.23084 -1.0198 10 0.51188 T 0.08 -25.8385 5.1776 0.15143 0.1407:0.6002:0.0:0.259 . 157 Q16633 OBF1_HUMAN T 157 ENSP00000376786:A157T ENSP00000376786:A157T A - 1 0 POU2AF1 110730498 0.018000 0.18449 0.001000 0.08648 0.845000 0.48019 0.185000 0.16958 0.189000 0.20188 0.563000 0.77884 GCC TCGA-IB-AAUU-01A-11D-A377-08 POU2AF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391002.1 0 0 0 6 24 0 18 0 0 0 1 0 18 2 0 0 0 0 0 2 1 9.705328e-01 6 24 0 17 2 0 0 0 0 18 2 -13.682250 1 1 120900 1 25 1 1 2 3 1.932710 1 0.370000 3.300000 0.468354 0.990000 5.800000e-01 1.000000 1.000000 0.954701 0.990000 1 0.900000 1.000000 PCSK7 9159 broad.mit.edu 37 11 117090363 117090363 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr11:117090363G>A ENST00000320934.3 - 10 1897 c.1267C>T c.(1267-1269)Cgg>Tgg p.R423W PCSK7_ENST00000540028.1_Missense_Mutation_p.R64W NM_004716.2 NP_004707.2 Q16549 PCSK7_HUMAN proprotein convertase subtilisin/kexin type 7 16 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) AGGCAGGGCCGCACCTGCAGC 0.627000 T IGH@ MLCLS Dom yes 11 11q23.3 9159 proprotein convertase subtilisin/kexin type 7 L 0 SO:0001583 missense ENST00000320934.3 0 1 hg19 CCDS8382.1 . . . . . . . . . . G 27.1 4.802841 0.90623 . . ENSG00000160613 ENST00000320934;ENST00000540028;ENST00000543900 D;D 0.87887 -2.31;-2.31 5.69 4.7 0.59300 Peptidase S8/S53, subtilisin/kexin/sedolisin (3); 0.000000 0.85682 D 0.000000 D 0.94305 0.8170 M 0.88979 2.995 0.58432 D 0.999999 D 0.89917 1.0 D 0.91635 0.999 D 0.94972 0.8118 10 0.72032 D 0.01 -34.1224 16.525 0.84328 0.0:0.0:0.8607:0.1393 . 423 Q16549 PCSK7_HUMAN W 423;64;423 ENSP00000325917:R423W;ENSP00000441944:R64W ENSP00000325917:R423W R - 1 2 PCSK7 116595573 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 6.085000 0.71343 2.696000 0.92011 0.557000 0.71058 CGG TCGA-IB-AAUU-01A-11D-A377-08 PCSK7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385529.2 0 0 0 4 222 0 34 0 5.459129e-01 0 90 0 34 2 0 0 0 0 0 2 1 8.890555e-01 4 220 0 34 2 0 0 0 0 34 2 -2.995169 1 1 0 0 1 1 2 3 1.932710 1 0.370000 3.300000 0.468354 0.120000 3.000000e-02 0.270000 0.120000 0.139730 0.120000 0 0.070000 0.200000 LRRC55 219527 broad.mit.edu 37 11 56950145 56950145 + Missense_Mutation SNP C C T rs143027441 byFrequency TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr11:56950145C>T ENST00000497933.1 + 1 925 c.778C>T c.(778-780)Cgc>Tgc p.R260C NM_001005210.2 NP_001005210.1 Q6ZSA7 LRC55_HUMAN leucine rich repeat containing 55 p.R260C(1) 25 CCGGATCCAGCGCTGTACAGC 0.607000 1 Substitution - Missense(1) SO:0001583 missense ENST00000497933.1 1 1 hg19 CCDS31539.1 . . . . . . . . . . C 17.57 3.421766 0.62622 2.27E-4 1.16E-4 ENSG00000183908 ENST00000497933 T 0.22743 1.94 5.53 5.53 0.82687 Cysteine-rich flanking region, C-terminal (1); 0.000000 0.64402 D 0.000016 T 0.33411 0.0862 L 0.43923 1.385 0.58432 D 0.999998 D 0.89917 1.0 P 0.55871 0.786 T 0.01363 -1.1374 10 0.54805 T 0.06 . 16.3896 0.83531 0.0:1.0:0.0:0.0 . 230 Q6ZSA7 LRC55_HUMAN C 260 ENSP00000419542:R260C ENSP00000419542:R260C R + 1 0 LRRC55 56706721 1.000000 0.71417 1.000000 0.80357 0.884000 0.51177 1.663000 0.37429 2.608000 0.88229 0.561000 0.74099 CGC TCGA-IB-AAUU-01A-11D-A377-08 LRRC55-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354503.2 1 0 1 53 384 0 67 0 7.739058e-02 0 4 0 67 2 0 0 0 0 0 2 1 1 52 375 0 67 2 0 0 0 0 67 2 -19.878260 1 1 0 0 1 2 2 4 2.222719 1 0.370000 3.300000 0.540146 0.890000 6.800000e-01 1.000000 1.000000 0.893641 0.890000 1 0.780000 1.000000 STIP1 10963 broad.mit.edu 37 11 63971050 63971050 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr11:63971050C>T ENST00000305218.4 + 13 1662 c.1515C>T c.(1513-1515)cgC>cgT p.R505R STIP1_ENST00000358794.5_Silent_p.R552R|STIP1_ENST00000538945.1_Silent_p.R481R NM_006819.2 NP_006810.1 P31948 STIP1_HUMAN stress-induced phosphoprotein 1 27 CAGCCATGCGCCTTATCCTGG 0.582000 0 SO:0001819 synonymous_variant ENST00000305218.4 1 1 hg19 CCDS8058.1 TCGA-IB-AAUU-01A-11D-A377-08 STIP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396289.2 1 0 1 54 135 0 28 1 1 220 227 0 28 2 0 0 0 0 0 2 1 1 54 131 0 28 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 1 2 3 1.932710 1 0.370000 3.300000 0.468354 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MUS81 80198 broad.mit.edu 37 11 65630663 65630663 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr11:65630663G>A ENST00000308110.4 + 7 1082 c.733G>A c.(733-735)Gct>Act p.A245T MUS81_ENST00000533035.1_Missense_Mutation_p.A170T|CFL1_ENST00000534769.1_5'Flank NM_025128.4 NP_079404.3 Q96NY9 MUS81_HUMAN MUS81 structure-specific endonuclease subunit 13 GCCAGGAGCAGCTTCAGCAGA 0.637000 Homologous recombination 0 SO:0001583 missense ENST00000308110.4 1 1 hg19 CCDS8115.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. g|g 9.761|9.761 1.170193|1.170193 0.21621|0.21621 .|. .|. ENSG00000172732|ENSG00000172732 ENST00000533035;ENST00000308110;ENST00000437855|ENST00000529374;ENST00000530111 T;T|. 0.14766|. 2.48;2.72|. 5.11|5.11 1.93|1.93 0.25924|0.25924 .|. 0.824135|. 0.11566|. N|. 0.551224|. T|T 0.34571|0.34571 0.0902|0.0902 L|L 0.41236|0.41236 1.265|1.265 0.09310|0.09310 N|N 1|1 B|. 0.10296|. 0.003|. B|. 0.06405|. 0.002|. T|T 0.21655|0.21655 -1.0239|-1.0239 10|5 0.08599|. T|. 0.76|. -6.8355|-6.8355 5.7461|5.7461 0.18120|0.18120 0.1806:0.0:0.6625:0.1569|0.1806:0.0:0.6625:0.1569 .|. 245|. Q96NY9|. MUS81_HUMAN|. T|N 170;245;245|169;140 ENSP00000432287:A170T;ENSP00000307853:A245T|. ENSP00000307853:A245T|. A|S +|+ 1|2 0|0 MUS81|MUS81 65387239|65387239 0.107000|0.107000 0.21998|0.21998 0.073000|0.073000 0.20177|0.20177 0.212000|0.212000 0.24457|0.24457 1.083000|1.083000 0.30815|0.30815 1.138000|1.138000 0.42230|0.42230 0.556000|0.556000 0.70494|0.70494 GCT|AGC TCGA-IB-AAUU-01A-11D-A377-08 MUS81-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390941.3 1 0 1 42 116 0 40 1 1 43 49 0 40 2 0 0 0 0 0 2 1 1 42 112 0 38 2 0 0 0 0 40 2 -20.000000 1 1 0 0 1 1 2 3 1.932710 1 0.370000 3.300000 0.468354 0.990000 9.900000e-01 1.000000 1.000000 0.999992 0.990000 1 0.990000 1.000000 DDX55 57696 broad.mit.edu 37 12 124090516 124090516 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr12:124090516C>T ENST00000238146.4 + 2 197 c.147C>T c.(145-147)gtC>gtT p.V49V DDX55_ENST00000538744.1_Silent_p.V49V NM_020936.1 NP_065987.1 Q8NHQ9 DDX55_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 14 all_neural(191;0.101)|Medulloblastoma(191;0.163) ACAAAGATGTCGCTGCAGAAG 0.498000 0 SO:0001819 synonymous_variant ENST00000238146.4 0 1 hg19 CCDS9251.1 TCGA-IB-AAUU-01A-11D-A377-08 DDX55-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400616.2 0 0 0 5 488 0 108 0 2.436109e-02 0 19 0 108 2 0 0 0 0 0 2 1 9.351190e-01 5 480 0 108 2 0 0 0 0 108 2 -2.425857 0 1 121412 6 41 1 0 3 3 1.750386 1 0.370000 3.300000 0.445862 0.070000 1.000000e-02 1.000000 0.060000 0.244820 0.070000 0 0.040000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 C G C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-AAUU-01A-11D-A377-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 70 233 0 67 1 9.967793e-01 17 15 0 67 2 1 1 93 272 0 347 2 1 1 69 232 0 67 2 1 1 2913 5108 0 67 2 -20.000000 1 1 0 0 1 2 5 7 2.124773 1 0.370000 3.300000 0.520730 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MYF5 4617 broad.mit.edu 37 12 81110965 81110965 + Silent SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr12:81110965G>A ENST00000228644.3 + 1 275 c.123G>A c.(121-123)gcG>gcA p.A41A NM_005593.2 NP_005584.2 P13349 MYF5_HUMAN myogenic factor 5 30 CCTTCGGAGCGCACAAAGCAG 0.617000 0 SO:0001819 synonymous_variant ENST00000228644.3 0 1 hg19 CCDS9020.1 TCGA-IB-AAUU-01A-11D-A377-08 MYF5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407757.1 0 0 0 4 165 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 8.899358e-01 4 164 0 36 2 0 0 0 0 38 2 -3.516685 1 1 0 0 1 0 3 3 1.750386 1 0.370000 3.300000 0.445862 0.180000 5.000000e-02 1.000000 0.140000 0.329815 0.180000 0 0.100000 1.000000 MYO16 23026 broad.mit.edu 37 13 109779791 109779791 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr13:109779791G>A ENST00000357550.2 + 30 3919 c.3878G>A c.(3877-3879)cGg>cAg p.R1293Q MYO16_ENST00000356711.2_Missense_Mutation_p.R1293Q|MYO16_ENST00000457511.2_Missense_Mutation_p.R805Q NM_001198950.1 NP_001185879.1 myosin XVI 121 all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104) BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201) CCGTCTCCACGGAAACAGCCC 0.662000 0 SO:0001583 missense ENST00000357550.2 0 1 hg19 CCDS32008.1 . . . . . . . . . . G 31 5.064283 0.93898 . . ENSG00000041515 ENST00000356711;ENST00000357550;ENST00000457511 T;T;T 0.50277 0.75;0.75;0.75 5.5 5.5 0.81552 . 0.000000 0.37178 U 0.002219 T 0.70684 0.3252 M 0.79258 2.445 0.54753 D 0.999983 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.994 T 0.71441 -0.4592 9 . . . . 18.4132 0.90559 0.0:0.0:1.0:0.0 . 805;1293 F8W883;Q9Y6X6 .;MYO16_HUMAN Q 1293;1293;805 ENSP00000349145:R1293Q;ENSP00000350160:R1293Q;ENSP00000401633:R805Q . R + 2 0 MYO16 108577792 1.000000 0.71417 0.998000 0.56505 0.874000 0.50279 8.813000 0.91963 2.584000 0.87258 0.563000 0.77884 CGG TCGA-IB-AAUU-01A-11D-A377-08 MYO16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045746.1 1 0 1 21 138 0 22 0 0 1 0 0 22 2 0 0 0 0 0 2 1 9.999983e-01 21 136 0 22 2 0 0 0 0 22 2 -20.000000 1 1 121410 1 28 1 2 2 4 2.202007 1 0.370000 3.300000 0.540146 0.980000 6.400000e-01 1.000000 1.000000 0.923909 0.980000 1 0.800000 1.000000 TFDP1 7027 broad.mit.edu 37 13 114277494 114277494 + Splice_Site SNP G G T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr13:114277494G>T ENST00000375370.5 + 4 291 c.e4-1 TFDP1_ENST00000544902.1_Splice_Site|TFDP1_ENST00000465174.1_Splice_Site|TFDP1_ENST00000538138.1_Splice_Site NM_007111.4 NP_009042.1 Q14186 TFDP1_HUMAN transcription factor Dp-1 26 Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153) all cancers(43;0.0576) TTGTGTTGCAGGCGTGGTGTC 0.532000 TSP Lung(29;0.18) 0 SO:0001630 splice_region_variant ENST00000375370.5 0 1 hg19 CCDS9538.1 . . . . . . . . . . G 13.43 2.235800 0.39498 . . ENSG00000198176 ENST00000375370;ENST00000408980;ENST00000453989 . . . 4.65 4.65 0.58169 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.5431 0.87853 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . TFDP1 113325495 1.000000 0.71417 0.997000 0.53966 0.174000 0.22865 8.046000 0.89438 2.125000 0.65367 0.491000 0.48974 . TCGA-IB-AAUU-01A-11D-A377-08 TFDP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045918.3 0 0 0 4 76 0 11 0 0 0 0 11 2 0 0 0 1 0 0 2 0 8.728445e-01 0 74 0 11 2 0 0 0 0 11 2 -7.858123 1 0 0 0 1 2 2 4 2.202007 1 0.370000 3.300000 0.540146 0.410000 1.400000e-01 0.850000 0.360000 0.445690 0.410000 0 0.250000 0.630000 TOX4 9878 broad.mit.edu 37 14 21961173 21961173 + Silent SNP T T C TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr14:21961173T>C ENST00000405508.1 + 8 1674 c.1398T>C c.(1396-1398)ccT>ccC p.P466P TOX4_ENST00000448790.2_Silent_p.P443P|TOX4_ENST00000262709.3_Silent_p.P466P O94842 TOX4_HUMAN TOX high mobility group box family member 4 18 all_cancers(95;0.000465) Epithelial(56;6.61e-06)|all cancers(55;5.15e-05) TGCAGCAGCCTCCTCCACTCC 0.552000 0 SO:0001819 synonymous_variant ENST00000405508.1 1 1 hg19 CCDS32043.1 TCGA-IB-AAUU-01A-11D-A377-08 TOX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317287.2 1 0 1 53 563 0 106 1 9.999993e-01 29 189 0 106 2 0 0 0 0 0 2 1 1 52 552 0 103 2 0 0 0 0 106 2 -14.466900 1 1 0 0 1 2 2 4 2.205976 1 0.370000 3.300000 0.540146 0.630000 4.800000e-01 0.810000 0.640000 0.646191 0.630000 0 0.550000 0.730000 LTB4R2 56413 broad.mit.edu 37 14 24780173 24780173 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr14:24780173C>T ENST00000528054.1 + 1 2013 c.396C>T c.(394-396)tgC>tgT p.C132C CIDEB_ENST00000336557.5_5'UTR|CIDEB_ENST00000555817.1_5'UTR|LTB4R2_ENST00000533293.1_Silent_p.C101C|LTB4R_ENST00000345363.3_5'Flank|CIDEB_ENST00000554411.1_5'Flank|LTB4R_ENST00000396789.4_5'Flank|CIDEB_ENST00000258807.5_5'UTR|LTB4R2_ENST00000543919.1_Silent_p.C101C Q9NPC1 LT4R2_HUMAN leukotriene B4 receptor 2 3 ACTACGTGTGCGCGCTCAGCA 0.721000 0 SO:0001819 synonymous_variant ENST00000528054.1 0 1 hg19 TCGA-IB-AAUU-01A-11D-A377-08 LTB4R2-001 KNOWN basic|appris_principal|readthrough_transcript protein_coding protein_coding OTTHUMT00000073194.4 1 0 0 35 255 0 20 0 7.811230e-02 1 3 0 20 2 0 0 0 0 0 2 1 1 35 254 0 20 2 0 0 0 0 20 2 -20.000000 1 1 117548 1 29 1 2 2 4 2.205976 1 0.370000 3.300000 0.540146 0.890000 6.400000e-01 1.000000 1.000000 0.886137 0.890000 1 0.760000 1.000000 L2HGDH 79944 broad.mit.edu 37 14 50704423 50704423 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr14:50704423G>A ENST00000261699.4 - 10 1234 c.1217C>T c.(1216-1218)cCg>cTg p.P406L Q9H9P8 L2HDH_HUMAN L-2-hydroxyglutarate dehydrogenase 10 all_epithelial(31;0.000599)|Breast(41;0.0102) TAGCCAGCTCGGTCCTCTCAC 0.517000 0 SO:0001583 missense ENST00000261699.4 0 1 hg19 . . . . . . . . . . G 15.45 2.835940 0.50951 . . ENSG00000087299 ENST00000261699 D 0.92699 -3.09 4.54 -1.11 0.09840 . . . . . D 0.93946 0.8062 . . . 0.09310 N 1 D 0.89917 1.0 D 0.78314 0.991 D 0.85113 0.0964 8 0.87932 D 0 . 4.3647 0.11218 0.4596:0.1691:0.3713:0.0 . 406 C9JVN9 . L 406 ENSP00000261699:P406L ENSP00000261699:P406L P - 2 0 L2HGDH 49774173 0.000000 0.05858 0.000000 0.03702 0.200000 0.23975 -0.086000 0.11233 -0.302000 0.08869 -1.446000 0.01064 CCG TCGA-IB-AAUU-01A-11D-A377-08 L2HGDH-002 KNOWN basic|exp_conf protein_coding protein_coding OTTHUMT00000276871.1 0 0 1 13 105 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 9.996151e-01 13 104 0 23 2 0 0 0 0 23 2 -3.321531 1 1 116142 1 29 1 2 2 4 2.205976 1 0.370000 3.300000 0.540146 0.830000 4.700000e-01 1.000000 1.000000 0.821978 0.830000 0 0.630000 1.000000 MAP3K9 4293 broad.mit.edu 37 14 71209085 71209085 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr14:71209085C>T ENST00000554752.2 - 6 1549 c.1550G>A c.(1549-1551)cGc>cAc p.R517H MAP3K9_ENST00000553414.1_Missense_Mutation_p.R211H|MAP3K9_ENST00000554146.1_Missense_Mutation_p.R254H|MAP3K9_ENST00000381250.4_Missense_Mutation_p.R517H|MAP3K9_ENST00000555993.2_Missense_Mutation_p.R517H NM_001284230.1 NP_001271159.1 P80192 M3K9_HUMAN mitogen-activated protein kinase kinase kinase 9 46 GAGGCTGATGCGGTTGCCATC 0.602000 GBM(114;411 1587 13539 28235 50070) 0 SO:0001583 missense ENST00000554752.2 0 1 hg19 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 12.47 1.947067 0.34377 . . ENSG00000006432 ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284 T;T;T;T 0.11495 2.77;2.77;2.77;2.77 6.06 5.17 0.71159 Protein kinase-like domain (1); 0.211843 0.49305 D 0.000141 T 0.07413 0.0187 N 0.25245 0.725 0.50171 D 0.999854 B;B;B;B 0.20261 0.001;0.025;0.043;0.005 B;B;B;B 0.20577 0.005;0.009;0.03;0.013 T 0.28332 -1.0047 10 0.35671 T 0.21 . 7.1057 0.25362 0.1401:0.71:0.0:0.1499 . 254;517;517;211 G3V4P9;P80192;P80192-4;G3V347 .;M3K9_HUMAN;.;. H 517;517;211;517;254;245 ENSP00000451612:R517H;ENSP00000451038:R211H;ENSP00000370649:R517H;ENSP00000451921:R254H ENSP00000005198:R517H R - 2 0 MAP3K9 70278838 1.000000 0.71417 1.000000 0.80357 0.716000 0.41182 3.617000 0.54181 1.577000 0.49804 -0.150000 0.13652 CGC TCGA-IB-AAUU-01A-11D-A377-08 MAP3K9-001 KNOWN basic protein_coding protein_coding OTTHUMT00000412550.2 0 0 0 5 463 2 69 0 1.112823e-03 0 4 2 69 2 0 0 0 0 0 2 0 9.027197e-06 5 448 2 66 29 0 0 0 2 69 2 -2.178743 0 1 121412 8 42 1 2 2 4 2.205976 1 0.370000 3.300000 0.540146 0.080000 1.000000e-02 0.180000 0.080000 0.093949 0.080000 0 0.040000 0.130000 YLPM1 56252 broad.mit.edu 37 14 75276279 75276279 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr14:75276279G>A ENST00000552421.1 + 6 2724 c.2600G>A c.(2599-2601)cGa>cAa p.R867Q YLPM1_ENST00000325680.7_Missense_Mutation_p.R1573Q|YLPM1_ENST00000238571.3_Missense_Mutation_p.R1378Q P49750 YLPM1_HUMAN YLP motif containing 1 62 KIRC - Kidney renal clear cell carcinoma(43;0.238) GAACAGGAACGATGGGATGAA 0.478000 0 SO:0001583 missense ENST00000552421.1 1 1 hg19 . . . . . . . . . . G 24.1 4.492754 0.84962 . . ENSG00000119596 ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680 . . . 5.54 5.54 0.83059 . 0.000000 0.64402 D 0.000008 T 0.66386 0.2784 L 0.27053 0.805 0.42961 D 0.994407 D;D 0.89917 0.997;1.0 D;D 0.81914 0.964;0.995 T 0.70139 -0.4954 9 0.72032 D 0.01 -5.0092 17.6519 0.88167 0.0:0.0:1.0:0.0 . 1378;1573 P49750-3;P49750-4 .;. Q 867;1573;1378;1286 . ENSP00000238571:R1378Q R + 2 0 YLPM1 74346032 1.000000 0.71417 1.000000 0.80357 0.902000 0.53008 6.826000 0.75298 2.588000 0.87417 0.591000 0.81541 CGA TCGA-IB-AAUU-01A-11D-A377-08 YLPM1-008 NOVEL not_organism_supported|basic|exp_conf protein_coding protein_coding OTTHUMT00000404450.1 1 0 1 27 85 0 20 1 9.997534e-01 19 27 0 20 2 0 0 0 0 0 2 1 1 26 85 0 20 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 2 2 4 2.205976 1 0.370000 3.300000 0.540146 0.990000 9.900000e-01 1.000000 1.000000 0.999938 0.990000 1 0.990000 1.000000 LRRK1 79705 broad.mit.edu 37 15 101586241 101586241 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr15:101586241C>T ENST00000388948.3 + 21 3378 c.3019C>T c.(3019-3021)Cgg>Tgg p.R1007W LRRK1_ENST00000284395.5_Missense_Mutation_p.R1004W|RP11-505E24.3_ENST00000558979.1_RNA NM_024652.3 NP_078928.3 leucine-rich repeat kinase 1 72 Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094) OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23) CCACGGTATGCGGCACCCCAC 0.562000 0 SO:0001583 missense ENST00000388948.3 0 1 hg19 CCDS42086.1 . . . . . . . . . . C 28.8 4.952657 0.92660 0.001224 0.0 ENSG00000154237 ENST00000388948;ENST00000284395 T;T 0.73152 -0.69;-0.72 5.58 5.58 0.84498 . 0.060599 0.64402 D 0.000003 T 0.72969 0.3527 L 0.55481 1.735 0.46185 D 0.998919 D 0.76494 0.999 P 0.50490 0.642 T 0.75634 -0.3250 10 0.66056 D 0.02 . 13.6371 0.62229 0.0:0.9197:0.0:0.0803 . 1007 Q38SD2 LRRK1_HUMAN W 1007;1004 ENSP00000373600:R1007W;ENSP00000284395:R1004W ENSP00000284395:R1004W R + 1 2 LRRK1 99403764 1.000000 0.71417 1.000000 0.80357 0.928000 0.56348 3.715000 0.54897 2.769000 0.95229 0.655000 0.94253 CGG TCGA-IB-AAUU-01A-11D-A377-08 LRRK1-003 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000384567.2 0 0 0 5 467 0 76 0 3.750867e-02 0 23 0 76 2 0 0 0 0 0 2 1 9.350053e-01 5 459 0 71 2 0 0 0 0 76 2 -1.878379 0 1 120976 11 45 1 2 2 4 2.228833 1 0.370000 3.300000 0.540146 0.080000 1.000000e-02 0.180000 0.080000 0.093135 0.080000 0 0.040000 0.130000 OCA2 4948 broad.mit.edu 37 15 28211955 28211955 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr15:28211955G>A ENST00000354638.3 - 15 1672 c.1517C>T c.(1516-1518)gCc>gTc p.A506V OCA2_ENST00000382996.2_Missense_Mutation_p.A506V|OCA2_ENST00000353809.5_Missense_Mutation_p.A482V NM_000275.2 NP_000266.2 Q04671 P_HUMAN oculocutaneous albinism II 85 all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234) AGTGAATCCGGCAAAGTCCAG 0.507000 Oculocutaneous Albinism 0 SO:0001583 missense Familial Cancer Database ENST00000354638.3 0 1 hg19 CCDS10020.1 . . . . . . . . . . G 19.87 3.907629 0.72868 . . ENSG00000104044 ENST00000354638;ENST00000353809;ENST00000382996 T;T;T 0.80480 -1.38;-1.38;-1.38 5.05 5.05 0.67936 Divalent ion symporter (1); 0.000000 0.85682 D 0.000000 T 0.76716 0.4026 N 0.16862 0.45 0.58432 D 0.999997 B;P 0.46621 0.196;0.881 B;P 0.51516 0.098;0.672 T 0.77451 -0.2583 10 0.38643 T 0.18 -19.0275 16.249 0.82472 0.0:0.0:1.0:0.0 . 482;506 Q04671-2;Q04671 .;P_HUMAN V 506;482;506 ENSP00000346659:A506V;ENSP00000261276:A482V;ENSP00000372457:A506V ENSP00000261276:A482V A - 2 0 OCA2 25885550 1.000000 0.71417 0.942000 0.38095 0.482000 0.33219 6.969000 0.76092 2.494000 0.84150 0.555000 0.69702 GCC TCGA-IB-AAUU-01A-11D-A377-08 OCA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250823.1 0 0 0 4 141 0 34 0 1.378930e-03 0 2 0 34 2 0 0 0 0 0 2 1 8.864814e-01 4 138 0 34 2 0 0 0 0 34 2 -6.256168 1 1 0 0 1 2 2 4 2.224059 1 0.370000 3.300000 0.540146 0.220000 7.000000e-02 0.480000 0.200000 0.250411 0.220000 0 0.130000 0.350000 HERC2 8924 broad.mit.edu 37 15 28517442 28517442 + Silent SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr15:28517442G>A ENST00000261609.7 - 9 1110 c.1002C>T c.(1000-1002)agC>agT p.S334S NM_004667.5 NP_004658.3 HECT and RLD domain containing E3 ubiquitin protein ligase 2 204 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) AAAGTGGGGCGCTGGTGCCCT 0.567000 0 SO:0001819 synonymous_variant ENST00000261609.7 0 1 hg19 CCDS10021.1 TCGA-IB-AAUU-01A-11D-A377-08 HERC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251358.2 0 0 0 10 358 0 46 0 1.018579e-01 0 18 0 46 2 0 0 0 0 0 2 1 9.965739e-01 10 349 0 44 2 0 0 0 0 46 2 -3.272530 1 1 121412 8 36 1 2 2 4 2.224059 1 0.370000 3.300000 0.540146 0.200000 9.000000e-02 0.350000 0.200000 0.219657 0.200000 0 0.140000 0.280000 CHRNA7 1139 broad.mit.edu 37 15 32460285 32460285 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr15:32460285G>A ENST00000306901.3 + 10 1232 c.1135G>A c.(1135-1137)Gcc>Acc p.A379T CHRNA7_ENST00000455693.2_Missense_Mutation_p.A198T|CHRNA7_ENST00000454250.3_Missense_Mutation_p.A408T NM_000746.5 NP_000737.1 P36544 ACHA7_HUMAN cholinergic receptor, nicotinic, alpha 7 (neuronal) 12 all_lung(180;6.35e-11) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273) GCCGCCGCCCGCCAGCAACGG 0.716000 Esophageal Squamous(193;529 2900 40232 43193) 0 SO:0001583 missense ENST00000306901.3 1 1 hg19 CCDS10027.1 . . . . . . . . . . g 3.425 -0.117298 0.06838 . . ENSG00000175344 ENST00000437966;ENST00000454250;ENST00000306901;ENST00000455693 T;T;T 0.19669 2.13;2.13;2.13 3.84 -0.555 0.11807 Neurotransmitter-gated ion-channel transmembrane domain (2); 2.523290 0.01582 N 0.021155 T 0.08179 0.0204 N 0.03000 -0.44 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.06405 0.002;0.001 T 0.20505 -1.0273 10 0.12766 T 0.61 . 3.6481 0.08192 0.494:0.0:0.3237:0.1823 . 408;379 B4DFS0;P36544 .;ACHA7_HUMAN T 289;408;379;198 ENSP00000407546:A408T;ENSP00000303727:A379T;ENSP00000405989:A198T ENSP00000303727:A379T A + 1 0 CHRNA7 30247577 0.000000 0.05858 0.001000 0.08648 0.477000 0.33069 -0.094000 0.11094 -0.091000 0.12440 0.650000 0.86243 GCC TCGA-IB-AAUU-01A-11D-A377-08 CHRNA7-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251410.2 0 0 0 55 225 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1 54 194 0 44 2 0 0 0 0 41 2 -3.045821 1 1 120386 8 36 1 2 2 4 2.203689 1 0.370000 3.300000 0.540146 0.990000 9.900000e-01 1.000000 1.000000 0.999918 0.990000 1 0.990000 1.000000 DET1 55070 broad.mit.edu 37 15 89070834 89070834 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr15:89070834G>A ENST00000268148.8 - 3 1412 c.1267C>T c.(1267-1269)Cgc>Tgc p.R423C DET1_ENST00000564406.1_Missense_Mutation_p.R434C|DET1_ENST00000444300.1_Missense_Mutation_p.R434C NM_001144074.1 NP_001137546.1 Q7L5Y6 DET1_HUMAN de-etiolated homolog 1 (Arabidopsis) p.R434C(1) 23 Lung NSC(78;0.105)|all_lung(78;0.182) BRCA - Breast invasive adenocarcinoma(143;0.188) GCTTACCGGCGCTGGATCTGC 0.443000 1 Substitution - Missense(1) SO:0001583 missense ENST00000268148.8 0 1 hg19 CCDS45344.1 . . . . . . . . . . G 20.6 4.014609 0.75161 . . ENSG00000140543 ENST00000444300;ENST00000268148 . . . 5.7 5.7 0.88788 . 0.049043 0.85682 D 0.000000 T 0.78953 0.4365 M 0.76574 2.34 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.64506 0.926;0.926 T 0.80725 -0.1254 9 0.87932 D 0 . 18.8293 0.92132 0.0:0.0:1.0:0.0 . 423;434 Q7L5Y6;B3KNN6 DET1_HUMAN;. C 434;423 . ENSP00000268148:R423C R - 1 0 DET1 86871838 1.000000 0.71417 1.000000 0.80357 0.971000 0.66376 7.036000 0.76524 2.683000 0.91414 0.655000 0.94253 CGC TCGA-IB-AAUU-01A-11D-A377-08 DET1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415442.2 0 0 0 4 229 1 41 0 2.156863e-03 0 11 1 41 3 0 0 0 0 0 2 0 1.489449e-03 4 225 1 41 18 0 0 0 1 41 2 -4.053565 1 0 120828 5 35 1 2 2 4 2.228833 1 0.370000 3.300000 0.540146 0.140000 4.000000e-02 0.310000 0.120000 0.156907 0.140000 0 0.080000 0.220000 SLC12A3 6559 broad.mit.edu 37 16 56920974 56920974 + Missense_Mutation SNP A A G TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr16:56920974A>G ENST00000563236.1 + 17 2172 c.2147A>G c.(2146-2148)gAc>gGc p.D716G SLC12A3_ENST00000262502.5_Missense_Mutation_p.D715G|SLC12A3_ENST00000438926.2_Missense_Mutation_p.D716G|SLC12A3_ENST00000566786.1_Missense_Mutation_p.D715G P55017 S12A3_HUMAN solute carrier family 12 (sodium/chloride transporter), member 3 50 Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325) ATTGCCGAGGACCTCCGCAGA 0.582000 0 SO:0001583 missense ENST00000563236.1 1 1 hg19 CCDS58464.1 . . . . . . . . . . A 14.91 2.675396 0.47781 . . ENSG00000070915 ENST00000438926;ENST00000262502 . . . 5.66 5.66 0.87406 . 0.153400 0.56097 D 0.000024 T 0.65575 0.2704 M 0.68317 2.08 0.80722 D 1 B;B;B 0.27910 0.193;0.006;0.011 B;B;B 0.34346 0.18;0.017;0.034 T 0.65598 -0.6129 9 0.52906 T 0.07 . 15.9025 0.79392 1.0:0.0:0.0:0.0 . 715;716;716 P55017-3;P55017;P55017-2 .;S12A3_HUMAN;. G 715;716 . ENSP00000262502:D716G D + 2 0 SLC12A3 55478475 1.000000 0.71417 1.000000 0.80357 0.524000 0.34500 6.121000 0.71602 2.155000 0.67459 0.450000 0.29827 GAC TCGA-IB-AAUU-01A-11D-A377-08 SLC12A3-005 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000432337.1 1 0 0 24 257 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 9.999997e-01 24 253 0 27 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 2 2 4 2.208062 1 0.370000 3.300000 0.540146 0.630000 4.200000e-01 0.900000 0.640000 0.651889 0.630000 0 0.520000 0.770000 HYDIN 54768 broad.mit.edu 37 16 70908762 70908762 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr16:70908762C>T ENST00000393567.2 - 63 10768 c.10618G>A c.(10618-10620)Gcg>Acg p.A3540T AC027281.1_ENST00000411384.1_RNA NM_001270974.1 NP_001257903.1 Q4G0P3 HYDIN_HUMAN HYDIN, axonemal central pair apparatus protein 43 Ovarian(137;0.0654) TAGATATACGCGGTGGTGGGC 0.507000 0 SO:0001583 missense ENST00000393567.2 1 1 hg19 CCDS59269.1 . . . . . . . . . . C 2.768 -0.256259 0.05829 . . ENSG00000157423 ENST00000393567;ENST00000316490 T 0.00882 5.58 4.66 0.836 0.18891 . 0.563128 0.13263 U 0.401146 T 0.00440 0.0014 N 0.03608 -0.345 0.80722 D 1 B 0.06786 0.001 B 0.01281 0.0 T 0.51028 -0.8757 10 0.17832 T 0.49 . 0.1104 0.00055 0.365:0.2089:0.1834:0.2427 . 3539 F8WD23 . T 3540;3539 ENSP00000377197:A3540T ENSP00000313052:A3539T A - 1 0 HYDIN 69466263 0.999000 0.42202 0.992000 0.48379 0.039000 0.13416 0.722000 0.25925 0.614000 0.30107 -0.463000 0.05309 GCG TCGA-IB-AAUU-01A-11D-A377-08 HYDIN-001 PUTATIVE not_organism_supported|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000398624.3 1 0 0 30 90 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 1 29 87 0 27 2 0 0 0 0 23 2 -19.998650 1 1 120804 5 34 1 2 2 4 2.208062 1 0.370000 3.300000 0.540146 0.990000 9.900000e-01 1.000000 1.000000 0.999983 0.990000 1 0.990000 1.000000 IRF8 3394 broad.mit.edu 37 16 85946826 85946826 + Silent SNP G G A rs146360039 byFrequency TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr16:85946826G>A ENST00000268638.5 + 5 959 c.537G>A c.(535-537)gcG>gcA p.A179A IRF8_ENST00000562492.1_5'Flank NM_002163.2 NP_002154.1 Q02556 IRF8_HUMAN interferon regulatory factor 8 24 Prostate(104;0.0771) ACTGGTGGGCGCAGCAGCCCA 0.617000 0 SO:0001819 synonymous_variant ENST00000268638.5 0 1 hg19 CCDS10956.1 TCGA-IB-AAUU-01A-11D-A377-08 IRF8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269100.2 0 0 0 6 400 0 49 0 5.519594e-01 0 113 0 49 2 0 0 0 0 0 2 1 9.638836e-01 6 395 0 48 2 0 0 0 0 49 2 -2.531501 1 1 121412 17 45 1 2 2 4 2.208062 1 0.370000 3.300000 0.540146 0.110000 3.000000e-02 0.230000 0.120000 0.126837 0.110000 0 0.070000 0.170000 COASY 80347 broad.mit.edu 37 17 40714771 40714771 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr17:40714771G>A ENST00000393818.2 + 1 587 c.131G>A c.(130-132)gGc>gAc p.G44D COASY_ENST00000420359.1_Missense_Mutation_p.G44D|RP11-400F19.8_ENST00000585572.1_RNA|COASY_ENST00000590958.1_Missense_Mutation_p.G73D|COASY_ENST00000449624.1_Intron|COASY_ENST00000421097.2_Missense_Mutation_p.G44D NM_025233.6 NP_079509.5 Q13057 COASY_HUMAN CoA synthase 21 all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344) CTGCAGCCGGGCATGAGCCTG 0.662000 0 SO:0001583 missense ENST00000393818.2 0 1 hg19 CCDS11429.1 . . . . . . . . . . G 19.21 3.783426 0.70222 4.54E-4 0.0 ENSG00000068120 ENST00000421097;ENST00000420359;ENST00000393818;ENST00000426807 T;T 0.33438 1.41;1.41 5.84 4.88 0.63580 . 0.000000 0.85682 D 0.000000 T 0.24736 0.0600 L 0.32530 0.975 0.80722 D 1 P;B 0.41041 0.736;0.043 B;B 0.38500 0.275;0.024 T 0.03068 -1.1076 10 0.48119 T 0.1 -18.0729 12.532 0.56120 0.0803:0.0:0.9197:0.0 . 73;44 Q13057-2;Q13057 .;COASY_HUMAN D 73;44;44;44 ENSP00000413338:G44D;ENSP00000377406:G44D ENSP00000377406:G44D G + 2 0 COASY 37968297 1.000000 0.71417 0.997000 0.53966 0.854000 0.48673 6.902000 0.75699 1.483000 0.48342 0.561000 0.74099 GGC TCGA-IB-AAUU-01A-11D-A377-08 COASY-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450409.1 0 0 0 6 507 0 69 0 4.133932e-01 0 107 0 69 2 0 0 0 0 0 2 1 9.631976e-01 6 498 0 69 2 0 0 0 0 69 2 -1.930375 0 1 121388 3 39 1 2 2 4 2.240639 1 0.370000 3.300000 0.540146 0.090000 2.000000e-02 0.180000 0.080000 0.100443 0.090000 0 0.050000 0.140000 DHX8 1659 broad.mit.edu 37 17 41570293 41570293 + Missense_Mutation SNP C C T rs146727331 TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr17:41570293C>T ENST00000262415.3 + 6 820 c.748C>T c.(748-750)Cgg>Tgg p.R250W DHX8_ENST00000540306.1_Missense_Mutation_p.R250W NM_004941.1 NP_004932.1 Q14562 DHX8_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 8 42 Breast(137;0.00908) GGATAGATGGCGGGATAAGCA 0.507000 NSCLC(56;1548 1661 49258 49987) 0 SO:0001583 missense ENST00000262415.3 1 1 hg19 CCDS11464.1 . . . . . . . . . . C 15.67 2.901639 0.52227 0.0 1.16E-4 ENSG00000067596 ENST00000540306;ENST00000262415 T;T 0.56611 0.45;0.45 5.33 0.831 0.18860 . 0.131203 0.50627 D 0.000103 T 0.35128 0.0921 N 0.08118 0 0.47183 D 0.999343 D;D 0.69078 0.997;0.995 P;P 0.51657 0.627;0.676 T 0.20672 -1.0268 10 0.59425 D 0.04 . 4.9162 0.13847 0.4807:0.3354:0.1111:0.0729 . 250;250 F5H658;Q14562 .;DHX8_HUMAN W 250 ENSP00000437886:R250W;ENSP00000262415:R250W ENSP00000262415:R250W R + 1 2 DHX8 38925819 1.000000 0.71417 1.000000 0.80357 0.493000 0.33554 3.269000 0.51592 0.205000 0.20568 -0.293000 0.09583 CGG TCGA-IB-AAUU-01A-11D-A377-08 DHX8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000453485.1 1 0 1 117 339 0 109 1 9.958452e-01 5 21 0 109 2 0 0 0 0 0 2 1 1 114 333 0 107 2 0 0 0 0 109 2 -20.000000 1 1 121412 7 42 1 2 2 4 2.240639 1 0.370000 3.300000 0.540146 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TANC2 26115 broad.mit.edu 37 17 61483573 61483573 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr17:61483573G>A ENST00000424789.2 + 19 3306 c.3302G>A c.(3301-3303)cGc>cAc p.R1101H AC015923.1_ENST00000431604.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.R1101H|RP11-269G24.3_ENST00000583552.1_RNA NM_025185.3 NP_079461.2 Q9HCD6 TANC2_HUMAN tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 44 AAGCAGGGCCGCACTCCCCTG 0.512000 OREG0024637 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000424789.2 0 1 hg19 CCDS45754.1 . . . . . . . . . . G 34 5.398436 0.96030 . . ENSG00000170921 ENST00000389520;ENST00000424789 T;T 0.66280 -0.2;-0.2 5.48 5.48 0.80851 Ankyrin repeat-containing domain (4); 0.055575 0.64402 D 0.000001 T 0.76357 0.3976 L 0.50919 1.6 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.992;0.996 T 0.77368 -0.2614 10 0.66056 D 0.02 . 19.3674 0.94469 0.0:0.0:1.0:0.0 . 1101;1101 Q9HCD6-2;Q9HCD6 .;TANC2_HUMAN H 1101 ENSP00000374171:R1101H;ENSP00000387593:R1101H ENSP00000374171:R1101H R + 2 0 TANC2 58837305 1.000000 0.71417 0.966000 0.40874 0.973000 0.67179 9.810000 0.99221 2.587000 0.87381 0.462000 0.41574 CGC TCGA-IB-AAUU-01A-11D-A377-08 TANC2-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444765.1 0 0 0 5 475 0 104 0 1.804077e-04 0 2 0 104 2 0 0 0 0 0 2 1 9.368114e-01 5 472 0 102 2 0 0 0 0 104 2 -2.083755 0 1 0 0 1 1 2 3 1.969332 1 0.370000 3.300000 0.468354 0.070000 1.000000e-02 0.150000 0.060000 0.079379 0.070000 0 0.040000 0.110000 DNAH2 146754 broad.mit.edu 37 17 7727588 7727588 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr17:7727588C>T ENST00000572933.1 + 76 13088 c.11628C>T c.(11626-11628)atC>atT p.I3876I DNAH2_ENST00000389173.2_Silent_p.I3876I Q9P225 DYH2_HUMAN dynein, axonemal, heavy chain 2 189 all_cancers(10;4.66e-07)|Prostate(122;0.081) AGGCCCCCATCGCTGCTCGGC 0.652000 0 SO:0001819 synonymous_variant ENST00000572933.1 1 1 hg19 CCDS32551.1 TCGA-IB-AAUU-01A-11D-A377-08 DNAH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000440241.1 1 0 1 23 114 0 44 1 6.289709e-01 8 4 0 44 2 0 0 0 0 0 2 1 9.999996e-01 23 111 0 42 2 0 0 0 0 44 2 -20.000000 1 1 121196 3 38 1 0 1 1 1.363146 1 0.370000 3.300000 0.226994 0.720000 4.800000e-01 0.950000 0.720000 0.729876 0.720000 0 0.590000 0.860000 ZNF700 90592 broad.mit.edu 37 19 12060731 12060731 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr19:12060731C>T ENST00000254321.5 + 4 2035 c.1892C>T c.(1891-1893)tCt>tTt p.S631F ZNF700_ENST00000482090.1_Missense_Mutation_p.S613F|ZNF763_ENST00000538752.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000590798.1_Intron NM_001271848.1|NM_144566.1 NP_001258777.1|NP_653167.1 Q9H0M5 ZN700_HUMAN zinc finger protein 700 ZNF700/MAST1_ENST00000251472(2) 33 GCCTTCAGATCTGCCTCAAAC 0.438000 0 SO:0001583 missense ENST00000254321.5 1 0 hg19 CCDS32915.1 . . . . . . . . . . c 0.399 -0.919390 0.02396 . . ENSG00000196757 ENST00000254321 T 0.03580 3.88 0.563 -1.13 0.09775 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.09024 0.0223 M 0.62723 1.935 0.09310 N 1 D 0.67145 0.996 D 0.64877 0.93 T 0.24512 -1.0158 9 0.10636 T 0.68 . 7.1331 0.25512 0.0:0.7162:0.2837:0.0 . 631 Q9H0M5 ZN700_HUMAN F 631 ENSP00000254321:S631F ENSP00000254321:S631F S + 2 0 ZNF700 11921731 0.000000 0.05858 0.001000 0.08648 0.011000 0.07611 -1.497000 0.02289 -0.437000 0.07243 0.313000 0.20887 TCT TCGA-IB-AAUU-01A-11D-A377-08 ZNF700-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344126.2 1 0 1 74 344 0 148 1 9.956576e-01 13 28 0 148 2 0 0 0 0 0 2 1 1 71 340 0 146 2 0 0 0 0 148 2 -3.201776 1 1 0 0 1 1 3 4 1.989907 1 0.370000 3.300000 0.486008 0.990000 9.500000e-01 1.000000 1.000000 0.997413 0.990000 1 0.990000 1.000000 HMG20B 10362 broad.mit.edu 37 19 3574395 3574395 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr19:3574395C>T ENST00000333651.6 + 4 237 c.162C>T c.(160-162)cgC>cgT p.R54R MFSD12_ENST00000591878.1_5'Flank NM_006339.2 NP_006330.2 Q9P0W2 HM20B_HUMAN high mobility group 20B 1 Hepatocellular(1079;0.137) TGAAGAAACGCGGCTGGCCCA 0.672000 0 SO:0001819 synonymous_variant ENST00000333651.6 0 1 hg19 CCDS45919.1 . . . . . . . . . . C 13.18 2.159407 0.38119 . . ENSG00000064961 ENST00000262949 . . . 4.03 -8.05 0.01106 . 0.000000 0.64402 U 0.000001 T 0.49745 0.1575 . . . 0.58432 D 0.999991 . . . . . . T 0.62067 -0.6932 6 0.72032 D 0.01 -7.5678 2.2814 0.04115 0.4628:0.0954:0.2597:0.182 . . . . W 59 . ENSP00000262949:R59W R + 1 2 HMG20B 3525395 0.000000 0.05858 0.325000 0.25375 0.925000 0.55904 -2.871000 0.00720 -3.088000 0.00248 0.491000 0.48974 CGG TCGA-IB-AAUU-01A-11D-A377-08 HMG20B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318088.1 1 0 0 11 33 0 12 1 9.999996e-01 34 90 0 12 2 0 0 0 0 0 2 1 9.987482e-01 10 32 0 12 2 0 0 0 0 12 2 -19.998840 1 1 0 0 1 0 3 3 1.729192 1 0.370000 3.300000 0.441316 0.990000 8.900000e-01 1.000000 1.000000 0.993476 0.990000 1 0.990000 1.000000 PSG6 5675 broad.mit.edu 37 19 43420517 43420517 + Missense_Mutation SNP T T C rs140507212 TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr19:43420517T>C ENST00000292125.2 - 2 231 c.187A>G c.(187-189)Act>Gct p.T63A PSG6_ENST00000187910.2_Missense_Mutation_p.T63A|PSG6_ENST00000601833.1_5'UTR|PSG6_ENST00000402603.4_Missense_Mutation_p.T63A NM_002782.4 NP_002773.1 Q00889 PSG6_HUMAN pregnancy specific beta-1-glycoprotein 6 44 Prostate(69;0.00899) ATGTAGCCAGTAAGATTCTGG 0.463000 0 SO:0001583 missense ENST00000292125.2 0 1 hg19 CCDS12613.1 . . . . . . . . . . N 0.008 -1.914902 0.00503 . . ENSG00000170848 ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456 T;T;T 0.01464 4.86;4.86;4.86 1.58 -3.16 0.05217 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1); . . . . T 0.00784 0.0026 N 0.11651 0.15 0.09310 N 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.11329 0.002;0.001;0.006 T 0.46020 -0.9221 9 0.05959 T 0.93 . 0.9301 0.01333 0.2963:0.2272:0.3254:0.1511 . 63;63;63 Q00889;Q00889-2;B5MCE1 PSG6_HUMAN;.;. A 63 ENSP00000187910:T63A;ENSP00000385736:T63A;ENSP00000292125:T63A ENSP00000187910:T63A T - 1 0 PSG6 48112357 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -4.985000 0.00163 -2.639000 0.00430 -1.366000 0.01203 ACT TCGA-IB-AAUU-01A-11D-A377-08 PSG6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321436.1 0 0 0 7 1311 0 353 0 0 0 0 353 2 0 0 0 0 0 2 1 9.789671e-01 6 1283 0 348 2 0 0 0 0 353 2 -4.032797 1 0 121316 16 48 1 1 3 4 2.057851 1 0.370000 3.300000 0.511097 0.030000 0 1.000000 0.040000 0.197100 0.030000 0 0.010000 1.000000 ERCC2 2068 broad.mit.edu 37 19 45867502 45867502 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr19:45867502G>A ENST00000391945.4 - 9 883 c.806C>T c.(805-807)aCg>aTg p.T269M ERCC2_ENST00000221481.6_3'UTR|ERCC2_ENST00000391944.3_Missense_Mutation_p.T191M|ERCC2_ENST00000391940.4_Missense_Mutation_p.T245M|ERCC2_ENST00000485403.2_Missense_Mutation_p.T245M NM_000400.3 NP_000391.1 P18074 ERCC2_HUMAN excision repair cross-complementation group 2 9 Ovarian(192;0.0728)|all_neural(266;0.112) CCTGAGCACCGTCTTCTGCAG 0.692000 Mis, N, F, S skin basal cell, skin squamous cell, melanoma Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (D) 19 19q13.2-q13.3 2068 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) E 0 SO:0001583 missense Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000391945.4 1 1 hg19 CCDS33049.1 . . . . . . . . . . G 17.83 3.485655 0.63962 . . ENSG00000104884 ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940 T;T;T 0.63913 -0.07;-0.07;-0.07 4.72 4.72 0.59763 Helicase-like, DEXD box c2 type (1);Domain of unknown function DUF1227 (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1); 0.359147 0.31071 N 0.008304 T 0.71091 0.3299 M 0.72118 2.19 0.80722 D 1 P;P;B 0.47841 0.468;0.901;0.04 B;P;B 0.51487 0.376;0.671;0.264 T 0.74748 -0.3560 10 0.59425 D 0.04 -24.3907 15.5543 0.76180 0.0:0.0:1.0:0.0 . 191;245;269 E7EVE9;Q7KZU6;P18074 .;.;ERCC2_HUMAN M 219;245;269;191;245 ENSP00000375809:T269M;ENSP00000375808:T191M;ENSP00000375804:T245M ENSP00000375804:T245M T - 2 0 ERCC2 50559342 1.000000 0.71417 0.997000 0.53966 0.662000 0.39071 4.390000 0.59646 2.601000 0.87937 0.561000 0.74099 ACG TCGA-IB-AAUU-01A-11D-A377-08 ERCC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109626.2 1 0 0 45 275 0 30 1 9.791805e-01 7 33 0 30 2 0 0 0 0 0 2 1 1 45 270 0 29 2 0 0 0 0 30 2 -20.000000 1 1 0 0 1 4 6 10 2.664688 1 0.370000 3.300000 0.618459 0.990000 9.600000e-01 1.000000 1.000000 0.997505 0.990000 1 0.990000 1.000000 KLK4 9622 broad.mit.edu 37 19 51411880 51411880 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr19:51411880C>T ENST00000324041.1 - 3 429 c.430G>A c.(430-432)Gcg>Acg p.A144T KLK4_ENST00000597441.1_5'Flank|KLK4_ENST00000431178.2_Missense_Mutation_p.A95T NM_004917.3 NP_004908.3 Q9Y5K2 KLK4_HUMAN kallikrein-related peptidase 4 19 all_neural(266;0.026) GAGTTCCCCGCGGTAGGGCAC 0.602000 0 SO:0001583 missense ENST00000324041.1 0 1 hg19 CCDS12809.1 . . . . . . . . . . c 6.881 0.532035 0.13127 . . ENSG00000167749 ENST00000324041;ENST00000431178 D;D 0.89415 -2.51;-2.51 3.99 -7.97 0.01139 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 1.234540 0.06113 N 0.667494 T 0.76307 0.3969 N 0.25201 0.72 0.09310 N 1 B;B 0.33964 0.434;0.248 B;B 0.27076 0.076;0.012 T 0.68296 -0.5446 10 0.41790 T 0.15 . 8.5105 0.33215 0.171:0.1988:0.5598:0.0703 . 95;144 Q96JD7;Q9Y5K2 .;KLK4_HUMAN T 144;95 ENSP00000326159:A144T;ENSP00000399448:A95T ENSP00000326159:A144T A - 1 0 KLK4 56103692 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -2.743000 0.00797 -2.474000 0.00527 -1.157000 0.01802 GCG TCGA-IB-AAUU-01A-11D-A377-08 KLK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464449.1 0 0 0 5 223 1 63 0 7.905138e-04 0 2 1 63 2 0 0 0 0 0 2 0 4.049618e-02 5 219 1 63 13 0 0 0 1 63 2 -3.084110 1 1 0 0 1 0 2 2 1.683231 1 0.370000 3.300000 0.370000 0.120000 4.000000e-02 0.260000 0.120000 0.139946 0.120000 0 0.070000 0.190000 ADORA3 140 broad.mit.edu 37 1 112042946 112042946 + Missense_Mutation SNP C C T rs143962803 byFrequency TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr1:112042946C>T ENST00000241356.4 - 2 988 c.583G>A c.(583-585)Gcc>Acc p.A195T ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_Intron|ADORA3_ENST00000369717.4_Intron NM_000677.3 NP_000668.1 P33765 AA3R_HUMAN adenosine A3 receptor p.A195T(1) 12 all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156) Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824) AGATAGATGGCGCACATGACA 0.433000 1 Substitution - Missense(1) SO:0001583 missense ENST00000241356.4 1 1 hg19 CCDS839.1 . . . . . . . . . . C 9.584 1.124357 0.20959 0.005447 1.16E-4 ENSG00000121933 ENST00000241356 T 0.37058 1.22 5.01 2.07 0.26955 GPCR, rhodopsin-like superfamily (1); . . . . T 0.10852 0.0265 L 0.39467 1.215 0.23174 N 0.998173 P 0.41784 0.762 B 0.36534 0.227 T 0.11717 -1.0576 9 0.27785 T 0.31 . 8.8535 0.35214 0.0:0.6997:0.0:0.3003 . 195 P33765 AA3R_HUMAN T 195 ENSP00000241356:A195T ENSP00000241356:A195T A - 1 0 ADORA3 111844469 0.077000 0.21312 0.173000 0.22940 0.021000 0.10359 1.197000 0.32211 0.227000 0.20999 0.655000 0.94253 GCC TCGA-IB-AAUU-01A-11D-A377-08 ADORA3-010 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033065.1 1 0 1 139 321 0 107 0 6.737607e-01 0 7 0 107 2 0 0 0 0 0 2 1 1 136 312 0 105 2 0 0 0 0 107 2 -3.017764 1 1 121412 56 51 1 1 2 3 1.940352 1 0.370000 3.300000 0.468354 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SPTA1 6708 broad.mit.edu 37 1 158585164 158585164 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr1:158585164C>T ENST00000368147.4 - 48 6810 c.6630G>A c.(6628-6630)aaG>aaA p.K2210K NM_003126.2 NP_003117.2 P02549 SPTA1_HUMAN spectrin, alpha, erythrocytic 1 307 all_hematologic(112;0.0378) TTAGTTGACGCTTCATCGCCT 0.483000 0 SO:0001819 synonymous_variant ENST00000368147.4 0 1 hg19 CCDS41423.1 TCGA-IB-AAUU-01A-11D-A377-08 SPTA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051851.3 0 0 0 6 704 0 119 0 0 0 0 119 2 0 0 0 0 0 2 1 9.625253e-01 6 688 0 116 2 0 0 0 0 119 2 -2.960638 1 1 0 0 1 2 2 4 2.208983 1 0.370000 3.300000 0.540146 0.060000 0 0.140000 0.080000 0.071525 0.060000 0 0.030000 0.100000 DCAF6 55827 broad.mit.edu 37 1 167960489 167960489 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr1:167960489C>T ENST00000312263.6 + 6 804 c.600C>T c.(598-600)tgC>tgT p.C200C DCAF6_ENST00000367843.3_Silent_p.C200C|DCAF6_ENST00000432587.2_Silent_p.C169C|DCAF6_ENST00000470919.1_3'UTR|DCAF6_ENST00000367840.3_Silent_p.C200C NM_001017977.2 NP_001017977.1 Q58WW2 DCAF6_HUMAN DDB1 and CUL4 associated factor 6 36 TTGCTATTTGCCCACCAATAC 0.393000 0 SO:0001819 synonymous_variant ENST00000312263.6 0 1 hg19 CCDS30933.1 TCGA-IB-AAUU-01A-11D-A377-08 DCAF6-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000083661.2 0 0 0 5 522 1 114 0 1.034541e-02 0 64 1 114 4 0 0 0 0 0 2 0 1.133879e-02 5 514 1 114 16 0 0 0 1 114 2 -2.291945 0 1 0 0 1 2 2 4 2.208983 1 0.370000 3.300000 0.540146 0.070000 1.000000e-02 0.160000 0.080000 0.083120 0.070000 0 0.030000 0.120000 HEATR1 55127 broad.mit.edu 37 1 236762848 236762848 + Nonsense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr1:236762848G>A ENST00000366582.3 - 4 550 c.436C>T c.(436-438)Cga>Tga p.R146* HEATR1_ENST00000483073.1_5'UTR|HEATR1_ENST00000366581.2_Nonsense_Mutation_p.R146* NM_018072.5 NP_060542.4 Q9H583 HEAT1_HUMAN HEAT repeat containing 1 87 Ovarian(103;0.0634)|Breast(184;0.133) all_cancers(173;0.0255)|Prostate(94;0.175) OV - Ovarian serous cystadenocarcinoma(106;0.00117) TGTATGACTCGCACAAATATT 0.368000 0 SO:0001587 stop_gained ENST00000366582.3 0 1 hg19 CCDS31066.1 . . . . . . . . . . G 38 7.045839 0.98025 . . ENSG00000119285 ENST00000366582;ENST00000366581 . . . 5.62 5.62 0.85841 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 15.6914 0.77457 0.0:0.0:0.855:0.145 . . . . X 146 . ENSP00000355540:R146X R - 1 2 HEATR1 234829471 1.000000 0.71417 0.945000 0.38365 0.991000 0.79684 1.649000 0.37281 2.812000 0.96745 0.561000 0.74099 CGA TCGA-IB-AAUU-01A-11D-A377-08 HEATR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096635.1 0 0 0 6 463 0 90 0 1.024651e-02 0 10 0 90 2 0 0 0 0 0 2 1 9.640146e-01 6 458 0 87 2 0 0 0 0 90 2 -2.380664 0 1 0 0 1 2 2 4 2.206397 1 0.370000 3.300000 0.540146 0.100000 2.000000e-02 0.200000 0.090000 0.109884 0.100000 0 0.060000 0.150000 ZNF362 149076 broad.mit.edu 37 1 33745956 33745956 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr1:33745956G>A ENST00000539719.1 + 5 751 c.581G>A c.(580-582)cGc>cAc p.R194H ZNF362_ENST00000373428.5_Missense_Mutation_p.R194H NM_152493.2 NP_689706.2 Q5T0B9 ZN362_HUMAN zinc finger protein 362 10 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211) GAACGCGGCCGCAAAAAGATC 0.647000 Pancreas(162;1431 2676 35353 38425) 0 SO:0001583 missense ENST00000539719.1 0 1 hg19 CCDS377.1 . . . . . . . . . . G 36 5.713649 0.96830 . . ENSG00000160094 ENST00000483388;ENST00000539719;ENST00000373428 T;T 0.09163 3.01;3.01 5.99 5.99 0.97316 . 0.468737 0.18085 N 0.152172 T 0.37404 0.1002 M 0.77103 2.36 0.80722 D 1 D 0.76494 0.999 D 0.76071 0.987 T 0.02512 -1.1148 10 0.87932 D 0 -36.2752 18.0311 0.89285 0.0:0.0:1.0:0.0 . 194 Q5T0B9 ZN362_HUMAN H 181;194;194 ENSP00000446335:R194H;ENSP00000362527:R194H ENSP00000362527:R194H R + 2 0 ZNF362 33518543 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.314000 0.96306 2.857000 0.98124 0.650000 0.86243 CGC TCGA-IB-AAUU-01A-11D-A377-08 ZNF362-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000011857.2 0 0 0 5 182 0 21 0 2.145633e-01 0 27 0 21 2 0 0 0 0 0 2 1 9.357119e-01 5 179 0 19 2 0 0 0 0 21 2 -2.743451 1 1 0 0 1 1 3 4 1.977741 1 0.370000 3.300000 0.479726 0.220000 7.000000e-02 1.000000 0.180000 0.395069 0.220000 0 0.130000 1.000000 GLMN 11146 broad.mit.edu 37 1 92755861 92755861 + Missense_Mutation SNP T T A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr1:92755861T>A ENST00000370360.3 - 5 369 c.288A>T c.(286-288)ttA>ttT p.L96F GLMN_ENST00000534881.1_Missense_Mutation_p.L96F NM_053274.2 NP_444504.1 Q92990 GLMN_HUMAN glomulin, FKBP associated protein 17 all_lung(203;0.00827)|Lung NSC(277;0.0295) TTGGATTGCATAACTATAAAA 0.308000 Multiple Glomus Tumors (of the Skin), Familial 0 SO:0001583 missense Familial Cancer Database Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma ENST00000370360.3 1 1 hg19 CCDS738.1 . . . . . . . . . . T 18.08 3.543108 0.65198 . . ENSG00000174842 ENST00000370360;ENST00000534881 T;T 0.50548 0.74;0.74 5.65 1.87 0.25490 . 0.418315 0.26231 N 0.025566 T 0.40067 0.1102 L 0.56769 1.78 0.47737 D 0.9995 D;D 0.59767 0.986;0.982 P;P 0.62813 0.907;0.875 T 0.50338 -0.8840 10 0.66056 D 0.02 -2.3571 0.2648 0.00223 0.2109:0.2274:0.2068:0.3549 . 96;96 B4DJ85;Q92990 .;GLMN_HUMAN F 96 ENSP00000359385:L96F;ENSP00000440156:L96F ENSP00000359385:L96F L - 3 2 GLMN 92528449 0.519000 0.26242 1.000000 0.80357 0.995000 0.86356 -0.704000 0.05058 1.033000 0.39918 0.533000 0.62120 TTA TCGA-IB-AAUU-01A-11D-A377-08 GLMN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000028358.1 0 0 1 50 256 0 98 0 2.786534e-02 0 2 0 98 2 0 0 0 0 0 2 1 1 50 252 0 99 2 0 0 0 0 98 2 -20.000000 1 1 121394 1 28 1 1 3 4 1.977741 1 0.370000 3.300000 0.479726 0.990000 8.300000e-01 1.000000 1.000000 0.982261 0.990000 1 0.960000 1.000000 PREX1 57580 broad.mit.edu 37 20 47262580 47262580 + Silent SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr20:47262580G>A ENST00000371941.3 - 26 3343 c.3321C>T c.(3319-3321)atC>atT p.I1107I PREX1_ENST00000396220.1_Silent_p.I1107I NM_020820.3 NP_065871 Q8TCU6 PREX1_HUMAN phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1 110 BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198) TGGGCTCTGTGATGGTGGACA 0.597000 0 SO:0001819 synonymous_variant ENST00000371941.3 1 1 hg19 CCDS13410.1 TCGA-IB-AAUU-01A-11D-A377-08 PREX1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079623.1 1 0 1 73 182 0 36 1 9.996427e-01 2 31 0 36 2 0 0 0 0 0 2 1 1 71 181 0 34 2 0 0 0 0 36 2 -20.000000 1 1 0 0 1 2 2 4 2.168958 1 0.370000 3.300000 0.532572 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 BACH1 571 broad.mit.edu 37 21 30699086 30699086 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr21:30699086C>T ENST00000399921.1 + 3 1184 c.941C>T c.(940-942)tCc>tTc p.S314F BACH1_ENST00000286800.3_Missense_Mutation_p.S314F NM_206866.1 NP_996749.1 Q9BX63 FANCJ_HUMAN BTB and CNC homology 1, basic leucine zipper transcription factor 1 27 CACAATTCTTCCATAGACCCT 0.388000 0 SO:0001583 missense ENST00000399921.1 1 1 hg19 CCDS13585.1 . . . . . . . . . . C 12.90 2.077636 0.36662 . . ENSG00000156273 ENST00000286800;ENST00000399921 T;T 0.72167 -0.63;-0.63 5.38 5.38 0.77491 . 0.248068 0.36034 N 0.002837 T 0.54695 0.1874 N 0.14661 0.345 0.09310 N 1 B 0.34372 0.451 B 0.26517 0.07 T 0.58233 -0.7672 10 0.72032 D 0.01 -16.0467 18.0715 0.89408 0.0:1.0:0.0:0.0 . 314 O14867 BACH1_HUMAN F 314 ENSP00000286800:S314F;ENSP00000382805:S314F ENSP00000286800:S314F S + 2 0 BACH1 29620957 0.098000 0.21812 0.093000 0.20910 0.624000 0.37722 4.125000 0.57931 2.813000 0.96785 0.655000 0.94253 TCC TCGA-IB-AAUU-01A-11D-A377-08 BACH1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171974.1 1 0 1 103 499 0 212 1 9.872332e-01 12 23 0 212 2 0 0 0 0 0 2 1 1 102 493 0 207 2 0 0 0 0 212 2 -20.000000 1 1 0 0 1 0 1 1 1.607975 0 0.370000 3.300000 0.368832 0.910000 7.600000e-01 1.000000 1.000000 0.917420 0.910000 1 0.830000 1.000000 DIP2A 23181 broad.mit.edu 37 21 47976980 47976980 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr21:47976980C>T ENST00000417564.2 + 30 3648 c.3627C>T c.(3625-3627)tgC>tgT p.C1209C DIP2A_ENST00000400274.1_Silent_p.C1205C|DIP2A_ENST00000318711.7_Silent_p.C1210C Q14689 DIP2A_HUMAN DIP2 disco-interacting protein 2 homolog A (Drosophila) 43 Breast(49;0.0933) GGTGTCTGTGCAGGTGAGTGC 0.612000 0 SO:0001819 synonymous_variant ENST00000417564.2 0 1 hg19 CCDS46655.1 TCGA-IB-AAUU-01A-11D-A377-08 DIP2A-012 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000376736.1 1 0 1 9 74 0 10 1 5.240832e-01 2 13 0 10 2 0 0 0 0 0 2 1 9.941661e-01 9 71 0 10 2 0 0 0 0 10 2 -15.453780 1 1 0 0 1 1 2 3 1.942018 0 0.370000 3.300000 0.468354 0.710000 3.600000e-01 1.000000 1.000000 0.726181 0.710000 0 0.510000 0.950000 ACR 49 broad.mit.edu 37 22 51182600 51182600 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr22:51182600C>T ENST00000216139.5 + 4 717 c.677C>T c.(676-678)gCg>gTg p.A226V ACR_ENST00000527761.1_3'UTR|AC002056.5_ENST00000532913.1_RNA NM_001097.2 NP_001088.2 P10323 ACRO_HUMAN acrosin 7 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) AATGTGTGCGCGGGGTATCCT 0.577000 0 SO:0001583 missense ENST00000216139.5 0 1 hg19 CCDS14101.1 . . . . . . . . . . N 13.55 2.272141 0.40194 . . ENSG00000100312 ENST00000216139 D 0.91124 -2.79 4.48 3.44 0.39384 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.000000 0.43416 D 0.000561 D 0.93455 0.7912 M 0.75884 2.315 0.32305 N 0.564555 D 0.89917 1.0 D 0.91635 0.999 D 0.92392 0.5922 10 0.66056 D 0.02 -19.6881 7.0808 0.25229 0.0:0.7985:0.0:0.2014 . 226 P10323 ACRO_HUMAN V 226 ENSP00000216139:A226V ENSP00000216139:A226V A + 2 0 ACR 49529466 0.988000 0.35896 0.865000 0.33974 0.031000 0.12232 3.250000 0.51445 2.335000 0.79485 0.450000 0.29827 GCG TCGA-IB-AAUU-01A-11D-A377-08 ACR-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000316605.2 0 0 0 8 386 0 78 0 5.724754e-04 0 2 0 78 2 0 0 0 0 0 2 1 9.883788e-01 7 377 0 84 2 0 0 0 0 78 2 -3.042878 1 1 121412 13 43 1 0 2 2 1.681803 1 0.370000 3.300000 0.370000 0.110000 4.000000e-02 0.210000 0.110000 0.122303 0.110000 0 0.070000 0.160000 SCN2A 6326 broad.mit.edu 37 2 166201198 166201198 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr2:166201198G>A ENST00000375437.2 + 16 2986 c.2696G>A c.(2695-2697)gGc>gAc p.G899D SCN2A_ENST00000357398.3_Missense_Mutation_p.G899D|SCN2A_ENST00000375427.2_Missense_Mutation_p.G899D|SCN2A_ENST00000283256.6_Missense_Mutation_p.G899D NM_001040142.1 NP_001035232.1 Q99250 SCN2A_HUMAN sodium channel, voltage-gated, type II, alpha subunit 118 Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909) GCTGTGGTCGGCATGCAGCTC 0.443000 0 SO:0001583 missense ENST00000375437.2 0 1 hg19 CCDS33314.1 . . . . . . . . . . G 31 5.064264 0.93898 . . ENSG00000136531 ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427 D;D;D;D 0.97688 -4.49;-4.49;-4.49;-4.49 5.74 5.74 0.90152 Ion transport (1); 0.000000 0.64402 D 0.000002 D 0.99444 0.9803 H 0.99391 4.545 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.98030 1.0376 10 0.87932 D 0 . 19.9329 0.97127 0.0:0.0:1.0:0.0 . 899;899 Q99250-2;Q99250 .;SCN2A_HUMAN D 899 ENSP00000364586:G899D;ENSP00000349973:G899D;ENSP00000283256:G899D;ENSP00000364576:G899D ENSP00000283256:G899D G + 2 0 SCN2A 165909444 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 9.735000 0.98825 2.714000 0.92807 0.650000 0.86243 GGC TCGA-IB-AAUU-01A-11D-A377-08 SCN2A-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000102659.2 0 0 0 7 784 0 170 0 0 0 0 170 2 0 0 0 0 0 2 1 9.785993e-01 7 764 0 169 2 0 0 0 0 170 2 -1.741427 0 1 0 0 1 2 2 4 2.162446 1 0.370000 3.300000 0.531285 0.060000 1.000000e-02 1.000000 0.080000 0.124319 0.060000 0 0.030000 0.110000 TTN 7273 broad.mit.edu 37 2 179407109 179407109 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr2:179407109C>T ENST00000591111.1 - 299 92675 c.92451G>A c.(92449-92451)acG>acA p.T30817T TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Silent_p.T29890T|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.T23393T|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Silent_p.T32458T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Silent_p.T23585T|TTN_ENST00000359218.5_Silent_p.T23518T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAAACTTAAACGTGGACCTAG 0.502000 0 SO:0001819 synonymous_variant ENST00000591111.1 1 1 hg19 TCGA-IB-AAUU-01A-11D-A377-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 51 134 0 36 0 0 0 1 0 36 2 0 0 0 0 0 2 1 1 50 132 0 36 2 0 0 0 0 36 2 -20.000000 1 1 0 0 1 2 2 4 2.162446 1 0.370000 3.300000 0.531285 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 HECW2 57520 broad.mit.edu 37 2 197187274 197187274 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr2:197187274C>T ENST00000260983.3 - 7 994 c.812G>A c.(811-813)cGt>cAt p.R271H HECW2_ENST00000409111.1_5'UTR NM_020760.1 NP_065811.1 Q9P2P5 HECW2_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 113 GATGATGGGACGGCTCTTGGC 0.423000 0 SO:0001583 missense ENST00000260983.3 1 1 hg19 CCDS33354.1 . . . . . . . . . . C 32 5.137069 0.94517 . . ENSG00000138411 ENST00000260983 T 0.46451 0.87 5.49 4.6 0.57074 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.191653 0.47455 D 0.000223 T 0.44973 0.1319 M 0.75447 2.3 0.58432 D 0.999998 B 0.29627 0.252 B 0.26614 0.071 T 0.51741 -0.8667 10 0.87932 D 0 . 14.9482 0.71050 0.0:0.9304:0.0:0.0696 . 271 Q9P2P5 HECW2_HUMAN H 271 ENSP00000260983:R271H ENSP00000260983:R271H R - 2 0 HECW2 196895519 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.912000 0.69948 2.878000 0.98634 0.650000 0.86243 CGT TCGA-IB-AAUU-01A-11D-A377-08 HECW2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335199.3 1 0 1 97 711 0 140 0 4.057401e-02 0 3 0 140 2 0 0 0 0 0 2 1 1 94 706 0 138 2 0 0 0 0 140 2 -20.000000 1 1 0 0 1 2 2 4 2.117468 1 0.370000 3.300000 0.520730 0.860000 7.000000e-01 1.000000 1.000000 0.873874 0.860000 1 0.770000 1.000000 HK2 3099 broad.mit.edu 37 2 75118049 75118049 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr2:75118049G>A ENST00000290573.2 + 18 3335 c.2735G>A c.(2734-2736)cGt>cAt p.R912H HK2_ENST00000409174.1_Missense_Mutation_p.R884H NM_000189.4 NP_000180.2 P52789 HXK2_HUMAN hexokinase 2 p.R912L(1) 43 TGCCGCATCCGTGAGGCTGGA 0.542000 1 Substitution - Missense(1) SO:0001583 missense ENST00000290573.2 0 1 hg19 CCDS1956.1 . . . . . . . . . . G 19.73 3.882526 0.72294 . . ENSG00000159399 ENST00000290573;ENST00000535740;ENST00000409174 D;D 0.97553 -4.43;-4.43 4.99 4.99 0.66335 . 0.056749 0.64402 D 0.000001 D 0.93926 0.8056 L 0.41079 1.255 0.80722 D 1 D 0.61080 0.989 B 0.39027 0.288 D 0.93726 0.7037 10 0.40728 T 0.16 -11.9165 15.8192 0.78626 0.0:0.0:1.0:0.0 . 912 P52789 HXK2_HUMAN H 912;912;884 ENSP00000290573:R912H;ENSP00000387140:R884H ENSP00000290573:R912H R + 2 0 HK2 74971557 1.000000 0.71417 0.961000 0.40146 0.996000 0.88848 4.459000 0.60102 2.609000 0.88269 0.561000 0.74099 CGT TCGA-IB-AAUU-01A-11D-A377-08 HK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252238.2 0 0 0 5 447 0 125 0 7.343498e-01 0 225 0 125 2 0 0 0 0 0 2 1 9.341313e-01 5 438 0 120 2 0 0 0 0 125 2 -3.139917 1 1 121412 1 28 1 2 2 4 2.171339 1 0.370000 3.300000 0.532572 0.080000 1.000000e-02 1.000000 0.080000 0.138256 0.080000 0 0.050000 0.150000 EPHB1 2047 broad.mit.edu 37 3 134884864 134884864 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr3:134884864C>T ENST00000398015.3 + 8 2010 c.1640C>T c.(1639-1641)gCg>gTg p.A547V EPHB1_ENST00000493838.1_Missense_Mutation_p.A108V NM_004441.4 NP_004432.1 P54762 EPHB1_HUMAN EPH receptor B1 130 GGCTCGGCAGCGGCCGGGGTC 0.567000 0 SO:0001583 missense ENST00000398015.3 0 1 hg19 CCDS46921.1 . . . . . . . . . . C 16.46 3.129979 0.56721 . . ENSG00000154928 ENST00000398015;ENST00000493838 T;T 0.10477 2.87;2.87 6.07 6.07 0.98685 . 0.056918 0.64402 D 0.000002 T 0.09598 0.0236 L 0.31065 0.9 0.80722 D 1 B 0.14805 0.011 B 0.11329 0.006 T 0.14117 -1.0484 10 0.02654 T 1 . 20.6439 0.99570 0.0:1.0:0.0:0.0 . 547 P54762 EPHB1_HUMAN V 547;108 ENSP00000381097:A547V;ENSP00000419574:A108V ENSP00000381097:A547V A + 2 0 EPHB1 136367554 1.000000 0.71417 0.879000 0.34478 0.743000 0.42351 7.794000 0.85869 2.884000 0.98904 0.655000 0.94253 GCG TCGA-IB-AAUU-01A-11D-A377-08 EPHB1-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357671.1 0 0 0 10 450 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 9.960064e-01 10 427 0 64 2 0 0 0 0 65 2 -2.612578 1 1 0 0 1 1 2 3 1.906089 1 0.370000 3.300000 0.468354 0.140000 6.000000e-02 0.250000 0.150000 0.152126 0.140000 0 0.100000 0.200000 CLSTN2 64084 broad.mit.edu 37 3 140178467 140178467 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr3:140178467G>A ENST00000458420.3 + 7 1268 c.1078G>A c.(1078-1080)Ggc>Agc p.G360S RP11-68L1.2_ENST00000503357.1_RNA|RP11-68L1.1_ENST00000483759.2_RNA NM_022131.2 NP_071414.2 Q9H4D0 CSTN2_HUMAN calsyntenin 2 87 CAAGTTTGACGGCAGGCAGGG 0.572000 HNSCC(16;0.037) GBM(45;858 913 3709 36904 37282) 0 SO:0001583 missense ENST00000458420.3 1 1 hg19 CCDS3112.1 . . . . . . . . . . G 34 5.305899 0.95629 . . ENSG00000158258 ENST00000458420 T 0.02863 4.13 5.41 5.41 0.78517 Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1); 0.000000 0.85682 D 0.000000 T 0.18341 0.0440 M 0.85630 2.765 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.00174 -1.1956 10 0.62326 D 0.03 -35.2726 16.6974 0.85339 0.0:0.0:1.0:0.0 . 360 Q9H4D0 CSTN2_HUMAN S 360 ENSP00000402460:G360S ENSP00000402460:G360S G + 1 0 CLSTN2 141661157 1.000000 0.71417 0.959000 0.39883 0.923000 0.55619 9.869000 0.99810 2.552000 0.86080 0.655000 0.94253 GGC TCGA-IB-AAUU-01A-11D-A377-08 CLSTN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359393.3 1 0 1 38 162 0 30 0 9.883776e-02 0 3 0 30 2 0 0 0 0 0 2 1 9.936295e-01 38 160 1 27 21 0 0 0 0 30 2 -3.356241 1 1 121412 7 40 1 1 2 3 1.906089 1 0.370000 3.300000 0.468354 0.990000 8.900000e-01 1.000000 1.000000 0.993423 0.990000 1 0.990000 1.000000 GRK7 131890 broad.mit.edu 37 3 141535562 141535562 + Missense_Mutation SNP G G T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr3:141535562G>T ENST00000264952.2 + 4 1469 c.1332G>T c.(1330-1332)aaG>aaT p.K444N NM_139209.2 NP_631948.1 Q8WTQ7 GRK7_HUMAN G protein-coupled receptor kinase 7 26 ACAGAGAAAAGTCTGATGATC 0.413000 0 SO:0001583 missense ENST00000264952.2 1 1 hg19 CCDS3120.1 . . . . . . . . . . G 10.19 1.281990 0.23392 . . ENSG00000114124 ENST00000264952 T 0.24350 1.86 5.4 -0.397 0.12423 Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.206992 0.43260 D 0.000593 T 0.07458 0.0188 N 0.03050 -0.425 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.17745 -1.0359 10 0.51188 T 0.08 -3.3201 0.3395 0.00331 0.2689:0.2271:0.2739:0.2301 . 444 Q8WTQ7 GRK7_HUMAN N 444 ENSP00000264952:K444N ENSP00000264952:K444N K + 3 2 GRK7 143018252 0.000000 0.05858 0.992000 0.48379 0.976000 0.68499 -0.314000 0.08092 -0.010000 0.14271 0.467000 0.42956 AAG TCGA-IB-AAUU-01A-11D-A377-08 GRK7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353168.1 1 0 1 42 287 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 1 41 286 0 97 2 0 0 0 0 97 2 -20.000000 1 1 120062 2 35 1 1 2 3 1.906089 1 0.370000 3.300000 0.468354 0.810000 6.000000e-01 1.000000 1.000000 0.824383 0.810000 0 0.700000 0.940000 P2RY12 64805 broad.mit.edu 37 3 151055628 151055628 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr3:151055628G>A ENST00000302632.3 - 3 1305 c.1006C>T c.(1006-1008)Cca>Tca p.P336S MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron NM_022788.4|NM_176876.2 NP_073625.1|NP_795345.1 Q9H244 P2Y12_HUMAN purinergic receptor P2Y, G-protein coupled, 12 17 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374) TCTTCATTTGGGTCACCACCA 0.368000 0 SO:0001583 missense ENST00000302632.3 0 1 hg19 CCDS3159.1 . . . . . . . . . . G 11.03 1.519990 0.27211 . . ENSG00000169313 ENST00000302632;ENST00000455408 T 0.59906 0.23 5.48 4.6 0.57074 . 0.944449 0.08953 N 0.869875 T 0.31734 0.0806 N 0.08118 0 0.09310 N 1 B 0.31026 0.304 B 0.23419 0.046 T 0.18808 -1.0325 10 0.15499 T 0.54 -2.2908 5.6313 0.17512 0.1514:0.0:0.6808:0.1678 . 336 Q9H244 P2Y12_HUMAN S 336;239 ENSP00000307259:P336S ENSP00000307259:P336S P - 1 0 P2RY12 152538318 0.161000 0.22892 0.037000 0.18230 0.021000 0.10359 0.759000 0.26461 1.435000 0.47434 -0.169000 0.13324 CCA TCGA-IB-AAUU-01A-11D-A377-08 P2RY12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357796.1 0 0 0 7 602 0 151 0 5.695090e-04 0 3 0 151 2 0 0 0 0 0 2 1 9.798811e-01 7 595 0 150 2 0 0 0 0 151 2 -2.364652 0 1 0 0 1 1 2 3 1.906089 1 0.370000 3.300000 0.468354 0.070000 2.000000e-02 0.150000 0.070000 0.083806 0.070000 0 0.040000 0.110000 GPR149 344758 broad.mit.edu 37 3 154055947 154055947 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr3:154055947C>T ENST00000389740.2 - 4 1836 c.1737G>A c.(1735-1737)ggG>ggA p.G579G NM_001038705.1 NP_001033794.1 Q86SP6 GP149_HUMAN G protein-coupled receptor 149 47 LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173) TTATTTTTTGCCCTTCTGCGC 0.458000 0 SO:0001819 synonymous_variant ENST00000389740.2 0 1 hg19 CCDS43162.1 TCGA-IB-AAUU-01A-11D-A377-08 GPR149-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353430.1 0 0 0 6 799 0 182 0 0 0 0 182 2 0 0 0 0 0 2 1 9.633826e-01 6 788 0 176 2 0 0 0 0 182 2 -1.673033 0 1 0 0 1 1 2 3 1.906089 1 0.370000 3.300000 0.468354 0.040000 0 0.100000 0.060000 0.054652 0.040000 0 0.020000 0.080000 PLCL2 23228 broad.mit.edu 37 3 17052241 17052241 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr3:17052241G>A ENST00000418129.2 + 2 1490 c.1025G>A c.(1024-1026)cGg>cAg p.R342Q PLCL2_ENST00000432376.1_Missense_Mutation_p.R342Q|PLCL2_ENST00000460467.1_Intron|PLCL2_ENST00000396755.2_Missense_Mutation_p.R342Q NM_001144382.1 NP_001137854.1 Q9UPR0 PLCL2_HUMAN phospholipase C-like 2 43 ATGGGTTGCCGGAGTGTTGAA 0.423000 0 SO:0001583 missense ENST00000418129.2 0 1 hg19 CCDS33713.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 26.8|26.8 4.776979|4.776979 0.90195|0.90195 .|. .|. ENSG00000154822|ENSG00000154822 ENST00000419842|ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376 .|T;T;T .|0.81163 .|-1.46;-1.46;-1.46 5.96|5.96 5.96|5.96 0.96718|0.96718 .|PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3); .|0.053332 .|0.64402 .|N .|0.000001 D|D 0.90841|0.90841 0.7123|0.7123 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|D .|0.89917 .|1.0 .|D .|0.97110 .|1.0 D|D 0.90920|0.90920 0.4782|0.4782 4|9 .|0.87932 .|D .|0 .|. 20.4008|20.4008 0.98991|0.98991 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|468 .|Q9UPR0 .|PLCL2_HUMAN R|Q 86|342;469;342;342 .|ENSP00000409637:R342Q;ENSP00000379979:R342Q;ENSP00000412836:R342Q .|ENSP00000285094:R469Q G|R +|+ 1|2 0|0 PLCL2|PLCL2 17027245|17027245 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.958000|0.958000 0.62258|0.62258 9.869000|9.869000 0.99810|0.99810 2.826000|2.826000 0.97356|0.97356 0.655000|0.655000 0.94253|0.94253 GGA|CGG TCGA-IB-AAUU-01A-11D-A377-08 PLCL2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340250.3 0 0 0 6 651 0 131 0 2.082527e-02 0 20 0 131 2 0 0 0 0 0 2 1 9.632171e-01 6 640 0 130 2 0 0 0 0 131 2 -2.288576 0 1 0 0 1 2 3 5 2.498643 1 0.370000 3.300000 0.593404 0.080000 1.000000e-02 0.170000 0.100000 0.087270 0.080000 0 0.040000 0.130000 ZFP42 132625 broad.mit.edu 37 4 188924640 188924640 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr4:188924640G>A ENST00000326866.4 + 4 1087 c.679G>A c.(679-681)Gtt>Att p.V227I ZFP42_ENST00000509524.1_Missense_Mutation_p.V227I NM_174900.3 NP_777560.2 Q96MM3 ZFP42_HUMAN ZFP42 zinc finger protein 27 all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227) GAAAGCGTTCGTTGAGAGCTC 0.502000 0 SO:0001583 missense ENST00000326866.4 1 1 hg19 CCDS3849.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 10.42 1.345682 0.24426 . . ENSG00000179059 ENST00000326866;ENST00000509524 T;T 0.41400 1.0;1.0 4.39 -8.78 0.00824 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 1.214960 0.06385 N 0.715986 T 0.16171 0.0389 N 0.16478 0.41 0.09310 N 1 B 0.27316 0.175 B 0.14023 0.01 T 0.08953 -1.0697 10 0.17832 T 0.49 . 1.3926 0.02253 0.1903:0.3391:0.2374:0.2333 . 227 Q96MM3 ZFP42_HUMAN I 227 ENSP00000317686:V227I;ENSP00000424662:V227I ENSP00000317686:V227I V + 1 0 ZFP42 189161634 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 0.295000 0.19065 -3.355000 0.00180 -0.892000 0.02923 GTT TCGA-IB-AAUU-01A-11D-A377-08 ZFP42-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359794.1 1 0 1 55 283 0 98 0 0 0 0 98 2 0 0 0 0 0 2 1 1 55 281 0 96 2 0 0 0 0 98 2 -3.162619 1 1 121412 2 32 1 1 2 3 1.922928 0 0.370000 3.300000 0.467523 0.990000 8.000000e-01 1.000000 1.000000 0.970440 0.990000 1 0.910000 1.000000 TBC1D1 23216 broad.mit.edu 37 4 38023260 38023260 + Missense_Mutation SNP G G T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr4:38023260G>T ENST00000261439.4 + 6 1486 c.1131G>T c.(1129-1131)caG>caT p.Q377H TBC1D1_ENST00000508802.1_Missense_Mutation_p.Q377H NM_001253914.1|NM_001253915.1|NM_015173.3 NP_001240843.1|NP_001240844.1|NP_055988.2 Q86TI0 TBCD1_HUMAN TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 36 CCGCAGTGCAGCAGACAGCTA 0.517000 0 SO:0001583 missense ENST00000261439.4 0 1 hg19 CCDS33972.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 17.32|17.32 3.358757|3.358757 0.61403|0.61403 .|. .|. ENSG00000065882|ENSG00000065882 ENST00000510573|ENST00000508802;ENST00000261439;ENST00000446803 .|T;T;T .|0.16196 .|2.36;2.36;2.36 5.76|5.76 4.01|4.01 0.46588|0.46588 .|Phosphotyrosine interaction domain (1); .|0.112392 .|0.39985 .|N .|0.001213 T|T 0.26738|0.26738 0.0654|0.0654 L|L 0.40543|0.40543 1.245|1.245 0.80722|0.80722 D|D 1|1 .|D;D;B;D .|0.89917 .|1.0;1.0;0.028;1.0 .|D;D;B;D .|0.81914 .|0.99;0.995;0.018;0.99 T|T 0.02713|0.02713 -1.1120|-1.1120 5|10 .|0.40728 .|T .|0.16 -24.9276|-24.9276 5.7525|5.7525 0.18154|0.18154 0.1938:0.0:0.6522:0.154|0.1938:0.0:0.6522:0.154 .|. .|377;377;109;377 .|B9A6J6;E9PGH8;Q6PJJ8;Q86TI0 .|.;.;.;TBCD1_HUMAN S|H 25|377;377;248 .|ENSP00000423651:Q377H;ENSP00000261439:Q377H;ENSP00000396877:Q248H .|ENSP00000261439:Q377H A|Q +|+ 1|3 0|2 TBC1D1|TBC1D1 37699655|37699655 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.671000|0.671000 0.39405|0.39405 6.142000|6.142000 0.71750|0.71750 0.761000|0.761000 0.33130|0.33130 0.591000|0.591000 0.81541|0.81541 GCA|CAG TCGA-IB-AAUU-01A-11D-A377-08 TBC1D1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317443.2 1 0 0 8 100 0 21 1 8.613083e-01 2 45 0 21 2 0 0 0 0 0 2 1 9.894837e-01 8 98 0 21 2 0 0 0 0 21 2 -12.812990 1 1 0 0 1 2 2 4 2.192112 1 0.370000 3.300000 0.538901 0.570000 2.700000e-01 1.000000 1.000000 0.596307 0.570000 0 0.400000 0.790000 SLAIN2 57606 broad.mit.edu 37 4 48379970 48379970 + Missense_Mutation SNP C C G TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr4:48379970C>G ENST00000264313.6 + 3 1014 c.596C>G c.(595-597)cCt>cGt p.P199R SLAIN2_ENST00000512093.1_Missense_Mutation_p.P6R|SLAIN2_ENST00000506375.1_3'UTR NM_020846.1 NP_065897.1 Q9P270 SLAI2_HUMAN SLAIN motif family, member 2 13 TACACCAGTCCTTACAGTCCA 0.413000 0 SO:0001583 missense ENST00000264313.6 1 1 hg19 CCDS47051.1 . . . . . . . . . . C 17.39 3.377180 0.61735 . . ENSG00000109171 ENST00000264313;ENST00000512093 . . . 5.76 5.76 0.90799 . 0.207938 0.42420 D 0.000708 T 0.52613 0.1745 L 0.29908 0.895 0.46131 D 0.998881 B 0.34200 0.441 B 0.36030 0.216 T 0.55866 -0.8073 9 0.87932 D 0 -3.4428 19.9601 0.97247 0.0:1.0:0.0:0.0 . 199 Q9P270 SLAI2_HUMAN R 199;6 . ENSP00000264313:P199R P + 2 0 SLAIN2 48074727 1.000000 0.71417 1.000000 0.80357 0.598000 0.36846 5.168000 0.64978 2.720000 0.93068 0.655000 0.94253 CCT TCGA-IB-AAUU-01A-11D-A377-08 SLAIN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365807.4 1 0 1 132 351 0 101 1 9.999582e-01 12 30 0 101 2 0 0 0 0 0 2 1 1 132 348 0 101 2 0 0 0 0 101 2 -7.211354 1 1 0 0 1 2 2 4 2.192112 1 0.370000 3.300000 0.538901 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 GRM6 2916 broad.mit.edu 37 5 178413350 178413350 + Silent SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr5:178413350G>A ENST00000517717.1 - 9 1943 c.1905C>T c.(1903-1905)taC>taT p.Y635Y RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.Y635Y O15303 GRM6_HUMAN glutamate receptor, metabotropic 6 55 all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351) all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) AGGTGATGGCGTAGATGAGGA 0.672000 0 SO:0001819 synonymous_variant ENST00000517717.1 1 1 hg19 CCDS4442.1 TCGA-IB-AAUU-01A-11D-A377-08 GRM6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253474.2 0 0 1 54 124 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 1 54 124 0 28 2 0 0 0 0 28 2 -3.222074 1 1 121406 42 44 1 1 2 3 1.913234 0 0.370000 3.300000 0.465014 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ITGA2 3673 broad.mit.edu 37 5 52356793 52356793 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr5:52356793G>A ENST00000296585.5 + 12 1518 c.1375G>A c.(1375-1377)Gca>Aca p.A459T NM_002203.3 NP_002194.2 P17301 ITA2_HUMAN integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 47 Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181) TGCTCCTCGGGCAAATTATAC 0.443000 0 SO:0001583 missense ENST00000296585.5 0 1 hg19 CCDS3957.1 . . . . . . . . . . G 17.08 3.297090 0.60086 . . ENSG00000164171 ENST00000296585 T 0.11169 2.8 5.77 3.84 0.44239 . 0.165528 0.56097 D 0.000037 T 0.07548 0.0190 L 0.46885 1.475 0.38632 D 0.951406 B;P 0.36412 0.104;0.552 B;B 0.27076 0.04;0.076 T 0.11591 -1.0581 10 0.37606 T 0.19 . 5.5765 0.17227 0.1627:0.0:0.5942:0.2431 . 459;459 E7ESP4;P17301 .;ITA2_HUMAN T 459 ENSP00000296585:A459T ENSP00000296585:A459T A + 1 0 ITGA2 52392550 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.461000 0.53035 2.720000 0.93068 0.650000 0.86243 GCA TCGA-IB-AAUU-01A-11D-A377-08 ITGA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253857.2 0 0 0 5 408 0 84 0 1.193541e-01 0 40 0 84 2 0 0 0 0 0 2 1 9.367007e-01 7 403 0 82 2 0 0 0 0 84 2 -2.526493 1 1 0 0 1 1 2 3 1.920332 0 0.370000 3.300000 0.462480 0.080000 2.000000e-02 1.000000 0.080000 0.141955 0.080000 0 0.040000 0.140000 TTBK1 84630 broad.mit.edu 37 6 43222815 43222815 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr6:43222815C>T ENST00000259750.4 + 7 688 c.605C>T c.(604-606)aCg>aTg p.T202M TTBK1_ENST00000304139.5_Missense_Mutation_p.T151M NM_032538.1 NP_115927.1 Q5TCY1 TTBK1_HUMAN tau tubulin kinase 1 53 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399) TTTCGAGGAACGGTTCGCTAT 0.617000 0 SO:0001583 missense ENST00000259750.4 0 1 hg19 CCDS34455.1 . . . . . . . . . . C 26.2 4.712948 0.89112 . . ENSG00000146216 ENST00000393984;ENST00000259750;ENST00000304139 T 0.76839 -1.05 4.83 4.83 0.62350 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 D 0.92756 0.7697 H 0.99336 4.52 0.58432 D 0.999996 D 0.89917 1.0 D 0.97110 1.0 D 0.95848 0.8872 10 0.87932 D 0 . 16.6948 0.85332 0.0:1.0:0.0:0.0 . 202 Q5TCY1 TTBK1_HUMAN M 151;202;151 ENSP00000259750:T202M ENSP00000259750:T202M T + 2 0 TTBK1 43330793 1.000000 0.71417 0.994000 0.49952 0.968000 0.65278 7.413000 0.80104 2.242000 0.73789 0.655000 0.94253 ACG TCGA-IB-AAUU-01A-11D-A377-08 TTBK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040584.3 0 0 0 5 214 0 39 0 8.560597e-04 0 2 0 39 2 0 0 0 0 0 2 1 9.367475e-01 5 212 0 38 2 0 0 0 0 39 2 -3.330339 1 1 121412 1 28 1 2 2 4 1.720841 1 0.370000 3.300000 0.411380 0.150000 5.000000e-02 1.000000 0.140000 0.278793 0.150000 0 0.090000 0.320000 DGKI 9162 broad.mit.edu 37 7 137263014 137263014 + Splice_Site SNP A A C TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr7:137263014A>C ENST00000288490.5 - 16 1699 c.e16+1 DGKI_ENST00000424189.2_Splice_Site|DGKI_ENST00000446122.1_Splice_Site|DGKI_ENST00000453654.2_Splice_Site NM_004717.2 NP_004708.1 O75912 DGKI_HUMAN diacylglycerol kinase, iota 84 ATGTATACCTACCCCTGCATA 0.313000 0 SO:0001630 splice_region_variant ENST00000288490.5 1 1 hg19 CCDS5845.1 . . . . . . . . . . A 22.2 4.262490 0.80358 . . ENSG00000157680 ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122 . . . 5.15 5.15 0.70609 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.9475 0.71044 1.0:0.0:0.0:0.0 . . . . . -1 . . . - . . DGKI 136913554 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 9.096000 0.94182 2.080000 0.62538 0.379000 0.24179 . TCGA-IB-AAUU-01A-11D-A377-08 DGKI-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341286.3 1 0 0 23 213 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 9.999994e-01 23 209 0 44 2 0 0 0 0 45 2 -20.000000 1 1 0 0 1 2 2 4 2.161656 1 0.370000 3.300000 0.531285 0.720000 4.700000e-01 1.000000 1.000000 0.742537 0.720000 0 0.580000 0.910000 ABCB5 340273 broad.mit.edu 37 7 20793112 20793112 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr7:20793112G>A ENST00000404938.2 + 27 4211 c.3559G>A c.(3559-3561)Gat>Aat p.D1187N ABCB5_ENST00000258738.6_Missense_Mutation_p.D742N NM_001163941.1 NP_001157413.1 Q2M3G0 ABCB5_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 5 77 TTCAGCCCTCGATAATGACAG 0.393000 0 SO:0001583 missense ENST00000404938.2 1 1 hg19 CCDS55090.1 . . . . . . . . . . G 25.2 4.614824 0.87359 . . ENSG00000004846 ENST00000404938;ENST00000258738 D;D 0.95756 -3.8;-3.8 5.16 4.26 0.50523 ATPase, AAA+ type, core (1);ABC transporter-like (1); 0.000000 0.56097 D 0.000024 D 0.98169 0.9395 H 0.96365 3.81 0.54753 D 0.999981 D;D 0.76494 0.999;0.999 D;D 0.65573 0.936;0.913 D 0.98395 1.0565 10 0.87932 D 0 . 13.0851 0.59135 0.0806:0.0:0.9194:0.0 . 1187;742 A7BKA4;Q2M3G0 .;ABCB5_HUMAN N 1187;742 ENSP00000384881:D1187N;ENSP00000258738:D742N ENSP00000258738:D742N D + 1 0 ABCB5 20759637 1.000000 0.71417 1.000000 0.80357 0.925000 0.55904 7.641000 0.83368 2.683000 0.91414 0.555000 0.69702 GAT TCGA-IB-AAUU-01A-11D-A377-08 ABCB5-004 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000326736.2 1 0 1 64 393 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 1 62 390 0 88 2 0 0 0 0 88 2 -3.075973 1 1 121410 4 34 1 2 2 4 2.177772 1 0.370000 3.300000 0.535124 0.990000 8.000000e-01 1.000000 1.000000 0.969155 0.990000 1 0.910000 1.000000 CPVL 54504 broad.mit.edu 37 7 29132283 29132283 + Silent SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr7:29132283G>A ENST00000409850.1 - 10 1144 c.498C>T c.(496-498)caC>caT p.H166H CPVL_ENST00000265394.5_Silent_p.H166H|CPVL_ENST00000396276.3_Silent_p.H166H Q9H3G5 CPVL_HUMAN carboxypeptidase, vitellogenic-like 28 CTGCATATCCGTGGGTATCAT 0.443000 0 SO:0001819 synonymous_variant ENST00000409850.1 1 1 hg19 CCDS5419.1 TCGA-IB-AAUU-01A-11D-A377-08 CPVL-009 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328305.1 1 0 1 31 219 0 42 1 9.999929e-01 30 104 0 42 2 0 0 0 0 0 2 1 1 30 217 0 41 2 0 0 0 0 42 2 -3.018182 1 1 121412 4 34 1 2 2 4 2.177772 1 0.370000 3.300000 0.535124 0.920000 6.400000e-01 1.000000 1.000000 0.897332 0.920000 1 0.770000 1.000000 PRSS55 203074 broad.mit.edu 37 8 10383123 10383123 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr8:10383123C>T ENST00000328655.3 + 1 68 c.28C>T c.(28-30)Ctg>Ttg p.L10L PRSS55_ENST00000522210.1_Silent_p.L10L|PRSS51_ENST00000523024.1_RNA NM_198464.3 NP_940866.2 Q6UWB4 PRS55_HUMAN protease, serine, 55 31 GTTGCTGCTCCTGTCCCTGGT 0.672000 0 SO:0001819 synonymous_variant ENST00000328655.3 1 1 hg19 CCDS5976.1 TCGA-IB-AAUU-01A-11D-A377-08 PRSS55-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251493.3 1 0 1 99 161 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 1 99 159 0 42 2 0 0 0 0 42 2 -20.000000 1 1 0 0 1 0 2 2 1.672263 1 0.370000 3.300000 0.370000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 WHSC1L1 54904 broad.mit.edu 37 8 38205614 38205614 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr8:38205614C>T ENST00000317025.8 - 2 593 c.76G>A c.(76-78)Gcc>Acc p.A26T WHSC1L1_ENST00000316985.3_Missense_Mutation_p.A26T|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.A26T|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.A26T NM_023034.1 NP_075447.1 Q9BZ95 NSD3_HUMAN Wolf-Hirschhorn syndrome candidate 1-like 1 24 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) CGGATGTTGGCGGAGTCAATG 0.453000 T NUP98 AML Dom yes 8 8p12 54904 Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3) L 0 SO:0001583 missense ENST00000317025.8 0 1 hg19 CCDS43729.1 . . . . . . . . . . C 34 5.358909 0.95854 . . ENSG00000147548 ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985;ENST00000529223 D;D;D;T;T 0.96651 -4.08;-4.02;-4.02;-0.76;0.39 5.56 5.56 0.83823 . 0.000000 0.47852 U 0.000201 D 0.97420 0.9156 L 0.46157 1.445 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.99;0.996;0.999;0.99 D 0.98006 1.0363 10 0.87932 D 0 . 19.8909 0.96929 0.0:1.0:0.0:0.0 . 26;26;26;26 B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95 .;.;.;NSD3_HUMAN T 26 ENSP00000393284:A26T;ENSP00000313983:A26T;ENSP00000434730:A26T;ENSP00000313410:A26T;ENSP00000435422:A26T ENSP00000313410:A26T A - 1 0 WHSC1L1 38324771 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.745000 0.68672 2.765000 0.95021 0.655000 0.94253 GCC TCGA-IB-AAUU-01A-11D-A377-08 WHSC1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381924.3 0 0 0 5 424 0 122 0 1.973842e-01 0 58 0 122 2 0 0 0 0 0 2 1 9.359450e-01 5 419 0 120 2 0 0 0 0 122 2 -2.224503 0 1 0 0 1 0 2 2 1.672263 1 0.370000 3.300000 0.370000 0.060000 1.000000e-02 0.140000 0.060000 0.074928 0.060000 0 0.030000 0.100000 ADAM2 2515 broad.mit.edu 37 8 39646232 39646232 + Missense_Mutation SNP C C A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr8:39646232C>A ENST00000265708.4 - 8 701 c.598G>T c.(598-600)Gtt>Ttt p.V200F ADAM2_ENST00000379853.2_Intron|ADAM2_ENST00000347580.4_Missense_Mutation_p.V181F|ADAM2_ENST00000521880.1_Missense_Mutation_p.V200F NM_001464.3 NP_001455.3 Q99965 ADAM2_HUMAN ADAM metallopeptidase domain 2 53 all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246) LUSC - Lung squamous cell carcinoma(45;0.000149) TGAGCGACAACAGTTGTATCA 0.274000 0 SO:0001583 missense ENST00000265708.4 1 1 hg19 CCDS34884.1 . . . . . . . . . . C 11.49 1.653517 0.29425 . . ENSG00000104755 ENST00000347580;ENST00000265708;ENST00000521880 T;T;T 0.64438 -0.1;-0.1;-0.1 4.7 -5.11 0.02901 Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2); . . . . T 0.72645 0.3486 M 0.71036 2.16 0.09310 N 1 P;P;P 0.41947 0.766;0.723;0.766 P;P;P 0.60609 0.877;0.73;0.824 T 0.70008 -0.4990 8 . . . . 12.6789 0.56910 0.0:0.1977:0.0:0.8023 . 200;181;200 B4DWY7;Q99965-2;Q99965 .;.;ADAM2_HUMAN F 181;200;200 ENSP00000343854:V181F;ENSP00000265708:V200F;ENSP00000429352:V200F . V - 1 0 ADAM2 39765389 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -2.932000 0.00688 -0.905000 0.03871 0.650000 0.86243 GTT TCGA-IB-AAUU-01A-11D-A377-08 ADAM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376926.1 1 0 0 40 479 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 1 40 476 0 61 2 0 0 0 0 62 2 -20.000000 1 1 0 0 1 1 7 8 3.766971 1 0.370000 3.300000 0.701422 0.880000 6.300000e-01 1.000000 1.000000 0.877360 0.880000 1 0.750000 1.000000 ZMAT4 79698 broad.mit.edu 37 8 40532370 40532370 + Missense_Mutation SNP C C G TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr8:40532370C>G ENST00000297737.6 - 5 576 c.430G>C c.(430-432)Gac>Cac p.D144H ZMAT4_ENST00000315769.7_Intron NM_024645.2 NP_078921.1 Q9H898 ZMAT4_HUMAN zinc finger, matrin-type 4 18 Ovarian(28;0.00724)|Colorectal(14;0.0468) all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152) LUSC - Lung squamous cell carcinoma(45;0.00722) CAGTATCTGTCTGAATCTCTT 0.507000 0 SO:0001583 missense ENST00000297737.6 1 1 hg19 CCDS34885.1 . . . . . . . . . . C 25.1 4.608201 0.87258 . . ENSG00000165061 ENST00000297737;ENST00000519406 T;T 0.42513 0.97;0.97 5.88 5.88 0.94601 Zinc finger, U1-type (1); 0.260803 0.46442 D 0.000283 T 0.34803 0.0910 N 0.24115 0.695 0.58432 D 0.999996 P 0.49961 0.93 P 0.44732 0.459 T 0.03773 -1.1005 10 0.15066 T 0.55 -30.1803 18.7792 0.91925 0.0:1.0:0.0:0.0 . 144 Q9H898 ZMAT4_HUMAN H 144 ENSP00000297737:D144H;ENSP00000428423:D144H ENSP00000297737:D144H D - 1 0 ZMAT4 40651527 1.000000 0.71417 0.999000 0.59377 0.937000 0.57800 7.376000 0.79658 2.782000 0.95742 0.557000 0.71058 GAC TCGA-IB-AAUU-01A-11D-A377-08 ZMAT4-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376950.1 1 0 0 228 2986 0 177 0 0 0 1 0 177 2 0 0 0 0 0 2 1 1 226 2952 0 175 2 0 0 0 0 177 2 -20.000000 1 1 0 0 1 1 15 16 7.312373 1 0.370000 3.300000 0.824513 0.990000 9.900000e-01 1.000000 1.000000 0.999998 0.990000 1 0.990000 1.000000 CHMP4C 92421 broad.mit.edu 37 8 82670525 82670525 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr8:82670525G>A ENST00000297265.4 + 4 825 c.632G>A c.(631-633)cGa>cAa p.R211Q NM_152284.3 NP_689497.1 Q96CF2 CHM4C_HUMAN charged multivesicular body protein 4C 10 CGTCGATCCCGAGCAGGTCTG 0.458000 0 SO:0001583 missense ENST00000297265.4 1 1 hg19 CCDS6233.1 . . . . . . . . . . G 11.74 1.727483 0.30593 . . ENSG00000164695 ENST00000297265 T 0.52526 0.66 6.17 5.3 0.74995 . 0.268617 0.28908 N 0.013750 T 0.25232 0.0613 N 0.08118 0 0.43334 D 0.995379 B 0.29037 0.231 B 0.17722 0.019 T 0.10497 -1.0627 10 0.15499 T 0.54 -2.4061 13.2245 0.59907 0.0759:0.0:0.9241:0.0 . 211 Q96CF2 CHM4C_HUMAN Q 211 ENSP00000297265:R211Q ENSP00000297265:R211Q R + 2 0 CHMP4C 82833080 0.991000 0.36638 0.925000 0.36789 0.351000 0.29236 1.321000 0.33678 1.633000 0.50488 0.655000 0.94253 CGA TCGA-IB-AAUU-01A-11D-A377-08 CHMP4C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379927.1 1 0 1 56 245 0 75 1 9.999999e-01 37 69 0 75 2 0 0 0 0 0 2 1 1 55 241 0 73 2 0 0 0 0 75 2 -2.893999 1 1 121402 2 33 1 1 2 3 1.874590 1 0.370000 3.300000 0.468354 0.990000 9.200000e-01 1.000000 1.000000 0.995640 0.990000 1 0.990000 1.000000 TGFBR1 7046 broad.mit.edu 37 9 101907091 101907091 + Missense_Mutation SNP G G C TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr9:101907091G>C ENST00000374994.4 + 6 1168 c.1051G>C c.(1051-1053)Gac>Cac p.D351H TGFBR1_ENST00000552516.1_Missense_Mutation_p.D355H|TGFBR1_ENST00000374990.2_Missense_Mutation_p.D274H|RNA5SP290_ENST00000517133.1_RNA|TGFBR1_ENST00000550253.1_Missense_Mutation_p.D282H NM_004612.2 NP_004603.1 P36897 TGFR1_HUMAN transforming growth factor, beta receptor 1 27 Acute lymphoblastic leukemia(62;0.0559) CTGTATTGCAGACTTAGGACT 0.358000 0 SO:0001583 missense ENST00000374994.4 0 1 hg19 CCDS6738.1 . . . . . . . . . . G 27.8 4.867703 0.91587 . . ENSG00000106799 ENST00000374994;ENST00000374990;ENST00000552516;ENST00000550253 D;D;D;D 0.93076 -3.16;-3.16;-3.16;-3.16 5.73 5.73 0.89815 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.042450 0.85682 N 0.000000 D 0.98726 0.9572 H 0.99964 5.085 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.99063 1.0831 10 0.87932 D 0 . 19.0403 0.92995 0.0:0.0:1.0:0.0 . 274;351 P36897-3;P36897 .;TGFR1_HUMAN H 351;274;355;282 ENSP00000364133:D351H;ENSP00000364129:D274H;ENSP00000447297:D355H;ENSP00000450052:D282H ENSP00000364129:D274H D + 1 0 TGFBR1 100946912 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.796000 0.99103 2.854000 0.98071 0.655000 0.94253 GAC TCGA-IB-AAUU-01A-11D-A377-08 TGFBR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053390.3 0 0 0 7 319 0 94 0 1.613972e-01 0 29 0 94 2 1 9.688136e-01 3 280 0 296 2 1 9.804713e-01 7 317 0 93 2 0 0 0 0 94 2 -7.506397 1 1 0 0 1 0 2 2 1.610059 1 0.370000 3.300000 0.370000 0.120000 4.000000e-02 0.230000 0.120000 0.131135 0.120000 0 0.080000 0.170000 MUSK 4593 broad.mit.edu 37 9 113547892 113547892 + Missense_Mutation SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr9:113547892C>T ENST00000374448.4 + 13 1806 c.1672C>T c.(1672-1674)Ccg>Tcg p.P558S MUSK_ENST00000416899.2_Missense_Mutation_p.P550S|MUSK_ENST00000189978.5_Missense_Mutation_p.P558S|MUSK_ENST00000374438.1_Missense_Mutation_p.P74S NM_001166281.1|NM_005592.3 NP_001159753.1|NP_005583.1 O15146 MUSK_HUMAN muscle, skeletal, receptor tyrosine kinase 49 CCAGAGGATGCCGCTCCTTCT 0.498000 0 SO:0001583 missense ENST00000374448.4 0 1 hg19 CCDS48005.1 . . . . . . . . . . C 21.0 4.084498 0.76642 . . ENSG00000030304 ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000374441;ENST00000416899;ENST00000374438 T;D 0.88664 -0.83;-2.41 5.86 5.86 0.93980 . 0.000000 0.85682 D 0.000000 D 0.92394 0.7586 L 0.45228 1.405 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.90595 0.4540 10 0.33940 T 0.23 . 19.1684 0.93567 0.0:1.0:0.0:0.0 . 558 O15146 MUSK_HUMAN S 564;558;558;472;472;74;556;74 ENSP00000363571:P558S;ENSP00000363561:P74S ENSP00000189978:P564S P + 1 0 MUSK 112587713 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.487000 0.81328 2.777000 0.95525 0.655000 0.94253 CCG TCGA-IB-AAUU-01A-11D-A377-08 MUSK-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 0 0 0 6 723 0 165 0 0 0 0 165 2 0 0 0 0 0 2 1 9.637002e-01 6 714 0 163 2 0 0 0 0 165 2 -1.857201 0 1 0 0 1 0 0 0 1.569305 0 0.370000 3.300000 0.348298 0.040000 0 0.090000 0.040000 0.049920 0.040000 0 0.020000 0.070000 LHX3 8022 broad.mit.edu 37 9 139090879 139090879 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr9:139090879G>A ENST00000371748.5 - 4 577 c.481C>T c.(481-483)Cgc>Tgc p.R161C LHX3_ENST00000371746.3_Missense_Mutation_p.R166C NM_178138.4 NP_835258.1 Q9UBR4 LHX3_HUMAN LIM homeobox 3 8 Myeloproliferative disorder(178;0.0511) ATGGTCGTGCGCGGCCGCTTG 0.761000 0 SO:0001583 missense ENST00000371748.5 1 0 hg19 CCDS6994.1 . . . . . . . . . . G 25.9 4.683978 0.88639 . . ENSG00000107187 ENST00000371748;ENST00000371746;ENST00000325195 D;D 0.99186 -5.53;-5.53 3.81 3.81 0.43845 Homeobox (3);Zinc finger, LIM-type (1);Homeodomain-like (1); 0.000000 0.85682 D 0.000000 D 0.99576 0.9847 H 0.99425 4.56 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.997;0.999 D 0.97659 1.0159 10 0.87932 D 0 . 10.2927 0.43605 0.0:0.0:0.8028:0.1972 . 161;166 Q9UBR4;F1T0D9 LHX3_HUMAN;. C 161;166;164 ENSP00000360813:R161C;ENSP00000360811:R166C ENSP00000319224:R164C R - 1 0 LHX3 138230700 1.000000 0.71417 1.000000 0.80357 0.970000 0.65996 6.984000 0.76186 1.959000 0.56917 0.555000 0.69702 CGC TCGA-IB-AAUU-01A-11D-A377-08 LHX3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000055048.3 1 0 0 19 57 0 9 0 0 0 0 9 2 0 0 0 0 0 2 1 9.999967e-01 19 57 0 9 2 0 0 0 0 9 2 -20.000000 1 1 0 0 1 0 2 2 1.649119 1 0.370000 3.300000 0.370000 0.990000 8.700000e-01 1.000000 1.000000 0.992339 0.990000 1 0.990000 1.000000 PDCD1LG2 80380 broad.mit.edu 37 9 5535034 5535034 + Silent SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chr9:5535034G>A ENST00000397747.3 + 3 593 c.345G>A c.(343-345)ctG>ctA p.L115L PDCD1LG2_ENST00000397745.2_Silent_p.L115L NM_025239.3 NP_079515.2 Q9BQ51 PD1L2_HUMAN programmed cell death 1 ligand 2 8 all_hematologic(13;0.158) Acute lymphoblastic leukemia(23;0.154) ACAAGTACCTGACTCTGAAAG 0.483000 0 SO:0001819 synonymous_variant ENST00000397747.3 1 1 hg19 CCDS6465.1 TCGA-IB-AAUU-01A-11D-A377-08 PDCD1LG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051634.1 1 0 1 9 77 0 30 0 1.404494e-02 0 2 0 30 2 0 0 0 0 0 2 1 9.950543e-01 9 77 0 28 2 0 0 0 0 30 2 -15.492490 1 1 0 0 1 0 2 2 1.586295 1 0.370000 3.300000 0.370000 0.570000 2.900000e-01 0.960000 1.000000 0.600135 0.570000 0 0.420000 0.770000 AMOT 154796 broad.mit.edu 37 X 112058796 112058796 + Silent SNP C C T TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chrX:112058796C>T ENST00000524145.1 - 3 1256 c.1182G>A c.(1180-1182)caG>caA p.Q394Q AMOT_ENST00000304758.1_5'UTR|AMOT_ENST00000371962.1_Silent_p.Q162Q|AMOT_ENST00000371959.3_Silent_p.Q394Q|AMOT_ENST00000371958.1_Silent_p.Q162Q Q4VCS5 AMOT_HUMAN angiomotin p.Q394Q(1) 43 gctgctgctgctgttgttggt 0.582000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000524145.1 0 1 hg19 CCDS48154.1 TCGA-IB-AAUU-01A-11D-A377-08 AMOT-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000378570.1 0 0 0 4 120 0 30 0 1.029019e-02 0 4 0 30 2 0 0 0 1 0 1 2 1 8.857989e-01 3 119 0 29 2 0 0 0 0 30 2 -2.472580 0 1 0 0 1 0 1 1 0.370000 3.300000 0.370000 0.090000 2.000000e-02 0.200000 0.090000 0.105781 0.090000 0 0.050000 0.150000 VGLL1 51442 broad.mit.edu 37 X 135630884 135630884 + Silent SNP G G A rs151216817 TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chrX:135630884G>A ENST00000370634.3 + 3 521 c.351G>A c.(349-351)ccG>ccA p.P117P MIR934_ENST00000401241.1_RNA NM_016267.3 NP_057351.1 Q99990 VGLL1_HUMAN vestigial-like family member 1 20 Acute lymphoblastic leukemia(192;0.000127) AGTTCTCACCGTCCCTGGCTA 0.592000 0 SO:0001819 synonymous_variant ENST00000370634.3 0 1 hg19 CCDS14658.1 . . . . . . . . . . G 0.012 -1.672630 0.00758 0.0 1.49E-4 ENSG00000102243 ENST00000440515 . . . 5.81 2.14 0.27477 . . . . . T 0.37945 0.1022 . . . 0.09310 N 1 . . . . . . T 0.23084 -1.0198 4 . . . 1.9921 10.4023 0.44237 0.224:0.0:0.776:0.0 . . . . I 82 . . V + 1 0 VGLL1 135458550 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 0.073000 0.14640 0.000000 0.14550 -2.015000 0.00435 GTC TCGA-IB-AAUU-01A-11D-A377-08 VGLL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058493.1 0 0 0 7 654 0 134 0 4.482178e-02 0 26 0 134 2 0 0 0 0 0 2 1 9.801466e-01 7 649 0 134 2 0 0 0 0 134 2 -2.230565 0 1 121410 9 46 1 0 1 1 0.370000 3.300000 0.370000 0.020000 0 0.060000 0.030000 0.032537 0.020000 0 0.010000 0.040000 FAM47C 442444 broad.mit.edu 37 X 37026745 37026745 + Missense_Mutation SNP G G A TCGA-IB-AAUU-01A-11D-A377-08 TCGA-IB-AAUU-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64433ce6-3172-4d93-97af-a61bc487b4d4 24455824-9f86-49b4-a078-ab7e8fdce629 g.chrX:37026745G>A ENST00000358047.3 + 1 314 c.262G>A c.(262-264)Gct>Act p.A88T NM_001013736.2 NP_001013758.1 Q5HY64 FA47C_HUMAN family with sequence similarity 47, member C 120 AGGTCCCCAAGCTGACCCCAA 0.532000 0 SO:0001583 missense ENST00000358047.3 1 1 hg19 CCDS35227.1 . . . . . . . . . . G 8.662 0.900661 0.17686 . . ENSG00000198173 ENST00000358047 T 0.20069 2.1 0.502 -0.96 0.10340 . . . . . T 0.18383 0.0441 L 0.43701 1.375 0.09310 N 1 B 0.28584 0.216 B 0.36959 0.237 T 0.38243 -0.9670 9 0.33940 T 0.23 . 5.7074 0.17915 0.0:0.3376:0.6624:0.0 . 88 Q5HY64 FA47C_HUMAN T 88 ENSP00000367913:A88T ENSP00000367913:A88T A + 1 0 FAM47C 36936666 0.001000 0.12720 0.002000 0.10522 0.010000 0.07245 0.310000 0.19356 -0.497000 0.06641 0.292000 0.19580 GCT TCGA-IB-AAUU-01A-11D-A377-08 FAM47C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060508.1 1 0 1 146 131 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1 143 130 0 55 2 0 0 0 0 55 2 -20.000000 1 1 0 0 1 0 1 1 0.370000 3.300000 0.370000 0.980000 9.400000e-01 1.000000 0.990000 0.989971 0.980000 1 0.970000 1.000000