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 PMEPA1 56937 broad.mit.edu 37 20 56227291 56227309 + Frame_Shift_Del DEL GCCCCTCCATGCGCCCGCC GCCCCTCCATGCGCCCGCC - TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 GCCCCTCCATGCGCCCGCC - GCCCCTCCATGCGCCCGCC GCCCCTCCATGCGCCCGCC Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr20:56227291_56227309delGCCCCTCCATGCGCCCGCC ENST00000341744.3 - 4 983_1001 c.664_682delGGCGGGCGCATGGAGGGGC c.(664-684)ggcgggcgcatggaggggccgfs p.GGRMEGP222fs PMEPA1_ENST00000395814.1_Frame_Shift_Del_p.GGRMEGP172fs|PMEPA1_ENST00000347215.4_Frame_Shift_Del_p.GGRMEGP187fs|PMEPA1_ENST00000265626.4_Frame_Shift_Del_p.GGRMEGP172fs|PMEPA1_ENST00000395816.3_Frame_Shift_Del_p.GGRMEGP172fs NM_020182.4 NP_064567.2 Q969W9 PMEPA_HUMAN prostate transmembrane protein, androgen induced 1 16 GTGGGCGGCGGCCCCTCCATGCGCCCGCCGCTGCCGTAG 0.694000 0 SO:0001589 frameshift_variant ENST00000341744.3 0 1 hg19 CCDS13463.1 TCGA-2J-AABA-01A-21D-A40W-08 PMEPA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079858.2 1 0 0 12 121 0 36 0 9.999954e-01 0 265 0 36 2 0 0 0 0 0 0 1 0.999358 18 118 0 34 2 -18.219060 1 1 0 0 1 0 1 1 2.057827 0 0.340000 1.830000 0.338876 0.530000 2.900000e-01 0.850000 0.520000 0.556949 0.530000 0 0.400000 0.700000 GTF3C3 9330 broad.mit.edu 37 2 197636516 197636516 + Frame_Shift_Del DEL T T - TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:197636516delT ENST00000263956.3 - 15 2305 c.2216delA c.(2215-2217)aatfs p.N739fs NM_012086.4 NP_036218.1 Q9Y5Q9 TF3C3_HUMAN general transcription factor IIIC, polypeptide 3, 102kDa 33 ATTGTGTCCATTTAAGACACA 0.428000 0 SO:0001589 frameshift_variant ENST00000263956.3 1 0 hg19 CCDS2316.1 TCGA-2J-AABA-01A-21D-A40W-08 GTF3C3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256104.1 1 0 0 41 260 0 67 0 7.994480e-01 1 20 0 67 2 0 0 0 0 0 0 1 1.000000 44 257 0 67 2 -20.000000 1 1 0 0 1 0 1 1 2.053808 0 0.340000 1.830000 0.338876 0.790000 5.800000e-01 1.000000 1.000000 0.805588 0.790000 0 0.680000 0.920000 APOB 338 broad.mit.edu 37 2 21225066 21225069 + Frame_Shift_Del DEL GACT GACT - TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:21225066_21225069delGACT ENST00000233242.1 - 29 13352_13355 c.13225_13228delAGTC c.(13225-13230)agtctgfs p.SL4409fs RP11-116D2.1_ENST00000567376.2_lincRNA NM_000384.2 NP_000375 P04114 APOB_HUMAN apolipoprotein B 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TTCTTGATCAGACTGACTATCTTT 0.373000 0 SO:0001589 frameshift_variant ENST00000233242.1 1 0 hg19 CCDS1703.1 TCGA-2J-AABA-01A-21D-A40W-08 APOB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207571.1 1 0 0 37 295 0 64 0 2.296132e-01 0 8 0 64 2 0 0 0 0 0 0 1 0.879521 51 304 3 63 31 -14.282990 1 0 0 0 1 0 0 0 2.048860 0 0.340000 1.830000 0.337748 0.650000 4.700000e-01 0.860000 0.650000 0.662996 0.650000 0 0.550000 0.760000 MLLT4 4301 broad.mit.edu 37 6 168299092 168299092 + Frame_Shift_Del DEL G G - TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr6:168299092delG ENST00000447894.2 + 11 1525 c.1525delG c.(1525-1527)gcafs p.A509fs MLLT4_ENST00000392108.3_Frame_Shift_Del_p.A509fs|MLLT4_ENST00000351017.4_Frame_Shift_Del_p.A509fs|MLLT4_ENST00000392112.1_Frame_Shift_Del_p.A493fs|MLLT4_ENST00000344191.4_Frame_Shift_Del_p.A509fs|MLLT4_ENST00000400822.3_Frame_Shift_Del_p.A508fs|MLLT4_ENST00000366806.2_Frame_Shift_Del_p.A509fs P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 65 Breast(66;1.07e-05)|Ovarian(120;0.024) TCATGCTCTTGCAAAAAGATC 0.438000 T MLL AL Dom yes 6 6q27 4301 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6) L 0 SO:0001589 frameshift_variant ENST00000447894.2 0 1 hg19 TCGA-2J-AABA-01A-21D-A40W-08 MLLT4-013 PUTATIVE basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000372077.1 1 0 0 26 202 0 56 0 7.183328e-02 1 3 0 56 2 0 0 0 0 0 0 1 1.000000 27 200 0 55 2 -20.000000 1 1 0 0 1 0 1 1 1.739085 1 0.340000 1.830000 0.206445 0.550000 3.700000e-01 0.760000 0.550000 0.564640 0.550000 0 0.450000 0.660000 NEBL 10529 broad.mit.edu 37 10 21158753 21158753 + Silent SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr10:21158753G>A ENST00000377122.4 - 6 894 c.498C>T c.(496-498)gaC>gaT p.D166D NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Silent_p.D166D NM_006393.2 NP_006384.1 O76041 NEBL_HUMAN nebulette 70 TGTCCTGCACGTCTTTCCTAT 0.358000 0 SO:0001819 synonymous_variant ENST00000377122.4 1 1 hg19 CCDS7134.1 TCGA-2J-AABA-01A-21D-A40W-08 NEBL-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000047113.1 1 0 0 62 256 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 1.000000 61 252 0 82 2 -20.000000 1 1 121400 6 41 1 0 1 1 1.772244 1 0.340000 1.830000 0.204819 0.900000 7.300000e-01 1.000000 0.940000 0.895666 0.900000 1 0.810000 0.970000 MUC2 4583 broad.mit.edu 37 11 1092201 1092201 + Silent SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr11:1092201G>A ENST00000441003.2 + 30 4047 c.4020G>A c.(4018-4020)tcG>tcA p.S1340S MUC2_ENST00000359061.5_Silent_p.S1341S|MUC2_ENST00000361558.6_Silent_p.S6S|MUC2_ENST00000333592.6_5'Flank NM_002457.2 NP_002448.2 Q02817 MUC2_HUMAN mucin 2, oligomeric mucus/gel-forming 102 all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191) Pranlukast(DB01411) AGTGCAGGTCGGTCAAGGATC 0.557000 0 SO:0001819 synonymous_variant ENST00000441003.2 1 1 hg19 TCGA-2J-AABA-01A-21D-A40W-08 MUC2-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000345894.2 1 0 1 19 105 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 0.999994 19 103 0 20 2 -12.141570 1 1 0 0 1 1 2 3 2.064705 0 0.340000 1.830000 0.341120 0.900000 5.700000e-01 1.000000 1.000000 0.877461 0.900000 1 0.720000 1.000000 STT3A 3703 broad.mit.edu 37 11 125476284 125476284 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr11:125476284G>A ENST00000529196.1 + 9 910 c.704G>A c.(703-705)cGg>cAg p.R235Q STT3A_ENST00000392708.4_Missense_Mutation_p.R235Q|STT3A_ENST00000531491.1_Missense_Mutation_p.R143Q P46977 STT3A_HUMAN STT3A, subunit of the oligosaccharyltransferase complex (catalytic) 33 all_hematologic(175;0.228) Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224) TTCTCTCACCGGATCTATGTG 0.493000 0 SO:0001583 missense ENST00000529196.1 0 1 hg19 CCDS8458.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 G 37 6.154801 0.97329 . . ENSG00000134910 ENST00000392708;ENST00000529196;ENST00000531491 . . . 6.03 6.03 0.97812 . 0.000000 0.85682 D 0.000000 D 0.85243 0.5652 M 0.88775 2.98 0.80722 D 1 D;D;D 0.76494 0.995;0.999;0.999 P;D;D 0.68765 0.74;0.96;0.96 D 0.86443 0.1768 9 0.66056 D 0.02 -15.5244 20.177 0.98182 0.0:0.0:1.0:0.0 . 143;143;235 B4DJ24;E9PNQ1;P46977 .;.;STT3A_HUMAN Q 235;235;143 . ENSP00000376472:R235Q R + 2 0 STT3A 124981494 1.000000 0.71417 0.998000 0.56505 0.999000 0.98932 7.912000 0.87465 2.854000 0.98071 0.655000 0.94253 CGG TCGA-2J-AABA-01A-21D-A40W-08 STT3A-002 PUTATIVE alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000386691.1 0 0 0 7 655 0 185 0 5.101609e-01 0 148 0 185 2 0 0 0 0 0 2 1 0.980255 7 650 0 177 2 -1.947696 0 1 121412 2 39 1 0 1 1 2.057508 0 0.340000 1.830000 0.338876 0.060000 2.000000e-02 0.120000 0.060000 0.070568 0.060000 0 0.030000 0.090000 ACCS 84680 broad.mit.edu 37 11 44089316 44089316 + Missense_Mutation SNP C C G TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr11:44089316C>G ENST00000263776.8 + 2 573 c.139C>G c.(139-141)Ctc>Gtc p.L47V ACCS_ENST00000432284.2_Missense_Mutation_p.L47V|ACCS_ENST00000533208.1_3'UTR NM_001127219.1|NM_032592.3 NP_001120691.1|NP_115981.1 Q96QU6 1A1L1_HUMAN 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional) 35 GCTGCCAGAGCTCCGTGGAGT 0.552000 Esophageal Squamous(158;148 1889 8077 23160 41213) 0 SO:0001583 missense ENST00000263776.8 1 1 hg19 CCDS7907.1 . . . . . . . . . . C 2.726 -0.265394 0.05754 . . ENSG00000110455 ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404 T;T;T;T 0.60548 1.21;0.18;1.21;0.82 4.94 -0.726 0.11170 . 1.197120 0.05715 N 0.596590 T 0.44095 0.1277 L 0.40543 1.245 0.09310 N 1 B;B 0.32829 0.386;0.099 B;B 0.34242 0.178;0.027 T 0.33727 -0.9857 10 0.38643 T 0.18 -1.6262 1.7604 0.02991 0.1416:0.4323:0.1391:0.287 . 47;47 B4E219;Q96QU6 .;1A1L1_HUMAN V 47 ENSP00000434156:L47V;ENSP00000263776:L47V;ENSP00000391775:L47V;ENSP00000435919:L47V ENSP00000263776:L47V L + 1 0 ACCS 44045892 0.000000 0.05858 0.001000 0.08648 0.101000 0.19017 -1.526000 0.02229 -0.001000 0.14495 0.655000 0.94253 CTC TCGA-2J-AABA-01A-21D-A40W-08 ACCS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389721.1 1 0 1 35 206 0 38 0 4.463793e-01 1 9 0 38 2 0 0 0 0 0 2 1 1.000000 35 205 0 38 2 -20.000000 1 1 0 0 1 1 2 3 2.064705 0 0.340000 1.830000 0.341120 0.850000 6.100000e-01 1.000000 1.000000 0.853770 0.850000 1 0.720000 1.000000 PAWR 5074 broad.mit.edu 37 12 79990331 79990331 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr12:79990331G>A ENST00000328827.4 - 5 1163 c.791C>T c.(790-792)tCa>tTa p.S264L NM_002583.2 NP_002574.2 Q96IZ0 PAWR_HUMAN PRKC, apoptosis, WT1, regulator 8 TGTGCTACTTGAAACCAGAGT 0.323000 0 SO:0001583 missense ENST00000328827.4 1 1 hg19 CCDS31863.1 . . . . . . . . . . G 15.10 2.732142 0.48939 . . ENSG00000177425 ENST00000328827 T 0.17370 2.28 5.21 5.21 0.72293 . 0.977772 0.08368 N 0.956530 T 0.17450 0.0419 L 0.29908 0.895 0.32789 N 0.501387 P 0.36535 0.557 B 0.39258 0.295 T 0.07481 -1.0770 9 . . . -0.0939 13.6695 0.62416 0.0:0.0:0.8453:0.1547 . 264 Q96IZ0 PAWR_HUMAN L 264 ENSP00000328088:S264L . S - 2 0 PAWR 78514462 1.000000 0.71417 0.985000 0.45067 0.148000 0.21650 4.049000 0.57397 2.601000 0.87937 0.585000 0.79938 TCA TCGA-2J-AABA-01A-21D-A40W-08 PAWR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407175.1 1 0 1 48 259 0 87 1 9.994344e-01 19 44 0 87 2 0 0 0 0 0 2 1 1.000000 47 254 0 83 2 -3.234357 1 1 0 0 1 0 0 0 2.005386 0 0.340000 1.830000 0.321546 0.890000 6.700000e-01 1.000000 1.000000 0.887011 0.890000 1 0.770000 1.000000 SLITRK5 26050 broad.mit.edu 37 13 88329453 88329453 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr13:88329453C>T ENST00000325089.6 + 2 2029 c.1810C>T c.(1810-1812)Cgc>Tgc p.R604C SLITRK5_ENST00000400028.3_Missense_Mutation_p.R363C NM_015567.1 NP_056382.1 O94991 SLIK5_HUMAN SLIT and NTRK-like family, member 5 p.R604C(1) 81 all_neural(89;0.101)|Medulloblastoma(90;0.163) GACCGACATGCGCTCCATTAA 0.567000 1 Substitution - Missense(1) SO:0001583 missense ENST00000325089.6 0 1 hg19 CCDS9465.1 . . . . . . . . . . C 16.04 3.011439 0.54468 0.0 1.16E-4 ENSG00000165300 ENST00000325089;ENST00000400028 T;T 0.61158 0.13;0.49 5.47 4.54 0.55810 Cysteine-rich flanking region, C-terminal (1); 0.000000 0.85682 D 0.000000 T 0.78033 0.4220 M 0.87971 2.92 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.79784 0.987;0.993 T 0.81450 -0.0927 9 . . . -15.1954 14.535 0.67953 0.1566:0.8434:0.0:0.0 . 363;604 B4DSH5;O94991 .;SLIK5_HUMAN C 604;363 ENSP00000366283:R604C;ENSP00000442244:R363C . R + 1 0 SLITRK5 87127454 1.000000 0.71417 0.999000 0.59377 0.994000 0.84299 3.167000 0.50793 2.554000 0.86153 0.555000 0.69702 CGC TCGA-2J-AABA-01A-21D-A40W-08 SLITRK5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045416.3 0 0 0 6 851 0 165 0 2.253067e-04 0 3 0 165 2 0 0 0 0 0 2 1 0.962799 7 833 0 158 2 -1.757131 0 1 121412 1 37 1 1 2 3 2.094580 0 0.340000 1.830000 0.346664 0.040000 0 1.000000 0.040000 0.092934 0.040000 0 0.020000 0.070000 PARP6 56965 broad.mit.edu 37 15 72557486 72557486 + Silent SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr15:72557486G>A ENST00000569795.1 - 7 951 c.264C>T c.(262-264)gtC>gtT p.V88V PARP6_ENST00000287196.9_Silent_p.V88V|PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000260376.7_Silent_p.V88V Q2NL67 PARP6_HUMAN poly (ADP-ribose) polymerase family, member 6 18 CTGTCCGGAGGACCTTCCAGG 0.473000 0 SO:0001819 synonymous_variant ENST00000569795.1 0 1 hg19 CCDS10241.2 TCGA-2J-AABA-01A-21D-A40W-08 PARP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257315.2 1 0 1 6 117 0 21 1 6.979104e-01 9 38 0 21 2 0 0 0 0 0 2 1 0.963480 6 114 0 20 2 -9.388886 1 1 0 0 1 1 2 3 2.068233 0 0.340000 1.830000 0.342236 0.300000 1.200000e-01 0.630000 0.290000 0.332014 0.300000 0 0.200000 0.450000 NF1 4763 broad.mit.edu 37 17 29559101 29559101 + Nonsense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr17:29559101C>T ENST00000358273.4 + 25 3591 c.3208C>T c.(3208-3210)Cag>Tag p.Q1070* NF1_ENST00000356175.3_Nonsense_Mutation_p.Q1070* NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 p.0?(8)|p.?(4) NF1/ACCN1(2) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) AGATTTGGACCAGGCAAGCAT 0.373000 D, Mis, N, F, S, O neurofibroma, glioma neurofibroma, glioma Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) yes Rec yes Neurofibromatosis type 1 17 17q12 4763 neurofibromatosis type 1 gene O 12 Whole gene deletion(8)|Unknown(4) SO:0001587 stop_gained Familial Cancer Database NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome ENST00000358273.4 0 1 hg19 CCDS42292.1 . . . . . . . . . . C 46 12.239175 0.99649 . . ENSG00000196712 ENST00000358273;ENST00000356175;ENST00000456735 . . . 5.35 5.35 0.76521 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.30078 T 0.28 . 19.0592 0.93080 0.0:1.0:0.0:0.0 . . . . X 1070;1070;736 . ENSP00000348498:Q1070X Q + 1 0 NF1 26583227 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 7.402000 0.79972 2.499000 0.84300 0.484000 0.47621 CAG TCGA-2J-AABA-01A-21D-A40W-08 NF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256351.2 0 0 1 12 53 0 12 0 3.994732e-02 1 1 0 12 2 0 0 0 0 0 2 1 0.999300 11 52 0 12 2 -19.996930 1 1 0 0 1 0 1 1 1.721658 1 0.340000 1.830000 0.204819 0.790000 4.700000e-01 0.990000 0.860000 0.784012 0.790000 0 0.630000 0.930000 SMAD4 4089 broad.mit.edu 37 18 48604705 48604705 + Nonsense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr18:48604705G>A ENST00000342988.3 + 12 2065 c.1527G>A c.(1525-1527)tgG>tgA p.W509* SMAD4_ENST00000588745.1_Nonsense_Mutation_p.W413*|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.W509* NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2)|p.W509*(1) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) TGAAAGGCTGGGGACCGGATT 0.473000 39 Whole gene deletion(36)|Unknown(2)|Substitution - Nonsense(1) GRCh37 CM086965 SMAD4 M SO:0001587 stop_gained ENST00000342988.3 0 1 hg19 CCDS11950.1 . . . . . . . . . . G 42 9.263344 0.99118 . . ENSG00000141646 ENST00000342988;ENST00000398417 . . . 6.08 6.08 0.98989 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 19.4362 0.94796 0.0:0.0:1.0:0.0 . . . . X 509 . ENSP00000341551:W509X W + 3 0 SMAD4 46858703 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.586000 0.98226 2.890000 0.99128 0.655000 0.94253 TGG TCGA-2J-AABA-01A-21D-A40W-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 56 250 0 50 1 9.986344e-01 24 23 0 50 2 1 1 125 607 1 1047 5 1 1.000000 55 250 0 47 2 -2.787374 1 1 0 0 1 0 1 1 1.734443 1 0.340000 1.830000 0.208063 0.870000 6.800000e-01 1.000000 1.000000 0.869917 0.870000 1 0.770000 0.960000 PSMD8 5714 broad.mit.edu 37 19 38874009 38874009 + Silent SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr19:38874009G>A ENST00000215071.4 + 7 1098 c.1032G>A c.(1030-1032)cgG>cgA p.R344R GGN_ENST00000591809.1_5'Flank|AC005789.9_ENST00000585411.1_RNA|PSMD8_ENST00000602911.1_Silent_p.R281R NM_002812.4 NP_002803.2 P48556 PSMD8_HUMAN proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 6 all_cancers(60;3.4e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) AGTATGCCCGGCAGCTGGAGA 0.562000 0 SO:0001819 synonymous_variant ENST00000215071.4 0 1 hg19 CCDS12515.2 TCGA-2J-AABA-01A-21D-A40W-08 PSMD8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319627.1 0 0 0 4 148 0 43 0 9.933983e-01 0 410 0 43 2 0 0 0 0 0 2 1 0.885046 4 144 0 42 2 -3.607143 1 1 0 0 1 0 0 0 2.039874 0 0.340000 1.830000 0.335481 0.160000 5.000000e-02 0.360000 0.150000 0.187231 0.160000 0 0.100000 0.260000 ZNF28 7576 broad.mit.edu 37 19 53304471 53304471 + Missense_Mutation SNP G G C TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr19:53304471G>C ENST00000457749.2 - 4 746 c.627C>G c.(625-627)caC>caG p.H209Q ZNF28_ENST00000414252.2_Missense_Mutation_p.H156Q|ZNF28_ENST00000360272.4_Missense_Mutation_p.H156Q|ZNF28_ENST00000438150.2_Missense_Mutation_p.H156Q NM_006969.3 NP_008900.3 P17035 ZNF28_HUMAN zinc finger protein 28 34 TTTCTCTCATGTGTACATTCC 0.333000 0 SO:0001583 missense ENST00000457749.2 1 1 hg19 CCDS33093.2 . . . . . . . . . . - 8.679 0.904585 0.17760 . . ENSG00000198538 ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783 T;T;T;T;T 0.41400 1.0;1.0;1.0;1.0;1.0 1.47 0.307 0.15811 . . . . . T 0.65863 0.2732 M 0.93720 3.45 0.09310 N 1 P 0.50156 0.932 D 0.63703 0.917 T 0.54629 -0.8265 9 0.87932 D 0 . 5.3957 0.16268 0.2136:0.0:0.7864:0.0 . 209 P17035 ZNF28_HUMAN Q 156;209;156;156;156 ENSP00000412143:H156Q;ENSP00000397693:H209Q;ENSP00000353410:H156Q;ENSP00000444965:H156Q;ENSP00000375661:H156Q ENSP00000353410:H156Q H - 3 2 ZNF28 57996283 0.009000 0.17119 0.001000 0.08648 0.036000 0.12997 0.142000 0.16096 -0.050000 0.13356 0.186000 0.17326 CAC TCGA-2J-AABA-01A-21D-A40W-08 ZNF28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336038.2 1 0 1 79 583 0 125 1 1.135772e-01 3 2 0 125 2 0 0 0 0 0 2 1 1.000000 79 575 0 124 2 -20.000000 1 1 0 0 1 0 1 1 2.054197 0 0.340000 1.830000 0.338876 0.690000 5.600000e-01 0.850000 0.700000 0.705427 0.690000 0 0.620000 0.780000 ZNF761 388561 broad.mit.edu 37 19 53960290 53960290 + RNA SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr19:53960290C>T ENST00000454407.1 + 0 2982 Q86XN6 ZN761_HUMAN zinc finger protein 761 30 TCGCACCTGGCACAACATGCT 0.438000 0 ENST00000454407.1 0 1 hg19 TCGA-2J-AABA-01A-21D-A40W-08 ZNF761-203 KNOWN basic processed_transcript processed_transcript 0 0 0 10 88 0 9 1 4.902955e-01 7 8 0 9 2 0 0 0 0 0 2 1 0.997085 10 86 0 8 2 -16.562990 1 1 0 0 1 0 1 1 2.054197 0 0.340000 1.830000 0.338876 0.610000 3.200000e-01 0.990000 1.000000 0.630304 0.610000 0 0.450000 0.800000 PSMB4 5692 broad.mit.edu 37 1 151372561 151372561 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr1:151372561G>A ENST00000290541.6 + 2 299 c.245G>A c.(244-246)cGc>cAc p.R82H NM_002796.2 NP_002787.2 P28070 PSB4_HUMAN proteasome (prosome, macropain) subunit, beta type, 4 14 Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) GCTCGTTTCCGCAACATCTCT 0.562000 0 SO:0001583 missense ENST00000290541.6 0 1 hg19 CCDS996.1 . . . . . . . . . . G 36 5.616730 0.96649 . . ENSG00000159377 ENST00000290541 T 0.23950 1.88 5.34 5.34 0.76211 Proteasome, beta-type subunit, conserved site (1); 0.000000 0.85682 D 0.000000 T 0.42765 0.1217 M 0.68952 2.095 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.985 T 0.23226 -1.0194 10 0.48119 T 0.1 -10.0508 17.6208 0.88080 0.0:0.0:1.0:0.0 . 82;82 B4DFL3;P28070 .;PSB4_HUMAN H 82 ENSP00000290541:R82H ENSP00000290541:R82H R + 2 0 PSMB4 149639185 1.000000 0.71417 1.000000 0.80357 0.979000 0.70002 9.420000 0.97426 2.502000 0.84385 0.561000 0.74099 CGC TCGA-2J-AABA-01A-21D-A40W-08 PSMB4-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034885.1 0 0 0 6 815 1 185 0 1.663031e-02 0 418 1 185 10 0 0 0 0 0 2 0 0.021741 6 793 1 178 16 -2.119973 0 1 0 0 1 1 2 3 2.061605 0 0.340000 1.830000 0.341120 0.040000 0 0.100000 0.040000 0.049969 0.040000 0 0.020000 0.070000 PIGM 93183 broad.mit.edu 37 1 160000872 160000872 + Missense_Mutation SNP T T C TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr1:160000872T>C ENST00000368090.2 - 1 911 c.658A>G c.(658-660)Aaa>Gaa p.K220E NM_145167.2 NP_660150.1 Q9H3S5 PIGM_HUMAN phosphatidylinositol glycan anchor biosynthesis, class M 17 all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) CACAGCCTTTTCAGGAGCTCG 0.493000 0 SO:0001583 missense ENST00000368090.2 0 1 hg19 CCDS1192.1 . . . . . . . . . . T 0.284 -0.984168 0.02180 . . ENSG00000143315 ENST00000368090 T 0.42513 0.97 5.01 -0.346 0.12620 . 1.434850 0.03898 N 0.279844 T 0.13157 0.0319 L 0.39898 1.24 0.09310 N 1 B 0.02656 0.0 B 0.09377 0.004 T 0.15009 -1.0452 9 . . . -16.8801 5.5481 0.17076 0.0:0.1892:0.4536:0.3572 . 220 Q9H3S5 PIGM_HUMAN E 220 ENSP00000357069:K220E . K - 1 0 PIGM 158267496 0.000000 0.05858 0.000000 0.03702 0.090000 0.18270 -0.053000 0.11846 0.035000 0.15519 0.379000 0.24179 AAA TCGA-2J-AABA-01A-21D-A40W-08 PIGM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060643.2 0 0 0 5 555 0 88 0 1.392864e-02 0 16 0 88 2 0 0 0 0 0 2 1 0.935104 4 548 0 87 2 -4.538811 1 0 0 0 1 1 2 3 2.061605 0 0.340000 1.830000 0.341120 0.050000 1.000000e-02 0.120000 0.060000 0.062660 0.050000 0 0.030000 0.090000 KIF21B 23046 broad.mit.edu 37 1 200950209 200950209 + Silent SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr1:200950209C>T ENST00000422435.2 - 29 4174 c.3858G>A c.(3856-3858)ccG>ccA p.P1286P KIF21B_ENST00000332129.2_Silent_p.P1273P|KIF21B_ENST00000461742.2_Silent_p.P1286P|KIF21B_ENST00000360529.5_Silent_p.P1273P NM_001252100.1 NP_001239029.1 O75037 KI21B_HUMAN kinesin family member 21B 83 CTCCTCCAACCGGGGAGATGA 0.637000 0 SO:0001819 synonymous_variant ENST00000422435.2 1 1 hg19 CCDS58056.1 TCGA-2J-AABA-01A-21D-A40W-08 KIF21B-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000382635.1 1 0 1 32 196 0 45 1 1.026975e-01 2 2 0 45 2 0 0 0 0 0 2 1 1.000000 32 191 0 43 2 -2.971653 1 1 121412 6 37 1 1 2 3 2.069687 0 0.340000 1.830000 0.342236 0.830000 5.800000e-01 1.000000 1.000000 0.832285 0.830000 0 0.700000 0.980000 ARID1A 8289 broad.mit.edu 37 1 27101342 27101342 + Nonsense_Mutation SNP G G T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr1:27101342G>T ENST00000324856.7 + 18 4995 c.4624G>T c.(4624-4626)Gaa>Taa p.E1542* ARID1A_ENST00000374152.2_Nonsense_Mutation_p.E1159*|ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000457599.2_Intron NM_006015.4 NP_006006.3 O14497 ARI1A_HUMAN AT rich interactive domain 1A (SWI-like) p.E1542*(1) ARID1A/MAST2_ENST00000361297(2) 411 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) GGCCAACCACGAAGGCTCGTG 0.642000 Mis, N, F, S, D clear cell ovarian carcinoma, RCC Rec yes 1 1p35.3 8289 AT rich interactive domain 1A (SWI-like) E 1 Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000324856.7 0 1 hg19 CCDS285.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 43|43 10.343878|10.343878 0.99388|0.99388 .|. .|. ENSG00000117713|ENSG00000117713 ENST00000324856;ENST00000374152|ENST00000430799 .|. .|. .|. 5.41|5.41 5.41|5.41 0.78517|0.78517 .|. 0.045702|. 0.85682|. D|. 0.000000|. .|T .|0.75287 .|0.3829 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.72743 .|-0.4201 .|4 0.42905|. T|. 0.14|. -7.5866|-7.5866 19.3941|19.3941 0.94598|0.94598 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|. .|. .|. X|L 1542;1159|438 .|. ENSP00000320485:E1542X|. E|R +|+ 1|2 0|0 ARID1A|ARID1A 26973929|26973929 1.000000|1.000000 0.71417|0.71417 0.994000|0.994000 0.49952|0.49952 0.479000|0.479000 0.33129|0.33129 9.144000|9.144000 0.94629|0.94629 2.822000|2.822000 0.97130|0.97130 0.557000|0.557000 0.71058|0.71058 GAA|CGA TCGA-2J-AABA-01A-21D-A40W-08 ARID1A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000011437.2 1 0 1 41 181 0 68 1 7.599884e-01 5 9 0 68 2 1 1 70 223 0 338 2 1 1.000000 40 166 0 64 2 -20.000000 1 1 0 0 1 0 1 1 1.733261 1 0.340000 1.830000 0.206445 0.860000 6.500000e-01 1.000000 1.000000 0.859098 0.860000 1 0.750000 0.960000 MFSD2A 84879 broad.mit.edu 37 1 40421012 40421012 + Silent SNP A A G TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr1:40421012A>G ENST00000372809.5 + 1 191 c.48A>G c.(46-48)ctA>ctG p.L16L MFSD2A_ENST00000372811.5_Silent_p.L16L|MFSD2A_ENST00000420632.2_5'UTR NM_001136493.1 NP_001129965.1 Q8NA29 NLS1_HUMAN major facilitator superfamily domain containing 2A 24 CGGGGCTGCTACCCACCAGCA 0.716000 0 SO:0001819 synonymous_variant ENST00000372809.5 0 1 hg19 CCDS44118.1 TCGA-2J-AABA-01A-21D-A40W-08 MFSD2A-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000025756.1 0 0 0 4 59 0 12 0 7.068444e-01 0 36 0 12 2 0 0 0 0 0 2 1 0.880764 4 56 0 10 2 -10.096200 1 1 0 0 1 1 2 3 2.071606 0 0.340000 1.830000 0.342236 0.410000 1.400000e-01 0.930000 0.370000 0.445072 0.410000 0 0.250000 0.630000 SGSM1 129049 broad.mit.edu 37 22 25264736 25264736 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr22:25264736C>T ENST00000400359.4 + 12 1212 c.1205C>T c.(1204-1206)gCc>gTc p.A402V SGSM1_ENST00000400358.4_Missense_Mutation_p.A402V NM_001039948.2|NM_133454.2 NP_001035037.1|NP_597711.1 Q2NKQ1 SGSM1_HUMAN small G protein signaling modulator 1 41 CAGGGTTCTGCCGAGTCCACA 0.512000 0 SO:0001583 missense ENST00000400359.4 0 1 hg19 CCDS46674.1 . . . . . . . . . . C 0.043 -1.275275 0.01410 . . ENSG00000167037 ENST00000403206;ENST00000400358;ENST00000400359 T;T 0.31510 1.49;1.49 4.97 2.9 0.33743 . 1.043230 0.07422 N 0.894208 T 0.08935 0.0221 N 0.01729 -0.75 0.09310 N 1 B;B;P;B 0.39665 0.05;0.102;0.682;0.007 B;B;B;B 0.30572 0.017;0.047;0.117;0.011 T 0.07385 -1.0775 10 0.08179 T 0.78 -10.6163 5.5656 0.17168 0.1576:0.6761:0.0:0.1663 . 402;518;535;402 Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1 .;.;.;SGSM1_HUMAN V 518;402;402 ENSP00000383211:A402V;ENSP00000383212:A402V ENSP00000383211:A402V A + 2 0 SGSM1 23594736 0.054000 0.20591 0.004000 0.12327 0.018000 0.09664 3.246000 0.51414 0.644000 0.30656 -0.218000 0.12543 GCC TCGA-2J-AABA-01A-21D-A40W-08 SGSM1-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000320282.1 0 0 0 6 476 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 0.962860 6 467 0 98 2 -2.104343 0 1 0 0 1 1 2 3 2.074349 0 0.340000 1.830000 0.342236 0.070000 2.000000e-02 0.170000 0.080000 0.093996 0.070000 0 0.040000 0.120000 NCKAP5 344148 broad.mit.edu 37 2 133541374 133541374 + Missense_Mutation SNP T T C TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:133541374T>C ENST00000409261.1 - 14 3383 c.3010A>G c.(3010-3012)Atc>Gtc p.I1004V NCKAP5_ENST00000317721.6_Missense_Mutation_p.I1004V|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank NM_207363.2 NP_997246.2 O14513 NCKP5_HUMAN NCK-associated protein 5 118 TGAGTGAAGATAGGCTTTTTG 0.537000 0 SO:0001583 missense ENST00000409261.1 1 1 hg19 CCDS46418.1 . . . . . . . . . . T 0.015 -1.544604 0.00934 . . ENSG00000176771 ENST00000409261;ENST00000317721 T;T 0.08458 3.09;3.09 5.07 -8.15 0.01065 . 1.865620 0.03556 N 0.226266 T 0.04092 0.0114 N 0.12182 0.205 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.34304 -0.9834 10 0.22706 T 0.39 . 7.2862 0.26340 0.0:0.3572:0.1999:0.4429 . 1004 O14513 NCKP5_HUMAN V 1004 ENSP00000387128:I1004V;ENSP00000380603:I1004V ENSP00000380603:I1004V I - 1 0 NCKAP5 133257844 0.000000 0.05858 0.000000 0.03702 0.692000 0.40212 -2.258000 0.01179 -2.146000 0.00800 -0.798000 0.03219 ATC TCGA-2J-AABA-01A-21D-A40W-08 NCKAP5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000331663.1 1 0 1 20 111 0 29 0 2.592302e-02 0 2 0 29 2 0 0 0 0 0 2 1 0.999996 20 107 0 29 2 -20.000000 1 1 120480 1 24 1 0 1 1 2.053808 0 0.340000 1.830000 0.338876 0.890000 5.800000e-01 1.000000 1.000000 0.874564 0.890000 1 0.720000 1.000000 TTN 7273 broad.mit.edu 37 2 179431867 179431867 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:179431867C>T ENST00000591111.1 - 276 74293 c.74069G>A c.(74068-74070)cGa>cAa p.R24690Q TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R23763Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R17266Q|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R26331Q|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R17458Q|TTN_ENST00000359218.5_Missense_Mutation_p.R17391Q|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) CCAGGCAAGTCGACTGGTTTC 0.413000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 16.16 3.045692 0.55110 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.56776 0.44;0.44;0.44;0.44 5.52 5.52 0.82312 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.74344 0.3704 M 0.76328 2.33 0.58432 D 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.87578 0.998;0.998;0.998;0.998 T 0.76844 -0.2809 9 0.87932 D 0 . 19.4392 0.94811 0.0:1.0:0.0:0.0 . 17266;17391;17458;24690 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN Q 23763;17266;17458;17391;17264 ENSP00000343764:R23763Q;ENSP00000434586:R17266Q;ENSP00000340554:R17458Q;ENSP00000352154:R17391Q ENSP00000340554:R17458Q R - 2 0 TTN 179140113 1.000000 0.71417 0.994000 0.49952 0.981000 0.71138 7.770000 0.85390 2.580000 0.87095 0.462000 0.41574 CGA TCGA-2J-AABA-01A-21D-A40W-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 1 95 395 1 96 0 0 0 1 96 2 0 0 0 0 0 2 1 1.000000 95 389 1 95 17 -20.000000 1 1 120842 5 40 1 0 1 1 2.053808 0 0.340000 1.830000 0.338876 0.990000 9.300000e-01 1.000000 1.000000 0.996259 0.990000 1 0.990000 1.000000 DNMT3A 1788 broad.mit.edu 37 2 25459873 25459873 + Splice_Site SNP G G A rs35824014 TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:25459873G>A ENST00000264709.3 - 21 2747 c.2410C>T c.(2410-2412)Ccg>Tcg p.P804S DNMT3A_ENST00000474887.1_Intron|DNMT3A_ENST00000380746.4_Splice_Site_p.P615S|DNMT3A_ENST00000402667.1_Splice_Site_p.P581S|DNMT3A_ENST00000321117.5_Splice_Site_p.P804S NM_175629.2 NP_783328.1 Q9Y6K1 DNM3A_HUMAN DNA (cytosine-5-)-methyltransferase 3 alpha p.R803fs*5(3)|p.P804S(2)|p.P615S(2) 1021 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) GATGCCAACGGCCTAGGAGGC 0.582000 Mis, F, N, S AML Rec yes 2 2p23 1788 DNA (cytosine-5-)-methyltransferase 3 alpha L 7 Substitution - Missense(4)|Deletion - Frameshift(3) SO:0001630 splice_region_variant ENST00000264709.3 1 0 hg19 CCDS33157.1 . . . . . . . . . . G 24.3 4.511478 0.85389 . . ENSG00000119772 ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667 D;D;D;D 0.97232 -4.3;-4.3;-4.3;-4.3 5.62 4.72 0.59763 . 0.047584 0.85682 D 0.000000 D 0.98391 0.9465 M 0.86651 2.83 0.80722 D 1 P;D 0.89917 0.729;1.0 B;D 0.75020 0.274;0.985 D 0.98630 1.0671 10 0.49607 T 0.09 -7.2591 14.0893 0.64980 0.0:0.1518:0.8482:0.0 . 804;615 Q9Y6K1;E9PEB8 DNM3A_HUMAN;. S 615;804;804;581 ENSP00000370122:P615S;ENSP00000324375:P804S;ENSP00000264709:P804S;ENSP00000384237:P581S ENSP00000264709:P804S P - 1 0 DNMT3A 25313377 1.000000 0.71417 0.997000 0.53966 0.995000 0.86356 9.624000 0.98398 1.325000 0.45301 0.655000 0.94253 CCG TCGA-2J-AABA-01A-21D-A40W-08 DNMT3A-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000211587.1 1 0 1 19 95 0 30 1 7.407874e-01 5 10 0 30 2 0 0 0 0 0 2 1 0.999993 18 93 0 30 2 -20.000000 1 1 0 0 1 0 0 0 2.048860 0 0.340000 1.830000 0.337748 0.970000 6.200000e-01 1.000000 1.000000 0.916529 0.970000 1 0.780000 1.000000 SLC8A1 6546 broad.mit.edu 37 2 40405540 40405540 + Missense_Mutation SNP C C A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:40405540C>A ENST00000403092.1 - 3 1935 c.1902G>T c.(1900-1902)atG>atT p.M634I SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1_ENST00000542024.1_Intron|SLC8A1_ENST00000406391.2_Intron|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.M634I|SLC8A1_ENST00000332839.4_Missense_Mutation_p.M634I|SLC8A1_ENST00000402441.1_Intron|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1_ENST00000405269.1_Intron|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1_ENST00000408028.2_Intron|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000405901.3_Missense_Mutation_p.M634I|SLC8A1_ENST00000406785.2_Intron P32418 NAC1_HUMAN solute carrier family 8 (sodium/calcium exchanger), member 1 100 Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159) TCTTCTCACTCATCTCCACCA 0.507000 0 SO:0001583 missense ENST00000403092.1 0 1 hg19 CCDS1806.1 . . . . . . . . . . C 9.553 1.116372 0.20795 . . ENSG00000183023 ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000332839 T;T;T;T 0.25749 1.78;1.79;1.78;1.79 5.39 5.39 0.77823 . 0.176546 0.50627 D 0.000106 T 0.24661 0.0598 L 0.40543 1.245 0.80722 D 1 B;B 0.13594 0.008;0.005 B;B 0.17979 0.02;0.007 T 0.02257 -1.1187 10 0.34782 T 0.22 . 16.6407 0.85098 0.0:1.0:0.0:0.0 . 634;634 F6VPY9;P32418 .;NAC1_HUMAN I 634 ENSP00000440727:M634I;ENSP00000384763:M634I;ENSP00000385678:M634I;ENSP00000332931:M634I ENSP00000332931:M634I M - 3 0 SLC8A1 40259044 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.616000 0.67709 2.506000 0.84524 0.591000 0.81541 ATG TCGA-2J-AABA-01A-21D-A40W-08 SLC8A1-010 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000326065.1 0 0 0 13 670 0 174 0 0 0 0 174 2 0 0 0 0 0 2 1 0.999467 13 656 0 169 2 -2.211063 0 1 0 0 1 0 0 0 2.048860 0 0.340000 1.830000 0.337748 0.110000 5.000000e-02 0.180000 0.110000 0.119468 0.110000 0 0.080000 0.150000 SLC3A1 6519 broad.mit.edu 37 2 44531289 44531289 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:44531289G>A ENST00000260649.6 + 7 1220 c.1144G>A c.(1144-1146)Ggg>Agg p.G382R SLC3A1_ENST00000409740.3_Missense_Mutation_p.G13R|SLC3A1_ENST00000409387.1_Missense_Mutation_p.G382R|SLC3A1_ENST00000409294.1_Missense_Mutation_p.G2R|SLC3A1_ENST00000409741.1_Missense_Mutation_p.G382R|SLC3A1_ENST00000409380.1_Missense_Mutation_p.G104R|SLC3A1_ENST00000409229.3_Missense_Mutation_p.G382R NM_000341.3 NP_000332.2 Q07837 SLC31_HUMAN solute carrier family 3 (amino acid transporter heavy chain), member 1 26 all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17) L-Cystine(DB00138) TAGGTTCATGGGGACTGAAGC 0.458000 0 SO:0001583 missense ENST00000260649.6 0 1 hg19 CCDS1819.1 . . . . . . . . . . G 21.9 4.213359 0.79352 . . ENSG00000138079 ENST00000260649;ENST00000409387;ENST00000540334;ENST00000409741;ENST00000409229;ENST00000541289;ENST00000409380;ENST00000409294;ENST00000409740 D;D;D;D;D;D;D 0.99474 -5.97;-5.97;-5.97;-5.97;-5.97;-4.58;-5.97 5.14 5.14 0.70334 Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1); 0.054269 0.64402 D 0.000001 D 0.99336 0.9767 L 0.60455 1.87 0.80722 D 1 D;D;D;D 0.76494 0.996;0.991;0.999;0.999 D;D;D;D 0.77004 0.959;0.959;0.989;0.98 D 0.99346 1.0913 10 0.66056 D 0.02 -16.9982 17.398 0.87451 0.0:0.0:1.0:0.0 . 382;382;382;382 Q07837;B8ZZK1;Q4J6B5;Q4J6B6 SLC31_HUMAN;.;.;. R 382;382;318;382;382;382;104;2;13 ENSP00000260649:G382R;ENSP00000387308:G382R;ENSP00000386954:G382R;ENSP00000386620:G382R;ENSP00000386709:G104R;ENSP00000386852:G2R;ENSP00000386677:G13R ENSP00000260649:G382R G + 1 0 SLC3A1 44384793 1.000000 0.71417 0.997000 0.53966 0.595000 0.36748 8.753000 0.91637 2.393000 0.81446 0.455000 0.32223 GGG TCGA-2J-AABA-01A-21D-A40W-08 SLC3A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250676.1 0 0 0 12 456 0 120 0 4.596796e-01 1 56 0 120 2 0 0 0 0 0 2 1 0.999067 12 450 0 115 2 -2.388793 0 1 0 0 1 0 0 0 2.048860 0 0.340000 1.830000 0.337748 0.150000 7.000000e-02 0.250000 0.150000 0.161472 0.150000 0 0.110000 0.200000 MOGS 7841 broad.mit.edu 37 2 74688883 74688883 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:74688883C>T ENST00000233616.4 - 4 2195 c.2033G>A c.(2032-2034)cGg>cAg p.R678Q MOGS_ENST00000462443.1_5'Flank|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.R572Q NM_006302.2 NP_006293.2 Q13724 MOGS_HUMAN mannosyl-oligosaccharide glucosidase 23 AGGTTGGGGCCGACCCACCAC 0.597000 0 SO:0001583 missense ENST00000233616.4 1 1 hg19 CCDS42700.1 . . . . . . . . . . C 6.851 0.526345 0.13066 . . ENSG00000115275 ENST00000233616;ENST00000452063 T;T 0.38240 1.15;1.15 5.01 5.01 0.66863 Six-hairpin glycosidase-like (1); 0.118143 0.52532 D 0.000072 T 0.39937 0.1097 L 0.31420 0.93 0.80722 D 1 D 0.89917 1.0 D 0.68353 0.957 T 0.09250 -1.0683 10 0.12430 T 0.62 -11.998 9.2712 0.37673 0.0:0.9044:0.0:0.0956 . 678 Q13724 MOGS_HUMAN Q 678;572 ENSP00000233616:R678Q;ENSP00000388201:R572Q ENSP00000233616:R678Q R - 2 0 MOGS 74542391 0.992000 0.36948 0.983000 0.44433 0.156000 0.22039 1.923000 0.40055 2.618000 0.88619 0.462000 0.41574 CGG TCGA-2J-AABA-01A-21D-A40W-08 MOGS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328382.1 1 0 1 54 319 0 84 1 9.999990e-01 42 80 0 84 2 0 0 0 0 0 2 1 1.000000 53 311 0 83 2 -19.999970 1 1 120878 1 35 1 0 0 0 2.048860 0 0.340000 1.830000 0.337748 0.840000 6.500000e-01 1.000000 1.000000 0.850258 0.840000 0 0.740000 0.960000 KIDINS220 57498 broad.mit.edu 37 2 8891668 8891668 + Missense_Mutation SNP C C A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:8891668C>A ENST00000256707.3 - 23 3299 c.3118G>T c.(3118-3120)Gtg>Ttg p.V1040L KIDINS220_ENST00000418530.1_Missense_Mutation_p.V998L|KIDINS220_ENST00000427284.1_Missense_Mutation_p.V1040L|KIDINS220_ENST00000473731.1_Missense_Mutation_p.V1040L NM_020738.2 NP_065789.1 Q9ULH0 KDIS_HUMAN kinase D-interacting substrate, 220kDa 60 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) TCTCGAGCCACAAGAACTGGG 0.353000 0 SO:0001583 missense ENST00000256707.3 1 1 hg19 CCDS42650.1 . . . . . . . . . . C 5.843 0.339815 0.11069 . . ENSG00000134313 ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000459813 T;T;T;T;T;T 0.64803 1.03;-0.12;-0.08;-0.02;-0.08;-0.06 5.07 5.07 0.68467 . 0.215268 0.42821 D 0.000645 T 0.41880 0.1178 N 0.12887 0.27 0.39550 D 0.968969 B;B;B;B;B 0.29552 0.012;0.001;0.058;0.165;0.248 B;B;B;B;B 0.34931 0.01;0.003;0.094;0.192;0.064 T 0.36648 -0.9739 10 0.06494 T 0.89 . 12.2106 0.54377 0.0:0.9213:0.0:0.0787 . 1041;1041;724;998;1040 B4DK94;E9PH70;B4DGY1;Q9ULH0-2;Q9ULH0 .;.;.;.;KDIS_HUMAN L 787;724;1040;1040;998;1040;1041;49 ENSP00000420364:V787L;ENSP00000256707:V1040L;ENSP00000411849:V1040L;ENSP00000414923:V998L;ENSP00000418974:V1040L;ENSP00000419964:V1041L ENSP00000256707:V1040L V - 1 0 KIDINS220 8809119 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 1.970000 0.40520 2.509000 0.84616 0.563000 0.77884 GTG TCGA-2J-AABA-01A-21D-A40W-08 KIDINS220-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323408.2 1 0 1 53 320 0 70 1 7.478136e-01 4 14 0 70 2 0 0 0 0 0 2 1 1.000000 52 284 0 60 2 -19.999930 1 1 0 0 1 0 0 0 2.048860 0 0.340000 1.830000 0.337748 0.820000 6.300000e-01 1.000000 1.000000 0.836070 0.820000 0 0.720000 0.940000 NCAPH 23397 broad.mit.edu 37 2 97019996 97019996 + Missense_Mutation SNP G G T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr2:97019996G>T ENST00000240423.4 + 9 1121 c.1078G>T c.(1078-1080)Gac>Tac p.D360Y NCAPH_ENST00000455200.1_Missense_Mutation_p.D349Y|NCAPH_ENST00000427946.1_Missense_Mutation_p.D224Y NM_001281710.1|NM_001281711.1|NM_015341.3 NP_001268639.1|NP_001268640.1|NP_056156.2 Q15003 CND2_HUMAN non-SMC condensin I complex, subunit H 28 Ovarian(717;0.0221) TGACGAGAGTGACTGTGGAGA 0.512000 0 SO:0001583 missense ENST00000240423.4 1 1 hg19 CCDS2021.1 . . . . . . . . . . G 10.56 1.384455 0.25031 . . ENSG00000121152 ENST00000240423;ENST00000427946;ENST00000435975;ENST00000455200 T;T;T;T 0.53857 0.67;0.68;0.6;0.67 5.38 4.48 0.54585 . 0.274240 0.42053 N 0.000768 T 0.51346 0.1669 M 0.78049 2.395 0.21064 N 0.999798 B;B;P;B 0.38148 0.19;0.19;0.62;0.19 B;B;B;B 0.39617 0.172;0.172;0.305;0.172 T 0.49588 -0.8924 10 0.06625 T 0.88 -9.4799 12.9558 0.58427 0.0:0.0:0.8368:0.1632 . 336;349;349;360 B4DRG7;E9PHA2;C9J470;Q15003 .;.;.;CND2_HUMAN Y 360;224;349;349 ENSP00000240423:D360Y;ENSP00000400774:D224Y;ENSP00000405237:D349Y;ENSP00000407308:D349Y ENSP00000240423:D360Y D + 1 0 NCAPH 96383723 1.000000 0.71417 0.003000 0.11579 0.320000 0.28249 5.587000 0.67510 1.215000 0.43411 0.561000 0.74099 GAC TCGA-2J-AABA-01A-21D-A40W-08 NCAPH-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000252842.2 1 0 1 92 584 0 121 0 9.358672e-02 1 3 0 121 2 0 0 0 0 0 2 1 1.000000 91 579 0 119 2 -20.000000 1 1 0 0 1 0 1 1 2.053808 0 0.340000 1.830000 0.338876 0.790000 6.500000e-01 0.950000 0.800000 0.802945 0.790000 0 0.720000 0.880000 ZBED2 79413 broad.mit.edu 37 3 111312977 111312977 + Silent SNP C C T rs145211272 TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr3:111312977C>T ENST00000317012.4 - 2 1080 c.72G>A c.(70-72)gaG>gaA p.E24E CD96_ENST00000438817.2_Intron|CD96_ENST00000352690.4_Intron|CD96_ENST00000283285.5_Intron NM_024508.4 NP_078784.2 Q9BTP6 ZBED2_HUMAN zinc finger, BED-type containing 2 6 TCTCTTCCTCCTCCTTCATCT 0.507000 0 SO:0001819 synonymous_variant ENST00000317012.4 1 1 hg19 CCDS2960.2 TCGA-2J-AABA-01A-21D-A40W-08 ZBED2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000157228.2 0 0 0 9 296 0 57 0 2.447040e-01 1 28 0 57 2 0 0 0 0 0 2 1 0.993678 9 288 0 53 2 -3.581752 1 1 0 0 1 1 2 3 2.059806 0 0.340000 1.830000 0.341120 0.170000 8.000000e-02 0.320000 0.180000 0.190721 0.170000 0 0.120000 0.250000 KLHL24 54800 broad.mit.edu 37 3 183368717 183368717 + Silent SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr3:183368717G>A ENST00000454652.2 + 4 959 c.573G>A c.(571-573)gcG>gcA p.A191A KLHL24_ENST00000242810.6_Silent_p.A191A|KLHL24_ENST00000476808.1_Silent_p.A191A NM_017644.3 NP_060114.2 Q6TFL4 KLH24_HUMAN kelch-like family member 24 27 all_cancers(143;2.88e-10)|Ovarian(172;0.0303) all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22) AAAATTTTGCGTTACAGACTT 0.368000 0 SO:0001819 synonymous_variant ENST00000454652.2 0 1 hg19 CCDS3246.1 TCGA-2J-AABA-01A-21D-A40W-08 KLHL24-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346586.2 0 0 0 8 391 1 84 0 2.610030e-02 0 11 1 84 2 0 0 0 0 0 2 0 0.048487 9 387 1 83 17 -2.787841 1 1 0 0 1 1 2 3 2.059806 0 0.340000 1.830000 0.341120 0.120000 5.000000e-02 0.230000 0.120000 0.131609 0.120000 0 0.080000 0.170000 ZNF35 7584 broad.mit.edu 37 3 44700479 44700479 + Silent SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr3:44700479C>T ENST00000396056.2 + 4 859 c.624C>T c.(622-624)ggC>ggT p.G208G ZNF35_ENST00000542250.1_Silent_p.G48G|ZNF35_ENST00000296092.3_3'UTR|RP11-944L7.4_ENST00000457331.1_RNA NM_003420.3 NP_003411.3 P13682 ZNF35_HUMAN zinc finger protein 35 p.G208G(1) 12 Ovarian(412;0.0228) TTAATTCTGGCGCTGTTAAAA 0.413000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000396056.2 0 1 hg19 CCDS2718.2 TCGA-2J-AABA-01A-21D-A40W-08 ZNF35-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256749.4 0 0 0 7 652 0 116 0 8.222551e-03 0 11 0 116 2 0 0 0 0 0 2 1 0.980146 7 648 0 113 2 -2.149243 0 1 121412 1 36 1 0 1 1 2.059351 0 0.340000 1.830000 0.338876 0.060000 2.000000e-02 0.120000 0.060000 0.070886 0.060000 0 0.040000 0.100000 MYL3 4634 broad.mit.edu 37 3 46902285 46902285 + Missense_Mutation SNP C C T rs139354105 TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr3:46902285C>T ENST00000395869.1 - 3 239 c.188G>A c.(187-189)cGc>cAc p.R63H MYL3_ENST00000292327.4_Missense_Mutation_p.R63H P08590 MYL3_HUMAN myosin, light chain 3, alkali; ventricular, skeletal, slow 3 CTTGGGTGTGCGGTCGAACAG 0.622000 Melanoma(166;130 1949 2249 18977 46142) 0 SO:0001583 missense ENST00000395869.1 0 1 hg19 CCDS2746.1 . . . . . . . . . . C 32 5.108683 0.94292 0.0 1.16E-4 ENSG00000160808 ENST00000395869;ENST00000292327 D;D 0.85861 -2.04;-2.04 4.36 4.36 0.52297 EF-hand-like domain (1); 0.000000 0.64402 D 0.000002 D 0.91341 0.7269 M 0.82323 2.585 0.80722 D 1 D 0.89917 1.0 P 0.60541 0.876 D 0.92718 0.6189 10 0.87932 D 0 -17.4592 14.7939 0.69863 0.0:1.0:0.0:0.0 . 63 P08590 MYL3_HUMAN H 63 ENSP00000379210:R63H;ENSP00000292327:R63H ENSP00000292327:R63H R - 2 0 MYL3 46877289 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 5.879000 0.69690 2.415000 0.81967 0.563000 0.77884 CGC TCGA-2J-AABA-01A-21D-A40W-08 MYL3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000259165.2 0 0 0 5 557 0 97 0 7.759968e-04 0 4 0 97 2 0 0 0 0 0 2 1 0.936018 5 551 0 95 2 -1.860039 0 1 121412 3 38 1 0 1 1 2.059351 0 0.340000 1.830000 0.338876 0.050000 1.000000e-02 0.120000 0.060000 0.062225 0.050000 0 0.030000 0.090000 IQCF2 389123 broad.mit.edu 37 3 51897313 51897313 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr3:51897313G>A ENST00000333127.3 + 3 451 c.422G>A c.(421-423)tGc>tAc p.C141Y IQCF2_ENST00000429548.1_3'UTR NM_203424.1 NP_982248.1 Q8IXL9 IQCF2_HUMAN IQ motif containing F2 10 TGCCAGACCTGCGCTCTCCTC 0.567000 0 SO:0001583 missense ENST00000333127.3 1 1 hg19 CCDS2835.1 . . . . . . . . . . G 16.90 3.250045 0.59212 . . ENSG00000184345 ENST00000333127 T 0.30448 1.53 5.22 5.22 0.72569 . 0.101398 0.44902 D 0.000401 T 0.44138 0.1279 L 0.36672 1.1 0.18873 N 0.999981 D 0.89917 1.0 D 0.68765 0.96 T 0.24119 -1.0169 10 0.54805 T 0.06 -19.2161 14.4799 0.67573 0.0:0.0:1.0:0.0 . 141 Q8IXL9 IQCF2_HUMAN Y 141 ENSP00000329904:C141Y ENSP00000329904:C141Y C + 2 0 IQCF2 51872353 0.948000 0.32251 0.293000 0.24932 0.943000 0.58893 2.580000 0.46068 2.866000 0.98385 0.650000 0.86243 TGC TCGA-2J-AABA-01A-21D-A40W-08 IQCF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346594.1 1 0 1 61 428 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 61 425 0 73 2 -19.999890 1 1 0 0 1 1 2 3 2.059806 0 0.340000 1.830000 0.341120 0.730000 5.700000e-01 0.920000 0.740000 0.741010 0.730000 0 0.640000 0.830000 QRFPR 84109 broad.mit.edu 37 4 122258001 122258001 + Silent SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr4:122258001G>A ENST00000394427.2 - 3 933 c.522C>T c.(520-522)gtC>gtT p.V174V QRFPR_ENST00000334383.5_Silent_p.V174V NM_198179.2 NP_937822.2 Q96P65 QRFPR_HUMAN pyroglutamylated RFamide peptide receptor 28 ATCCTACGATGACTGCCACCA 0.413000 0 SO:0001819 synonymous_variant ENST00000394427.2 1 1 hg19 CCDS3719.1 TCGA-2J-AABA-01A-21D-A40W-08 QRFPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256641.2 1 0 1 152 724 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 150 709 0 143 2 -20.000000 1 1 0 0 1 1 2 3 2.063727 0 0.340000 1.830000 0.341120 0.990000 8.700000e-01 1.000000 1.000000 0.980720 0.990000 1 0.940000 1.000000 FBXW7 55294 broad.mit.edu 37 4 153244139 153244139 + Nonsense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr4:153244139C>T ENST00000281708.4 - 12 3247 c.2018G>A c.(2017-2019)tGg>tAg p.W673* FBXW7_ENST00000296555.5_Nonsense_Mutation_p.W555*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.W593*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.W673*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.W497*|FBXW7_ENST00000603548.1_Nonsense_Mutation_p.W673*|RP11-461L13.3_ENST00000603766.1_lincRNA NM_033632.3 NP_361014.1 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase p.?(1) 462 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) TCTGATCCGCCACACAACTCC 0.498000 Mis, N, D, F colorectal, endometrial, T-ALL Rec yes 4 4q31.3 55294 F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila) E, L 1 Unknown(1) SO:0001587 stop_gained ENST00000281708.4 0 1 hg19 CCDS3777.1 . . . . . . . . . . C 27.4 4.827871 0.90955 . . ENSG00000109670 ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956 . . . 5.67 5.67 0.87782 . 0.119994 0.64402 D 0.000003 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -8.4663 19.7667 0.96346 0.0:1.0:0.0:0.0 . . . . X 673;555;593;497 . ENSP00000263981:W593X W - 2 0 FBXW7 153463589 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.794000 0.85869 2.681000 0.91329 0.655000 0.94253 TGG TCGA-2J-AABA-01A-21D-A40W-08 FBXW7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000469956.1 1 0 0 89 624 0 113 1 6.466035e-01 4 13 0 113 2 1 1 129 584 0 759 2 1 1.000000 87 613 0 110 2 -20.000000 1 1 0 0 1 1 2 3 2.063727 0 0.340000 1.830000 0.341120 0.730000 5.900000e-01 0.890000 0.740000 0.739678 0.730000 0 0.660000 0.810000 JAKMIP1 152789 broad.mit.edu 37 4 6107417 6107417 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr4:6107417G>A ENST00000282924.5 - 3 892 c.407C>T c.(406-408)gCg>gTg p.A136V JAKMIP1_ENST00000410077.2_Intron|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.A136V|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.A136V|JAKMIP1_ENST00000457227.2_Intron|JAKMIP1_ENST00000409371.3_Intron NM_144720.3 NP_653321.1 Q96N16 JKIP1_HUMAN janus kinase and microtubule interacting protein 1 42 CTCCTCGCGCGCCTCGGTCAG 0.706000 0 SO:0001583 missense ENST00000282924.5 1 1 hg19 CCDS3385.1 . . . . . . . . . . G 17.64 3.438645 0.62955 . . ENSG00000152969 ENST00000409021;ENST00000418227;ENST00000425341;ENST00000282924;ENST00000409831 T;T;T 0.06687 3.27;3.27;3.27 4.6 3.74 0.42951 . 0.081594 0.51477 D 0.000100 T 0.09598 0.0236 L 0.54323 1.7 0.80722 D 1 B;B;B 0.28850 0.225;0.01;0.225 B;B;B 0.20767 0.031;0.005;0.031 T 0.07731 -1.0757 10 0.72032 D 0.01 . 12.6579 0.56797 0.0865:0.0:0.9135:0.0 . 136;136;136 F2Z2K5;Q96N16-2;Q96N16 .;.;JKIP1_HUMAN V 136 ENSP00000386711:A136V;ENSP00000282924:A136V;ENSP00000386925:A136V ENSP00000282924:A136V A - 2 0 JAKMIP1 6158318 1.000000 0.71417 0.981000 0.43875 0.781000 0.44180 6.134000 0.71689 2.259000 0.74868 0.484000 0.47621 GCG TCGA-2J-AABA-01A-21D-A40W-08 JAKMIP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000246816.2 1 0 1 15 62 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 0.999903 15 59 0 13 2 -20.000000 1 1 0 0 1 1 2 3 2.063727 0 0.340000 1.830000 0.341120 0.990000 6.900000e-01 1.000000 1.000000 0.962237 0.990000 1 0.900000 1.000000 DMP1 1758 broad.mit.edu 37 4 88583927 88583927 + Missense_Mutation SNP G G A rs147275271 byFrequency TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr4:88583927G>A ENST00000339673.6 + 6 1096 c.997G>A c.(997-999)Gta>Ata p.V333I RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Missense_Mutation_p.V317I|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA NM_004407.3 NP_004398.1 Q13316 DMP1_HUMAN dentin matrix acidic phosphoprotein 1 32 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227) GAGCCAAAACGTAGATGGTCC 0.547000 0 SO:0001583 missense ENST00000339673.6 1 1 hg19 CCDS3623.1 . . . . . . . . . . G 3.132 -0.178230 0.06380 0.002043 1.16E-4 ENSG00000152592 ENST00000339673;ENST00000282479 T;T 0.51325 0.71;0.71 5.11 -4.38 0.03622 . 2.186990 0.01837 N 0.035040 T 0.25791 0.0628 L 0.27053 0.805 0.09310 N 1 B;P 0.34662 0.407;0.462 B;B 0.29785 0.065;0.107 T 0.05954 -1.0854 10 0.21540 T 0.41 1.4837 0.1494 0.00091 0.3024:0.2321:0.2291:0.2365 . 317;333 Q13316-2;Q13316 .;DMP1_HUMAN I 333;317 ENSP00000340935:V333I;ENSP00000282479:V317I ENSP00000282479:V317I V + 1 0 DMP1 88802951 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.407000 0.07178 -0.887000 0.03961 -1.724000 0.00704 GTA TCGA-2J-AABA-01A-21D-A40W-08 DMP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253047.1 1 0 1 33 235 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 33 234 0 38 2 -6.470585 1 1 121412 31 48 1 1 2 3 2.063727 0 0.340000 1.830000 0.341120 0.720000 5.100000e-01 0.980000 0.720000 0.735711 0.720000 0 0.610000 0.850000 SQSTM1 8878 broad.mit.edu 37 5 179247944 179247944 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr5:179247944C>T ENST00000389805.4 + 1 186 c.8C>T c.(7-9)tCg>tTg p.S3L SQSTM1_ENST00000360718.5_5'Flank|SQSTM1_ENST00000402874.3_5'UTR|SQSTM1_ENST00000376929.3_Intron|SQSTM1_ENST00000510187.1_Missense_Mutation_p.S3L NM_003900.4 NP_003891.1 Q13501 SQSTM_HUMAN sequestosome 1 SQSTM1/ALK(2) 13 all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243) all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GCTATGGCGTCGCTCACCGTG 0.711000 0 SO:0001583 missense ENST00000389805.4 1 1 hg19 CCDS34317.1 . . . . . . . . . . C 19.75 3.885955 0.72410 . . ENSG00000161011 ENST00000389805;ENST00000504627;ENST00000510187 D;T;T 0.84944 -1.92;1.3;2.08 4.57 0.299 0.15771 Phox/Bem1p (1); 0.320727 0.25402 U 0.030926 T 0.72479 0.3465 L 0.58101 1.795 0.80722 D 1 P;B 0.51351 0.944;0.065 B;B 0.30179 0.112;0.004 T 0.68078 -0.5504 10 0.72032 D 0.01 -10.7097 4.5537 0.12126 0.1172:0.5961:0.1275:0.1592 . 3;3 Q13501;E7EMC7 SQSTM_HUMAN;. L 3 ENSP00000374455:S3L;ENSP00000425957:S3L;ENSP00000424477:S3L ENSP00000374455:S3L S + 2 0 SQSTM1 179180550 1.000000 0.71417 0.428000 0.26697 0.461000 0.32589 2.655000 0.46707 0.309000 0.22966 0.462000 0.41574 TCG TCGA-2J-AABA-01A-21D-A40W-08 SQSTM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319344.1 1 0 0 7 83 0 23 1 9.999971e-01 171 298 0 23 2 0 0 0 0 0 2 1 0.981287 6 83 0 22 2 -12.156160 1 1 118576 2 29 1 1 2 3 2.127722 0 0.340000 1.830000 0.352115 0.500000 2.200000e-01 1.000000 0.460000 0.553409 0.500000 0 0.340000 0.770000 CMYA5 202333 broad.mit.edu 37 5 79029066 79029066 + Missense_Mutation SNP A A G TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr5:79029066A>G ENST00000446378.2 + 2 4509 c.4478A>G c.(4477-4479)gAc>gGc p.D1493G NM_153610.3 NP_705838.3 Q8N3K9 CMYA5_HUMAN cardiomyopathy associated 5 128 Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262) AGGGTAGAAGACAAACAAGAT 0.398000 0 SO:0001583 missense ENST00000446378.2 1 1 hg19 CCDS47238.1 . . . . . . . . . . A 0.115 -1.132640 0.01756 . . ENSG00000164309 ENST00000446378 T 0.44881 0.91 5.32 2.9 0.33743 . 0.493610 0.17051 N 0.188919 T 0.21347 0.0514 N 0.14661 0.345 0.09310 N 1 B 0.10296 0.003 B 0.08055 0.003 T 0.17592 -1.0364 10 0.15952 T 0.53 . 6.9254 0.24412 0.8161:0.0:0.1839:0.0 . 1493 Q8N3K9 CMYA5_HUMAN G 1493 ENSP00000394770:D1493G ENSP00000394770:D1493G D + 2 0 CMYA5 79064822 0.000000 0.05858 0.042000 0.18584 0.034000 0.12701 0.586000 0.23894 1.058000 0.40530 0.533000 0.62120 GAC TCGA-2J-AABA-01A-21D-A40W-08 CMYA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369497.1 1 0 1 79 532 0 128 0 0 0 0 128 2 0 0 0 0 0 2 1 1.000000 79 526 0 125 2 -20.000000 1 1 0 0 1 1 2 3 2.127722 0 0.340000 1.830000 0.352115 0.780000 6.200000e-01 1.000000 0.780000 0.799112 0.780000 0 0.690000 0.900000 RNF8 9025 broad.mit.edu 37 6 37349011 37349011 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr6:37349011G>A ENST00000373479.4 + 7 1515 c.1322G>A c.(1321-1323)cGg>cAg p.R441Q RNF8_ENST00000469731.1_Intron NM_003958.3|NM_183078.2 NP_003949.1|NP_898901.1 O76064 RNF8_HUMAN ring finger protein 8, E3 ubiquitin protein ligase 13 CCCATTTGTCGGAAGGACATT 0.413000 0 SO:0001583 missense ENST00000373479.4 0 1 hg19 CCDS4834.1 . . . . . . . . . . G 35 5.473197 0.96274 . . ENSG00000112130 ENST00000373479 T 0.60797 0.16 6.08 6.08 0.98989 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1); 0.068846 0.64402 D 0.000015 T 0.78136 0.4236 M 0.87180 2.865 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.79631 -0.1723 10 0.66056 D 0.02 -13.1243 19.6603 0.95864 0.0:0.0:1.0:0.0 . 441 O76064 RNF8_HUMAN Q 441 ENSP00000362578:R441Q ENSP00000362578:R441Q R + 2 0 RNF8 37456989 1.000000 0.71417 1.000000 0.80357 0.803000 0.45373 9.869000 0.99810 2.894000 0.99253 0.591000 0.81541 CGG TCGA-2J-AABA-01A-21D-A40W-08 RNF8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040403.2 0 0 0 5 428 1 95 0 1.003162e-02 0 29 1 95 3 0 0 0 0 0 2 0 0.012078 5 427 1 92 16 -2.516899 1 1 121412 1 39 1 0 0 0 1.970790 0 0.340000 1.830000 0.309479 0.060000 2.000000e-02 0.140000 0.070000 0.077150 0.060000 0 0.040000 0.110000 GUCA1B 2979 broad.mit.edu 37 6 42152645 42152645 + Missense_Mutation SNP G G T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr6:42152645G>T ENST00000230361.3 - 4 606 c.511C>A c.(511-513)Cgt>Agt p.R171S NM_002098.5 NP_002089.4 Q9UMX6 GUC1B_HUMAN guanylate cyclase activator 1B (retina) 8 Colorectal(47;0.196) Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177) TTGTCCCGACGGGCACCTTCA 0.577000 0 SO:0001583 missense ENST00000230361.3 0 1 hg19 CCDS4865.1 . . . . . . . . . . G 23.5 4.425131 0.83667 . . ENSG00000112599 ENST00000230361;ENST00000372949 T 0.54866 0.55 4.12 4.12 0.48240 EF-hand-like domain (1); 0.052845 0.85682 D 0.000000 T 0.38026 0.1025 L 0.46157 1.445 0.80722 D 1 P 0.50369 0.934 B 0.43194 0.411 T 0.48958 -0.8988 10 0.87932 D 0 . 14.6554 0.68828 0.0:0.0:1.0:0.0 . 171 Q9UMX6 GUC1B_HUMAN S 171;163 ENSP00000230361:R171S ENSP00000230361:R171S R - 1 0 GUCA1B 42260623 1.000000 0.71417 0.998000 0.56505 0.980000 0.70556 4.425000 0.59875 2.243000 0.73865 0.655000 0.94253 CGT TCGA-2J-AABA-01A-21D-A40W-08 GUCA1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040550.1 0 0 0 5 301 0 58 0 2.557718e-03 0 4 0 58 2 0 0 0 0 0 2 1 0.933599 5 293 0 58 2 -2.782677 1 1 0 0 1 0 0 0 1.970790 0 0.340000 1.830000 0.309479 0.090000 3.000000e-02 0.200000 0.090000 0.108731 0.090000 0 0.060000 0.150000 LY86 9450 broad.mit.edu 37 6 6589102 6589102 + Splice_Site SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr6:6589102C>T ENST00000379953.2 + 2 487 c.135C>T c.(133-135)tgC>tgT p.C45C LY86-AS1_ENST00000429345.1_RNA|LY86_ENST00000230568.4_Splice_Site_p.C45C|LY86-AS1_ENST00000447858.1_RNA|LY86-AS1_ENST00000435641.1_RNA O95711 LY86_HUMAN lymphocyte antigen 86 8 Ovarian(93;0.0377) ACCAGAGTTGCGGTAAGCCCT 0.587000 0 SO:0001630 splice_region_variant ENST00000379953.2 1 0 hg19 CCDS4498.1 TCGA-2J-AABA-01A-21D-A40W-08 LY86-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039762.2 1 0 1 50 184 0 56 0 5.399564e-01 0 8 0 56 2 0 0 0 0 0 2 1 1.000000 50 179 0 54 2 -3.627983 1 1 121412 55 47 1 0 1 1 1.713140 1 0.340000 1.830000 0.204819 0.920000 7.500000e-01 1.000000 0.990000 0.916664 0.920000 1 0.840000 0.980000 RREB1 6239 broad.mit.edu 37 6 7230223 7230223 + Missense_Mutation SNP G G A TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr6:7230223G>A ENST00000349384.6 + 10 2205 c.1891G>A c.(1891-1893)Ggc>Agc p.G631S RREB1_ENST00000379938.2_Missense_Mutation_p.G631S|RREB1_ENST00000334984.6_Missense_Mutation_p.G631S|RREB1_ENST00000379933.3_Missense_Mutation_p.G631S NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) GACAGCGCCCGGCGGCAAGAA 0.637000 0 SO:0001583 missense ENST00000349384.6 0 1 hg19 CCDS34336.1 . . . . . . . . . . A 0.003 -2.475359 0.00167 . . ENSG00000124782 ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150 T;T;T;T;T 0.11604 2.97;2.94;2.97;2.76;2.86 5.13 0.216 0.15258 . 0.747822 0.12041 N 0.505003 T 0.01800 0.0057 N 0.16478 0.41 0.09310 N 1 B;B;B 0.29188 0.236;0.039;0.007 B;B;B 0.19148 0.024;0.005;0.006 T 0.42515 -0.9447 10 0.33141 T 0.24 -14.9214 10.9984 0.47591 0.4186:0.0:0.5814:0.0 . 631;631;631 Q92766-3;Q92766;Q92766-2 .;RREB1_HUMAN;. S 631 ENSP00000369265:G631S;ENSP00000369270:G631S;ENSP00000305560:G631S;ENSP00000335574:G631S;ENSP00000419511:G631S ENSP00000335574:G631S G + 1 0 RREB1 7175222 0.000000 0.05858 0.002000 0.10522 0.012000 0.07955 -0.002000 0.12924 -0.418000 0.07450 -0.977000 0.02584 GGC TCGA-2J-AABA-01A-21D-A40W-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 0 0 0 4 110 0 15 0 1.961137e-02 0 5 0 15 2 0 0 0 0 0 2 1 0.889606 4 109 0 13 2 -7.045847 1 1 0 0 1 0 1 1 1.713140 1 0.340000 1.830000 0.204819 0.180000 6.000000e-02 0.390000 0.170000 0.203336 0.180000 0 0.110000 0.290000 EPHA7 2045 broad.mit.edu 37 6 93967819 93967819 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr6:93967819C>T ENST00000369303.4 - 11 2292 c.2108G>A c.(2107-2109)aGa>aAa p.R703K NM_004440.3 NP_004431.1 Q15375 EPHA7_HUMAN EPH receptor A7 112 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) ATATCTACCTCTTGTAACAAC 0.343000 0 SO:0001583 missense ENST00000369303.4 1 1 hg19 CCDS5031.1 . . . . . . . . . . C 13.52 2.260255 0.39995 . . ENSG00000135333 ENST00000369303 D 0.81659 -1.52 6.06 6.06 0.98353 Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.72503 0.3468 N 0.17723 0.515 0.80722 D 1 P;D;D 0.62365 0.747;0.989;0.991 P;P;P 0.62089 0.778;0.837;0.898 T 0.68172 -0.5479 10 0.02654 T 1 . 20.6314 0.99525 0.0:1.0:0.0:0.0 . 699;698;703 Q15375-4;Q15375-2;Q15375 .;.;EPHA7_HUMAN K 703 ENSP00000358309:R703K ENSP00000358309:R703K R - 2 0 EPHA7 94024540 1.000000 0.71417 1.000000 0.80357 0.580000 0.36256 6.063000 0.71162 2.885000 0.99019 0.579000 0.79373 AGA TCGA-2J-AABA-01A-21D-A40W-08 EPHA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041545.1 1 0 1 44 183 0 59 1 1.019112e-01 3 0 0 59 2 0 0 0 0 0 2 1 1.000000 43 178 0 57 2 -3.323014 1 1 0 0 1 0 1 1 1.714906 1 0.340000 1.830000 0.204819 0.880000 6.800000e-01 1.000000 0.930000 0.878528 0.880000 1 0.780000 0.960000 INTS1 26173 broad.mit.edu 37 7 1522220 1522220 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr7:1522220C>T ENST00000404767.3 - 27 3750 c.3665G>A c.(3664-3666)cGc>cAc p.R1222H INTS1_ENST00000389470.4_Missense_Mutation_p.R1384H NM_001080453.2 NP_001073922.2 Q8N201 INT1_HUMAN integrator complex subunit 1 62 Ovarian(82;0.0253) ACGGATCATGCGCAGCTTCAG 0.667000 0 SO:0001583 missense ENST00000404767.3 1 1 hg19 CCDS47526.1 . . . . . . . . . . C 35 5.597216 0.96602 2.36E-4 0.0 ENSG00000164880 ENST00000404767;ENST00000389470 T;T 0.59502 0.26;0.39 4.67 4.67 0.58626 . 0.000000 0.45606 U 0.000346 T 0.70824 0.3268 M 0.69823 2.125 0.58432 D 0.999999 D 0.69078 0.997 P 0.56042 0.79 T 0.76599 -0.2900 10 0.87932 D 0 . 17.5786 0.87958 0.0:1.0:0.0:0.0 . 1222 Q8N201 INT1_HUMAN H 1222;1384 ENSP00000385722:R1222H;ENSP00000374121:R1384H ENSP00000374121:R1384H R - 2 0 INTS1 1488746 1.000000 0.71417 0.999000 0.59377 0.968000 0.65278 7.540000 0.82074 2.154000 0.67381 0.561000 0.74099 CGC TCGA-2J-AABA-01A-21D-A40W-08 INTS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323683.1 1 0 0 64 241 1 44 1 9.258303e-01 12 27 1 44 5 0 0 0 0 0 2 1 1.000000 63 235 1 42 21 -20.000000 1 1 121046 2 32 1 1 2 3 2.088232 0 0.340000 1.830000 0.345563 0.990000 9.800000e-01 1.000000 1.000000 0.998649 0.990000 1 0.990000 1.000000 HOXA4 3201 broad.mit.edu 37 7 27169037 27169037 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr7:27169037C>T ENST00000360046.5 - 2 835 c.770G>A c.(769-771)cGc>cAc p.R257H HOXA3_ENST00000317201.2_5'Flank|HOXA4_ENST00000428284.2_Missense_Mutation_p.R257H|HOXA-AS2_ENST00000521687.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000521159.1_RNA|HOXA3_ENST00000521401.1_Intron|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000517550.1_RNA NM_002141.4 NP_002132.3 Q00056 HXA4_HUMAN homeobox A4 12 CTTGACCTGGCGCTCAGACAA 0.572000 0 SO:0001583 missense ENST00000360046.5 1 1 hg19 CCDS5405.1 . . . . . . . . . . C 27.5 4.837480 0.91117 0.0 1.16E-4 ENSG00000197576 ENST00000360046;ENST00000428284 D;D 0.96802 -4.13;-4.13 5.29 5.29 0.74685 Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1); 0.000000 0.64402 D 0.000011 D 0.98438 0.9480 M 0.88775 2.98 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.99494 1.0951 10 0.87932 D 0 . 18.9816 0.92757 0.0:1.0:0.0:0.0 . 257 Q00056 HXA4_HUMAN H 257 ENSP00000353151:R257H;ENSP00000408845:R257H ENSP00000353151:R257H R - 2 0 HOXA4 27135562 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.728000 0.84847 2.485000 0.83878 0.555000 0.69702 CGC TCGA-2J-AABA-01A-21D-A40W-08 HOXA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059534.4 1 0 1 83 416 0 110 0 7.997745e-01 1 16 0 110 2 0 0 0 0 0 2 1 1.000000 83 413 0 107 2 -3.156128 1 1 121412 16 46 1 1 2 3 2.088232 0 0.340000 1.830000 0.345563 0.980000 8.000000e-01 1.000000 1.000000 0.957452 0.980000 1 0.880000 1.000000 HECW1 23072 broad.mit.edu 37 7 43590047 43590047 + Missense_Mutation SNP A A G TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr7:43590047A>G ENST00000395891.2 + 27 4857 c.4252A>G c.(4252-4254)Acg>Gcg p.T1418A HECW1_ENST00000453890.1_Missense_Mutation_p.T1384A NM_015052.3 NP_055867.3 Q76N89 HECW1_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 125 CTACAAGGTCACGGAAAGGGA 0.507000 0 SO:0001583 missense ENST00000395891.2 0 1 hg19 CCDS5469.2 . . . . . . . . . . A 24.0 4.487153 0.84854 . . ENSG00000002746 ENST00000395891;ENST00000453890;ENST00000265522 T;T 0.57273 0.41;0.41 5.62 5.62 0.85841 HECT (4); 0.000000 0.85682 D 0.000000 T 0.60715 0.2290 L 0.31926 0.97 0.80722 D 1 D;B 0.55605 0.972;0.048 D;B 0.67231 0.95;0.027 T 0.56432 -0.7980 10 0.25751 T 0.34 . 15.8276 0.78727 1.0:0.0:0.0:0.0 . 1384;1418 B4DH42;Q76N89 .;HECW1_HUMAN A 1418;1384;1418 ENSP00000379228:T1418A;ENSP00000407774:T1384A ENSP00000265522:T1418A T + 1 0 HECW1 43556572 1.000000 0.71417 0.986000 0.45419 0.929000 0.56500 8.962000 0.93254 2.122000 0.65172 0.533000 0.62120 ACG TCGA-2J-AABA-01A-21D-A40W-08 HECW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250893.2 0 0 0 5 105 0 19 0 2.879528e-02 0 5 0 19 2 0 0 0 0 0 2 1 0.939019 5 105 0 19 2 -8.669340 1 1 0 0 1 1 2 3 2.088232 0 0.340000 1.830000 0.345563 0.290000 1.100000e-01 1.000000 0.270000 0.338492 0.290000 0 0.180000 0.460000 BLVRA 644 broad.mit.edu 37 7 43810766 43810766 + Silent SNP A A T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr7:43810766A>T ENST00000402924.1 + 3 172 c.9A>T c.(7-9)gcA>gcT p.A3A BLVRA_ENST00000265523.4_Silent_p.A3A NM_001253823.1 NP_001240752.1 P53004 BIEA_HUMAN biliverdin reductase A 12 AGATGAATGCAGAGGTGAGTT 0.463000 0 SO:0001819 synonymous_variant ENST00000402924.1 1 1 hg19 CCDS5472.1 TCGA-2J-AABA-01A-21D-A40W-08 BLVRA-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000339006.1 1 0 1 43 199 0 61 1 9.997526e-01 14 47 0 61 2 0 0 0 0 0 2 1 1.000000 42 196 0 61 2 -19.999950 1 1 0 0 1 1 2 3 2.088232 0 0.340000 1.830000 0.345563 0.990000 7.900000e-01 1.000000 1.000000 0.969903 0.990000 1 0.910000 1.000000 RIMS2 9699 broad.mit.edu 37 8 105263381 105263381 + Missense_Mutation SNP A A C TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr8:105263381A>C ENST00000436393.2 + 27 4116 c.3875A>C c.(3874-3876)aAa>aCa p.K1292T RIMS2_ENST00000507740.1_Missense_Mutation_p.K1088T|RIMS2_ENST00000406091.3_Missense_Mutation_p.K1274T|RIMS2_ENST00000339750.2_Missense_Mutation_p.K210T|RIMS2_ENST00000262231.10_Missense_Mutation_p.K1113T Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 144 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) CCACAAGGAAAAGTTTTACAG 0.368000 HNSCC(12;0.0054) 0 SO:0001583 missense ENST00000436393.2 0 1 hg19 . . . . . . . . . . A 20.2 3.951323 0.73787 . . ENSG00000176406 ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000436393;ENST00000523362;ENST00000339750 T;T;T;T;T;T 0.68903 -0.36;-0.36;-0.36;-0.36;-0.36;-0.36 5.24 4.03 0.46877 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); . . . . T 0.79143 0.4396 M 0.72624 2.21 0.58432 D 0.999998 D;P;P;D;D 0.76494 0.994;0.787;0.933;0.999;0.999 D;P;D;D;D 0.85130 0.994;0.69;0.963;0.997;0.997 T 0.79811 -0.1646 9 0.66056 D 0.02 . 11.4916 0.50383 0.9278:0.0:0.0722:0.0 . 1336;1292;1113;1088;1274 Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47 RIMS2_HUMAN;.;.;.;. T 1311;1274;1336;1113;1088;1292;210;210 ENSP00000384892:K1274T;ENSP00000262231:K1113T;ENSP00000423559:K1088T;ENSP00000390665:K1292T;ENSP00000428478:K210T;ENSP00000342051:K210T ENSP00000262231:K1113T K + 2 0 RIMS2 105332557 1.000000 0.71417 0.904000 0.35570 0.985000 0.73830 7.451000 0.80668 0.889000 0.36185 0.477000 0.44152 AAA TCGA-2J-AABA-01A-21D-A40W-08 RIMS2-007 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000367217.1 1 0 1 13 67 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.999688 13 67 0 12 2 -19.999850 1 1 0 0 1 0 1 1 2.053834 0 0.340000 1.830000 0.338876 0.950000 5.500000e-01 1.000000 1.000000 0.894287 0.950000 1 0.730000 1.000000 WRN 7486 broad.mit.edu 37 8 30924630 30924630 + Missense_Mutation SNP C C T TCGA-2J-AABA-01A-21D-A40W-08 TCGA-2J-AABA-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 61e9c5f2-e782-404f-92f1-ecc78d28b285 702e85b0-5c6e-4945-a20a-37568587f243 g.chr8:30924630C>T ENST00000298139.5 + 6 835 c.586C>T c.(586-588)Cgc>Tgc p.R196C NM_000553.4 NP_000544.2 Q14191 WRN_HUMAN Werner syndrome, RecQ helicase-like 60 Breast(100;0.195) CAAGTCTATCCGCTGTAGCAA 0.413000 Mis, N, F, S osteosarcoma, meningioma, others Genes defective in diseases associated with sensitivity to DNA damaging agents Werner syndrome Ovarian(18;161 598 2706 14834 27543) yes Rec Werner Syndrome 8 8p12-p11.2 7486 Werner syndrome (RECQL2) L, E, M, O 0 SO:0001583 missense Familial Cancer Database WS, Adult Progeria ENST00000298139.5 1 1 hg19 CCDS6082.1 . . . . . . . . . . C 28.1 4.886939 0.91814 2.27E-4 0.0 ENSG00000165392 ENST00000298139 T 0.63913 -0.07 5.82 5.82 0.92795 -5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2); 0.056461 0.64402 N 0.000001 D 0.85444 0.5698 M 0.93638 3.44 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.88398 0.3013 10 0.87932 D 0 -10.7416 19.6956 0.96023 0.0:1.0:0.0:0.0 . 196 Q14191 WRN_HUMAN C 196 ENSP00000298139:R196C ENSP00000298139:R196C R + 1 0 WRN 31044172 1.000000 0.71417 0.992000 0.48379 0.966000 0.64601 6.162000 0.71874 2.757000 0.94681 0.561000 0.74099 CGC TCGA-2J-AABA-01A-21D-A40W-08 WRN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376248.1 1 0 1 48 274 0 66 0 2.326686e-02 1 1 0 66 2 0 0 0 0 0 2 1 1.000000 48 272 0 66 2 -2.527547 1 1 121412 1 29 1 0 1 1 2.053834 0 0.340000 1.830000 0.338876 0.870000 6.600000e-01 1.000000 1.000000 0.872277 0.870000 1 0.760000 0.990000