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 NFKBIZ 64332 broad.mit.edu 37 3 101575980 101575980 + Frame_Shift_Del DEL C C - TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 C - C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr3:101575980delC ENST00000326172.5 + 10 2003 c.1888delC c.(1888-1890)cgcfs p.R630fs NFKBIZ_ENST00000394054.2_Frame_Shift_Del_p.R530fs|NFKBIZ_ENST00000326151.5_Frame_Shift_Del_p.R508fs NM_031419.3 NP_113607.1 Q9BYH8 IKBZ_HUMAN nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta 24 GGAACTCATTCGCCTCTTTTT 0.463000 0 SO:0001589 frameshift_variant ENST00000326172.5 1 1 hg19 CCDS2946.1 TCGA-IB-AAUO-01A-12D-A38G-08 NFKBIZ-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000353793.1 1 0 0 48 424 0 202 1 9.999883e-01 45 103 0 202 2 0 0 0 0 0 0 1 1.000000 58 431 1 208 10 0 0 0 0 0 0 -15.511920 1 1 0 0 1 0 1 1 1.716026 1 0.380000 1.860000 0.234568 0.420000 0.320000 0.550000 0.430000 0.437665 0.420000 0 0.370000 0.490000 PKD2L1 9033 broad.mit.edu 37 10 102057186 102057186 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr10:102057186G>A ENST00000318222.3 - 5 1291 c.909C>T c.(907-909)atC>atT p.I303I PKD2L1_ENST00000353274.3_Silent_p.I303I|PKD2L1_ENST00000338519.3_Intron NM_001253837.1|NM_016112.2 NP_001240766.1|NP_057196.2 Q9P0L9 PK2L1_HUMAN polycystic kidney disease 2-like 1 43 Colorectal(252;0.117) CTGAGAAGTCGATGAACACCA 0.567000 0 SO:0001819 synonymous_variant ENST00000318222.3 1 1 hg19 CCDS7492.1 TCGA-IB-AAUO-01A-12D-A38G-08 PKD2L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049863.2 0 0 1 37 280 1 118 0 0 0 1 118 2 0 0 0 0 0 2 1 0.999979 37 275 1 118 11 0 0 0 1 118 2 -15.167500 1 1 121412 1 35 1 1 2 3 2.064821 0 0.380000 1.860000 0.381176 0.610000 0.440000 0.820000 0.620000 0.624935 0.610000 0 0.520000 0.720000 C10orf82 143379 broad.mit.edu 37 10 118425205 118425205 + Missense_Mutation SNP G G C TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr10:118425205G>C ENST00000369210.3 - 3 242 c.188C>G c.(187-189)gCc>gGc p.A63G C10orf82_ENST00000588184.1_Missense_Mutation_p.A63G NM_144661.2 NP_653262.1 Q8WW14 CJ082_HUMAN chromosome 10 open reading frame 82 7 CAGTTTCGGGGCAGTGGCCAC 0.562000 0 SO:0001583 missense ENST00000369210.3 1 1 hg19 CCDS7596.1 . . . . . . . . . . G 16.52 3.146601 0.57044 . . ENSG00000165863 ENST00000369210;ENST00000388884 T 0.64260 -0.09 5.16 4.25 0.50352 . 0.715143 0.13142 N 0.410531 T 0.66015 0.2747 M 0.65975 2.015 0.09310 N 1 P;D 0.56521 0.884;0.976 B;P 0.49085 0.42;0.6 T 0.57106 -0.7868 10 0.49607 T 0.09 -4.1516 9.7479 0.40457 0.096:0.0:0.904:0.0 . 63;63 Q8WW14-3;Q8WW14 .;CJ082_HUMAN G 63 ENSP00000358212:A63G ENSP00000358212:A63G A - 2 0 C10orf82 118415195 0.014000 0.17966 0.010000 0.14722 0.031000 0.12232 1.748000 0.38308 1.161000 0.42604 0.561000 0.74099 GCC TCGA-IB-AAUO-01A-12D-A38G-08 C10orf82-001 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000050527.1 1 0 1 51 258 0 118 0 0 0 0 118 2 0 0 0 0 0 2 1 1.000000 51 250 0 118 2 0 0 0 0 118 2 -20.000000 1 1 0 0 1 1 2 3 2.064821 0 0.380000 1.860000 0.381176 0.860000 0.660000 1.000000 1.000000 0.868711 0.860000 1 0.760000 0.990000 KIAA1217 56243 broad.mit.edu 37 10 24831899 24831899 + Nonsense_Mutation SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr10:24831899G>T ENST00000376454.3 + 19 3730 c.3700G>T c.(3700-3702)Gaa>Taa p.E1234* KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Nonsense_Mutation_p.E917*|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376452.3_Intron NM_019590.3 NP_062536.2 Q5T5P2 SKT_HUMAN KIAA1217 70 AAGAACATCAGAATATAAAAC 0.413000 0 SO:0001587 stop_gained ENST00000376454.3 0 1 hg19 CCDS31165.1 . . . . . . . . . . G 42 9.260198 0.99117 . . ENSG00000120549 ENST00000442879;ENST00000376454;ENST00000450158;ENST00000376451 . . . 5.42 4.5 0.54988 . 0.360938 0.28062 N 0.016754 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.56958 D 0.05 . 15.1525 0.72713 0.0:0.1417:0.8583:0.0 . . . . X 917;1234;917;917 . ENSP00000365634:E917X E + 1 0 KIAA1217 24871905 0.993000 0.37304 0.790000 0.31976 0.868000 0.49771 2.681000 0.46926 1.264000 0.44198 0.561000 0.74099 GAA TCGA-IB-AAUO-01A-12D-A38G-08 KIAA1217-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047223.2 1 0 1 41 153 0 105 1 7.549167e-01 4 8 0 105 2 0 0 0 0 0 2 1 1.000000 41 150 0 106 2 0 0 0 0 105 2 -20.000000 1 1 0 0 1 0 1 1 1.666965 1 0.380000 1.860000 0.234568 0.850000 0.650000 0.990000 0.890000 0.855220 0.850000 1 0.750000 0.950000 DIP2C 22982 broad.mit.edu 37 10 410376 410376 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr10:410376G>A ENST00000280886.6 - 20 2502 c.2415C>T c.(2413-2415)aaC>aaT p.N805N DIP2C_ENST00000381496.3_3'UTR|DIP2C_ENST00000540204.1_Silent_p.N126N NM_014974.2 NP_055789.1 Q9Y2E4 DIP2C_HUMAN DIP2 disco-interacting protein 2 homolog C (Drosophila) 81 all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235) OV - Ovarian serous cystadenocarcinoma(33;0.136) TGTCGTCGGCGTTGTGCCTGC 0.602000 0 SO:0001819 synonymous_variant ENST00000280886.6 1 1 hg19 CCDS7054.1 TCGA-IB-AAUO-01A-12D-A38G-08 DIP2C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046389.1 1 0 1 59 267 1 120 0 2.289787e-01 0 5 1 120 2 0 0 0 0 0 2 1 1.000000 59 262 1 119 11 0 0 0 1 120 2 -20.000000 1 1 121412 18 44 1 0 1 1 2.049863 0 0.380000 1.860000 0.378820 0.940000 0.740000 1.000000 1.000000 0.929680 0.940000 1 0.830000 1.000000 ALOX5 240 broad.mit.edu 37 10 45878098 45878098 + Silent SNP C C T rs150281723 by1000genomes TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr10:45878098C>T ENST00000374391.2 + 2 371 c.318C>T c.(316-318)ggC>ggT p.G106G ALOX5_ENST00000542434.1_Silent_p.G106G NM_000698.3|NM_001256153.1 NP_000689.1|NP_001243082.1 P09917 LOX5_HUMAN arachidonate 5-lipoxygenase p.G106G(1) 37 Lung SC(717;0.0257) Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744) GGATCACCGGCGATGTCGAGG 0.592000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000374391.2 1 1 hg19 CCDS7212.1 TCGA-IB-AAUO-01A-12D-A38G-08 ALOX5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047780.1 1 0 1 15 94 0 53 1 1 119 191 0 53 2 0 0 0 0 0 2 1 0.999883 13 92 0 53 2 0 0 0 0 53 2 -4.328109 1 1 121412 109 48 1 0 1 1 2.051288 0 0.380000 1.860000 0.378820 0.720000 0.430000 1.000000 1.000000 0.738615 0.720000 0 0.560000 0.910000 C11orf70 85016 broad.mit.edu 37 11 101953816 101953816 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:101953816G>A ENST00000434758.2 + 7 718 c.690G>A c.(688-690)atG>atA p.M230I NM_032930.2 NP_116319.2 Q9BRQ4 CK070_HUMAN chromosome 11 open reading frame 70 12 all_epithelial(12;0.0137) Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137) Lung(13;0.245) CTGCTGGTATGTGCTATCCTT 0.294000 0 SO:0001583 missense ENST00000434758.2 1 1 hg19 CCDS8313.2 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 10.29 1.310068 0.23821 0.0 9.3E-4 ENSG00000137691 ENST00000434758;ENST00000423732 . . . 5.85 3.99 0.46301 . 0.448291 0.26062 N 0.026578 T 0.46600 0.1401 L 0.50333 1.59 0.80722 D 1 B 0.12013 0.005 B 0.10450 0.005 T 0.36578 -0.9742 9 0.23891 T 0.37 0.0275 7.5577 0.27833 0.1437:0.0:0.7203:0.1361 . 230 Q9BRQ4 CK070_HUMAN I 230;192 . ENSP00000392150:M192I M + 3 0 C11orf70 101459026 0.991000 0.36638 0.996000 0.52242 0.588000 0.36517 0.758000 0.26447 1.487000 0.48415 0.585000 0.79938 ATG TCGA-IB-AAUO-01A-12D-A38G-08 C11orf70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394144.1 0 0 0 115 443 0 186 0 1.114614e-01 1 2 0 186 2 0 0 0 0 0 2 1 1.000000 112 435 0 184 2 0 0 0 0 186 2 -2.958174 1 1 121410 50 50 1 1 2 3 2.062376 0 0.380000 1.860000 0.381176 0.990000 0.910000 1.000000 1.000000 0.992752 0.990000 1 0.990000 1.000000 DYNC2H1 79659 broad.mit.edu 37 11 103027117 103027117 + Splice_Site SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:103027117G>T ENST00000375735.2 + 26 3889 c.3745G>T c.(3745-3747)Gat>Tat p.D1249Y DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Splice_Site_p.D1249Y NM_001080463.1|NM_001377.2 NP_001073932.1|NP_001368.2 Q8NCM8 DYHC2_HUMAN dynein, cytoplasmic 2, heavy chain 1 33 Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348) TGTTAAATAGGATTTAAATAG 0.284000 0 SO:0001630 splice_region_variant ENST00000375735.2 1 0 hg19 CCDS53701.1 . . . . . . . . . . G 17.09 3.300875 0.60195 . . ENSG00000187240 ENST00000375735;ENST00000398093 T;T 0.62639 0.01;0.01 5.27 5.27 0.74061 Dynein heavy chain, domain-2 (1); 0.197764 0.33895 N 0.004459 T 0.76140 0.3946 M 0.88181 2.935 0.80722 D 1 B;B 0.33171 0.4;0.348 B;B 0.43123 0.409;0.301 T 0.76817 -0.2819 9 . . . . 18.8855 0.92376 0.0:0.0:1.0:0.0 . 1249;1249 Q8NCM8;Q8NCM8-2 DYHC2_HUMAN;. Y 1249 ENSP00000364887:D1249Y;ENSP00000381167:D1249Y . D + 1 0 DYNC2H1 102532327 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 7.376000 0.79658 2.472000 0.83506 0.563000 0.77884 GAT TCGA-IB-AAUO-01A-12D-A38G-08 DYNC2H1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387196.1 1 0 1 21 102 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 0.999999 20 102 0 53 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.062376 0 0.380000 1.860000 0.381176 0.900000 0.590000 1.000000 1.000000 0.878325 0.900000 1 0.730000 1.000000 ARHGAP20 57569 broad.mit.edu 37 11 110451075 110451075 + Silent SNP T T C TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:110451075T>C ENST00000260283.4 - 16 2879 c.2595A>G c.(2593-2595)tcA>tcG p.S865S ARHGAP20_ENST00000528829.1_Silent_p.S829S|ARHGAP20_ENST00000527598.1_Silent_p.S829S|ARHGAP20_ENST00000529591.1_Silent_p.S408S|ARHGAP20_ENST00000533353.1_Silent_p.S839S|ARHGAP20_ENST00000524756.1_Silent_p.S842S|ARHGAP20_ENST00000357139.3_Silent_p.S839S NM_020809.3 NP_065860.2 Q9P2F6 RHG20_HUMAN Rho GTPase activating protein 20 60 all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544) GTTGTTTCTTTGAATAAATTC 0.493000 0 SO:0001819 synonymous_variant ENST00000260283.4 1 1 hg19 CCDS31673.1 TCGA-IB-AAUO-01A-12D-A38G-08 ARHGAP20-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000390628.1 1 0 1 108 479 0 214 0 0 0 1 0 214 2 0 0 0 0 0 2 1 1.000000 108 468 0 213 2 0 0 0 0 214 2 -20.000000 1 1 0 0 1 1 2 3 2.062376 0 0.380000 1.860000 0.381176 0.960000 0.800000 1.000000 1.000000 0.951003 0.960000 1 0.880000 1.000000 ZBTB16 7704 broad.mit.edu 37 11 114027126 114027126 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:114027126C>T ENST00000335953.4 + 3 1716 c.1336C>T c.(1336-1338)Cgg>Tgg p.R446W ZBTB16_ENST00000392996.2_Missense_Mutation_p.R446W NM_006006.4 NP_005997.2 Q05516 ZBT16_HUMAN zinc finger and BTB domain containing 16 6 all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438) GGATAGTTTGCGGCTGAGAAT 0.547000 0 SO:0001583 missense ENST00000335953.4 0 1 hg19 CCDS8367.1 . . . . . . . . . . C 23.2 4.389876 0.82902 . . ENSG00000109906 ENST00000335953;ENST00000392996;ENST00000310883 T;T 0.15372 2.43;2.43 4.81 4.81 0.61882 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.64402 D 0.000001 T 0.38134 0.1029 M 0.62723 1.935 0.51767 D 0.999937 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.998 T 0.10245 -1.0638 10 0.72032 D 0.01 -2.7332 13.0927 0.59174 0.1603:0.8397:0.0:0.0 . 446;451 Q05516;Q59H43 ZBT16_HUMAN;. W 446;446;323 ENSP00000338157:R446W;ENSP00000376721:R446W ENSP00000309507:R323W R + 1 2 ZBTB16 113532336 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.419000 0.66435 2.500000 0.84329 0.655000 0.94253 CGG TCGA-IB-AAUO-01A-12D-A38G-08 ZBTB16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398940.1 0 0 0 4 216 0 81 0 6.059872e-04 0 2 0 81 2 0 0 0 0 0 2 1 0.885690 4 211 0 80 2 0 0 0 0 81 2 -2.672181 1 1 0 0 1 1 2 3 2.062376 0 0.380000 1.860000 0.381176 0.100000 0.030000 0.240000 0.100000 0.117887 0.100000 0 0.060000 0.170000 DPAGT1 1798 broad.mit.edu 37 11 118972344 118972344 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:118972344G>A ENST00000409993.2 - 3 1573 c.22C>T c.(22-24)Ccc>Tcc p.P8S DPAGT1_ENST00000432443.2_5'UTR|DPAGT1_ENST00000445653.1_5'UTR|DPAGT1_ENST00000354202.4_Missense_Mutation_p.P8S Q9H3H5 GPT_HUMAN dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase) 17 all_hematologic(175;0.0977) Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) AGCGGCATGGGCAATTCCGAG 0.632000 OREG0021396 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000409993.2 0 1 hg19 CCDS8411.1 . . . . . . . . . . G 15.61 2.884783 0.51908 . . ENSG00000172269 ENST00000409993;ENST00000354202 D;D 0.91011 -2.77;-2.77 4.79 3.87 0.44632 . 0.000000 0.85682 D 0.000000 T 0.80628 0.4659 N 0.19112 0.55 0.80722 D 1 P 0.35174 0.488 B 0.27380 0.079 T 0.78725 -0.2092 10 0.27082 T 0.32 -2.6285 12.3966 0.55389 0.0:0.0:0.8312:0.1688 . 8 Q9H3H5 GPT_HUMAN S 8 ENSP00000386597:P8S;ENSP00000346142:P8S ENSP00000346142:P8S P - 1 0 DPAGT1 118477554 . . 0.973000 0.42090 0.691000 0.40173 . . 1.602000 0.50124 0.655000 0.94253 CCC TCGA-IB-AAUO-01A-12D-A38G-08 DPAGT1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331527.2 0 0 0 5 289 0 112 0 2.477637e-01 0 47 0 112 2 0 0 0 0 0 2 1 0.935214 5 284 0 110 2 0 0 0 0 112 2 -2.631334 1 1 0 0 1 1 2 3 2.062376 0 0.380000 1.860000 0.381176 0.090000 0.030000 0.210000 0.090000 0.106304 0.090000 0 0.050000 0.150000 KIRREL3 84623 broad.mit.edu 37 11 126432761 126432761 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:126432761C>T ENST00000525144.2 - 2 351 c.102G>A c.(100-102)atG>atA p.M34I KIRREL3_ENST00000533026.2_5'UTR|KIRREL3_ENST00000525704.2_Missense_Mutation_p.M34I|KIRREL3-AS1_ENST00000548204.1_RNA|KIRREL3_ENST00000529097.2_Missense_Mutation_p.M34I NM_032531.3 NP_115920.1 Q8IZU9 KIRR3_HUMAN kin of IRRE like 3 (Drosophila) 29 all_hematologic(175;0.145) Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224) TGTCCTTGGCCATGTAGCCCA 0.547000 0 SO:0001583 missense ENST00000525144.2 1 1 hg19 CCDS53723.1 . . . . . . . . . . C 16.07 3.017523 0.54576 . . ENSG00000149571 ENST00000525144;ENST00000529097;ENST00000525704 T;T;T 0.70516 -0.49;-0.26;-0.35 5.62 5.62 0.85841 . 0.078542 0.53938 D 0.000046 T 0.54255 0.1847 N 0.08118 0 0.80722 D 1 B;B;B 0.26547 0.048;0.152;0.077 B;B;B 0.26614 0.025;0.071;0.019 T 0.52719 -0.8538 10 0.37606 T 0.19 . 17.8583 0.88773 0.0:1.0:0.0:0.0 . 34;34;34 Q8IZU9-2;E9PRX9;Q8IZU9 .;.;KIRR3_HUMAN I 34 ENSP00000435466:M34I;ENSP00000434081:M34I;ENSP00000435094:M34I ENSP00000435466:M34I M - 3 0 KIRREL3 125937971 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.770000 0.62309 2.645000 0.89757 0.650000 0.86243 ATG TCGA-IB-AAUO-01A-12D-A38G-08 KIRREL3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000386479.2 1 0 1 31 207 0 72 0 0 0 1 0 72 2 0 0 0 0 0 2 1 1.000000 31 203 0 72 2 0 0 0 0 72 2 -3.320078 1 1 0 0 1 1 2 3 2.062376 0 0.380000 1.860000 0.381176 0.680000 0.480000 0.940000 0.680000 0.697943 0.680000 0 0.570000 0.810000 MUC5B 727897 broad.mit.edu 37 11 1268340 1268340 + Silent SNP A A T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr11:1268340A>T ENST00000529681.1 + 31 10288 c.10230A>T c.(10228-10230)ccA>ccT p.P3410P MUC5B_ENST00000447027.1_Silent_p.P3413P|RP11-532E4.2_ENST00000532061.2_RNA NM_002458.2 NP_002449.2 Q9HC84 MUC5B_HUMAN mucin 5B, oligomeric mucus/gel-forming 137 all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) cctcaactccagggacaactc 0.637000 0 SO:0001819 synonymous_variant ENST00000529681.1 0 1 hg19 CCDS44515.2 TCGA-IB-AAUO-01A-12D-A38G-08 MUC5B-002 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000390041.2 0 0 0 3 29 0 14 0 4.481793e-02 0 3 0 14 2 0 0 0 0 0 2 1 0.779939 3 26 0 13 2 0 0 0 0 14 2 -0.923199 0 1 114872 183 46 1 0 1 1 2.051225 0 0.380000 1.860000 0.378820 0.540000 0.160000 1.000000 1.000000 0.573597 0.540000 0 0.310000 0.840000 SSH1 54434 broad.mit.edu 37 12 109186420 109186420 + Missense_Mutation SNP C C T rs146699038 by1000genomes TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr12:109186420C>T ENST00000326495.5 - 14 1628 c.1535G>A c.(1534-1536)cGg>cAg p.R512Q SSH1_ENST00000551165.1_Missense_Mutation_p.R512Q|SSH1_ENST00000326470.5_Missense_Mutation_p.R523Q|SSH1_ENST00000360239.3_Missense_Mutation_p.R200Q NM_018984.3 NP_061857.3 Q8WYL5 SSH1_HUMAN slingshot protein phosphatase 1 38 TGAGAGTCGCCGGAAACAGCA 0.637000 0 SO:0001583 missense ENST00000326495.5 0 1 hg19 CCDS9121.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 C 14.68 2.607225 0.46527 0.001817 0.0 ENSG00000084112 ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470 T;T;T;T 0.15834 2.39;2.4;2.49;2.46 5.48 4.6 0.57074 . 3.113600 0.01024 N 0.004037 T 0.23054 0.0557 M 0.71581 2.175 0.39015 D 0.959636 P;B;P;P 0.39624 0.681;0.218;0.569;0.681 B;B;B;B 0.26614 0.071;0.016;0.07;0.071 T 0.39563 -0.9608 10 0.37606 T 0.19 -25.6956 12.894 0.58089 0.0:0.9248:0.0:0.0752 . 523;512;512;200 Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4 .;.;SSH1_HUMAN;. Q 200;512;512;523 ENSP00000353374:R200Q;ENSP00000315713:R512Q;ENSP00000448824:R512Q;ENSP00000326107:R523Q ENSP00000326107:R523Q R - 2 0 SSH1 107710549 0.990000 0.36364 0.815000 0.32552 0.069000 0.16628 2.653000 0.46691 1.460000 0.47911 -0.136000 0.14681 CGG TCGA-IB-AAUO-01A-12D-A38G-08 SSH1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000403724.1 0 0 0 7 256 0 119 0 8.719772e-02 1 15 0 119 2 0 0 0 0 0 2 1 0.979070 7 249 0 117 2 0 0 0 0 119 2 -3.215354 1 1 121338 22 43 1 0 0 0 2.013098 0 0.380000 1.860000 0.365534 0.140000 0.060000 0.270000 0.130000 0.154241 0.140000 0 0.090000 0.200000 GPR133 283383 broad.mit.edu 37 12 131476784 131476784 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr12:131476784G>A ENST00000261654.5 + 8 1372 c.813G>A c.(811-813)atG>atA p.M271I RP11-76C10.5_ENST00000542980.1_lincRNA|GPR133_ENST00000535015.1_Missense_Mutation_p.M303I NM_198827.3 NP_942122.2 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 67 all_neural(191;0.0982)|Medulloblastoma(191;0.163) TCTTTCAGATGCCCACAGATG 0.393000 0 SO:0001583 missense ENST00000261654.5 1 1 hg19 CCDS9272.1 . . . . . . . . . . G 2.052 -0.417574 0.04766 . . ENSG00000111452 ENST00000261654;ENST00000542091;ENST00000535015;ENST00000537600 T;T 0.38887 1.11;1.11 5.62 2.61 0.31194 . 1.491050 0.03428 N 0.207351 T 0.30727 0.0774 L 0.29908 0.895 0.22081 N 0.999377 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.16512 -1.0400 10 0.27785 T 0.31 . 3.881 0.09079 0.1601:0.1364:0.5778:0.1257 . 303;271 B7ZLF7;Q6QNK2 .;GP133_HUMAN I 271;211;303;30 ENSP00000261654:M271I;ENSP00000444425:M303I ENSP00000261654:M271I M + 3 0 GPR133 130042737 0.174000 0.23070 0.228000 0.23943 0.043000 0.13939 0.405000 0.21015 1.350000 0.45770 0.655000 0.94253 ATG TCGA-IB-AAUO-01A-12D-A38G-08 GPR133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399356.1 0 0 0 24 951 0 356 0 0 0 0 356 2 0 0 0 0 0 2 1 1.000000 24 930 0 355 2 0 0 0 0 356 2 -2.688130 1 1 0 0 1 0 0 0 2.013098 0 0.380000 1.860000 0.365534 0.120000 0.070000 0.180000 0.130000 0.131366 0.120000 0 0.090000 0.160000 RECQL 5965 broad.mit.edu 37 12 21644543 21644543 + Missense_Mutation SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr12:21644543G>T ENST00000444129.2 - 3 592 c.124C>A c.(124-126)Ctg>Atg p.L42M RECQL_ENST00000421138.2_Missense_Mutation_p.L42M NM_002907.3|NM_032941.2 NP_002898.2|NP_116559.1 P46063 RECQ1_HUMAN RecQ helicase-like 17 TTCTTTGTCAGGACTTTTTTT 0.378000 Other identified genes with known or suspected DNA repair function 0 SO:0001583 missense ENST00000444129.2 1 0 hg19 CCDS31756.1 . . . . . . . . . . G 11.66 1.704990 0.30232 . . ENSG00000004700 ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240;ENST00000536964;ENST00000539672 T;T;T;T;D;D;D;D 0.87256 0.29;0.29;0.55;0.54;-2.23;-2.23;-2.23;-1.68 4.33 3.42 0.39159 . 0.087041 0.48767 D 0.000177 D 0.92195 0.7525 M 0.83953 2.67 0.24809 N 0.992651 D 0.89917 1.0 D 0.73380 0.98 D 0.84614 0.0680 10 0.72032 D 0.01 -4.8901 8.4221 0.32707 0.0843:0.0:0.7589:0.1568 . 42 P46063 RECQ1_HUMAN M 42 ENSP00000416739:L42M;ENSP00000395449:L42M;ENSP00000379400:L42M;ENSP00000318727:L42M;ENSP00000445555:L42M;ENSP00000439069:L42M;ENSP00000446036:L42M;ENSP00000440700:L42M ENSP00000318727:L42M L - 1 2 RECQL 21535810 0.652000 0.27349 0.372000 0.25991 0.193000 0.23685 0.781000 0.26774 1.123000 0.41961 0.655000 0.94253 CTG TCGA-IB-AAUO-01A-12D-A38G-08 RECQL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402371.1 1 0 1 69 392 0 174 1 8.603249e-01 5 17 0 174 2 0 0 0 0 0 2 1 1.000000 67 382 0 172 2 0 0 0 0 174 2 -2.922170 1 1 0 0 1 0 0 0 2.013098 0 0.380000 1.860000 0.365534 0.760000 0.600000 0.940000 0.770000 0.774454 0.760000 0 0.680000 0.860000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-AAUO-01A-12D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 51 227 0 107 1 4.524297e-01 2 6 0 107 2 1 1 59 312 0 333 2 1 1.000000 50 221 0 107 2 1 1 1697 6340 0 107 2 -20.000000 1 1 121404 2 44 1 0 0 0 2.013098 0 0.380000 1.860000 0.365534 0.930000 0.720000 1.000000 1.000000 0.922427 0.930000 1 0.820000 1.000000 ACSM4 341392 broad.mit.edu 37 12 7469871 7469871 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr12:7469871C>T ENST00000399422.4 + 4 807 c.759C>T c.(757-759)tgC>tgT p.C253C NM_001080454.1 NP_001073923.1 P0C7M7 ACSM4_HUMAN acyl-CoA synthetase medium-chain family member 4 21 TCACCCTCTGCGGAAGGTAGG 0.463000 0 SO:0001819 synonymous_variant ENST00000399422.4 0 1 hg19 CCDS44825.1 TCGA-IB-AAUO-01A-12D-A38G-08 ACSM4-001 NOVEL not_organism_supported|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000337866.2 0 0 0 7 26 0 9 0 0 0 0 9 2 0 0 0 0 0 2 1 0.984761 7 26 0 9 2 0 0 0 0 9 2 -15.874150 1 1 116028 9 32 1 0 0 0 2.013098 0 0.380000 1.860000 0.365534 0.990000 0.520000 1.000000 1.000000 0.916676 0.990000 1 0.760000 1.000000 SEL1L 6400 broad.mit.edu 37 14 81950645 81950645 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr14:81950645G>A ENST00000336735.4 - 19 2086 c.1970C>T c.(1969-1971)gCt>gTt p.A657V NM_005065.5 NP_005056.3 Q9UBV2 SE1L1_HUMAN sel-1 suppressor of lin-12-like (C. elegans) 28 CTGCTCAGAAGCCAGACGGTA 0.428000 0 SO:0001583 missense ENST00000336735.4 1 1 hg19 CCDS9876.1 . . . . . . . . . . G 36 5.610409 0.96637 . . ENSG00000071537 ENST00000336735;ENST00000261258 T 0.65178 -0.14 5.92 5.92 0.95590 Tetratricopeptide-like helical (1); 0.000000 0.85682 D 0.000000 D 0.85191 0.5640 M 0.92219 3.285 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.87620 0.2509 10 0.87932 D 0 . 20.3167 0.98654 0.0:0.0:1.0:0.0 . 657 Q9UBV2 SE1L1_HUMAN V 657;18 ENSP00000337053:A657V ENSP00000261258:A18V A - 2 0 SEL1L 81020398 1.000000 0.71417 0.916000 0.36221 0.980000 0.70556 9.335000 0.96500 2.809000 0.96659 0.557000 0.71058 GCT TCGA-IB-AAUO-01A-12D-A38G-08 SEL1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413325.1 0 0 0 46 1233 0 514 0 6.003873e-02 1 10 0 514 2 0 0 0 0 0 2 1 1.000000 45 1208 0 512 2 0 0 0 0 514 2 -3.687732 1 1 0 0 1 0 0 0 2.033170 0 0.380000 1.860000 0.375252 0.180000 0.130000 0.250000 0.190000 0.191390 0.180000 0 0.150000 0.220000 CHGA 1113 broad.mit.edu 37 14 93396099 93396099 + Missense_Mutation SNP C C A rs150929444 byFrequency TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr14:93396099C>A ENST00000216492.5 + 5 574 c.294C>A c.(292-294)agC>agA p.S98R CHGA_ENST00000334654.4_Missense_Mutation_p.S98R|CHGA_ENST00000553866.1_3'UTR NM_001275.3 NP_001266.1 P10645 CMGA_HUMAN chromogranin A (parathyroid secretory protein 1) 8 all_cancers(154;0.0843) AGAAACACAGCGGTTTTGAAG 0.542000 Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204) 0 SO:0001583 missense ENST00000216492.5 1 1 hg19 CCDS9906.1 . . . . . . . . . . C 8.843 0.942786 0.18281 . . ENSG00000100604 ENST00000216492;ENST00000334654 T;T 0.07021 4.56;3.23 4.78 1.53 0.23141 . 0.334049 0.33382 N 0.004968 T 0.09468 0.0233 L 0.53249 1.67 0.09310 N 0.999998 B;P 0.36162 0.057;0.54 B;B 0.40677 0.028;0.337 T 0.14392 -1.0474 10 0.41790 T 0.15 -6.3264 5.9182 0.19067 0.1371:0.545:0.0:0.3179 . 98;98 G5E968;P10645 .;CMGA_HUMAN R 98 ENSP00000216492:S98R;ENSP00000334023:S98R ENSP00000216492:S98R S + 3 2 CHGA 92465852 0.008000 0.16893 0.012000 0.15200 0.675000 0.39556 0.091000 0.15046 0.466000 0.27193 -0.221000 0.12465 AGC TCGA-IB-AAUO-01A-12D-A38G-08 CHGA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412411.1 1 0 0 19 197 0 77 0 4.318480e-01 0 16 0 77 2 0 0 0 0 0 2 1 0.999991 19 193 0 77 2 0 0 0 0 77 2 -3.017770 1 1 0 0 1 0 0 0 2.033170 0 0.380000 1.860000 0.375252 0.460000 0.290000 0.670000 0.450000 0.475512 0.460000 0 0.360000 0.570000 PLCB2 5330 broad.mit.edu 37 15 40581489 40581489 + Missense_Mutation SNP C C G TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr15:40581489C>G ENST00000260402.3 - 31 3587 c.3338G>C c.(3337-3339)cGg>cCg p.R1113P PLCB2_ENST00000557821.1_Missense_Mutation_p.R1109P|PLCB2_ENST00000456256.2_Missense_Mutation_p.R1098P NM_001284297.1|NM_004573.2 NP_001271226.1|NP_004564.2 Q00722 PLCB2_HUMAN phospholipase C, beta 2 39 all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) TTCCATCTCCCGTATCTGTTC 0.582000 0 SO:0001583 missense ENST00000260402.3 1 1 hg19 CCDS42020.1 . . . . . . . . . . C 15.50 2.852673 0.51270 . . ENSG00000137841 ENST00000260402;ENST00000456256 T;T 0.45668 0.89;0.89 5.05 -0.161 0.13371 PLC-beta, C-terminal (1); 0.561271 0.17537 N 0.170673 T 0.33177 0.0854 N 0.22421 0.69 0.80722 D 1 P;B;P 0.37122 0.523;0.451;0.583 P;B;P 0.46299 0.509;0.333;0.511 T 0.06180 -1.0841 10 0.33141 T 0.24 . 8.7765 0.34765 0.0:0.4418:0.0:0.5582 . 1098;1109;1113 B9EGH5;Q00722-2;Q00722 .;.;PLCB2_HUMAN P 1113;1098 ENSP00000260402:R1113P;ENSP00000411991:R1098P ENSP00000260402:R1113P R - 2 0 PLCB2 38368781 0.889000 0.30405 0.991000 0.47740 0.983000 0.72400 -0.086000 0.11233 -0.207000 0.10187 0.561000 0.74099 CGG TCGA-IB-AAUO-01A-12D-A38G-08 PLCB2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000418430.1 0 0 0 12 392 0 173 0 8.674163e-01 0 118 0 173 2 0 0 0 0 0 2 1 0.999005 11 383 0 170 2 0 0 0 0 173 2 -2.211676 0 1 0 0 1 1 2 3 2.055270 0 0.380000 1.860000 0.381176 0.150000 0.080000 0.270000 0.160000 0.168167 0.150000 0 0.110000 0.210000 DUOX1 53905 broad.mit.edu 37 15 45433521 45433521 + Nonsense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr15:45433521C>T ENST00000321429.4 + 15 2004 c.1597C>T c.(1597-1599)Cga>Tga p.R533* DUOX1_ENST00000389037.3_Nonsense_Mutation_p.R533*|DUOX1_ENST00000561166.1_Nonsense_Mutation_p.R179* NM_017434.3 NP_059130.2 Q9NRD9 DUOX1_HUMAN dual oxidase 1 57 all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027) TGAAGAAATCCGAAATACCAC 0.527000 0 SO:0001587 stop_gained ENST00000321429.4 0 1 hg19 CCDS32221.1 . . . . . . . . . . C 37 6.140306 0.97320 . . ENSG00000137857 ENST00000431588;ENST00000321429;ENST00000389037 . . . 4.53 2.15 0.27550 . 0.095326 0.64402 D 0.000001 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -15.0907 10.5604 0.45142 0.4411:0.5589:0.0:0.0 . . . . X 533 . ENSP00000317997:R533X R + 1 2 DUOX1 43220813 1.000000 0.71417 1.000000 0.80357 0.027000 0.11550 2.572000 0.45999 0.336000 0.23639 -0.271000 0.10264 CGA TCGA-IB-AAUO-01A-12D-A38G-08 DUOX1-006 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416251.1 0 0 0 11 274 0 120 1 7.740379e-02 2 9 0 120 2 0 0 0 0 0 2 1 0.998258 11 269 0 118 2 0 0 0 0 120 2 -2.927638 1 1 121412 3 37 1 1 2 3 2.055270 0 0.380000 1.860000 0.381176 0.200000 0.100000 0.360000 0.200000 0.219229 0.200000 0 0.150000 0.280000 IDH2 3418 broad.mit.edu 37 15 90630448 90630448 + Missense_Mutation SNP C C A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr15:90630448C>A ENST00000330062.3 - 7 976 c.863G>T c.(862-864)cGg>cTg p.R288L IDH2_ENST00000539790.1_Missense_Mutation_p.R158L|IDH2_ENST00000540499.2_Missense_Mutation_p.R236L|IDH2_ENST00000559482.1_Missense_Mutation_p.R179L NM_002168.2 NP_002159.2 P48735 IDHP_HUMAN isocitrate dehydrogenase 2 (NADP+), mitochondrial 1109 Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04) BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106) ATCAATGAGCCGGTGCTCATA 0.527000 M GBM OREG0023466 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) Dom yes 15 15q26.1 3418 socitrate dehydrogenase 2 (NADP+), mitochondrial M 0 SO:0001583 missense ENST00000330062.3 0 1 hg19 CCDS10359.1 . . . . . . . . . . C 24.0 4.476860 0.84640 . . ENSG00000182054 ENST00000330062;ENST00000539790;ENST00000540499 T;T;T 0.76316 -1.01;-1.01;-1.01 5.73 5.73 0.89815 Isopropylmalate dehydrogenase-like domain (2); 0.000000 0.85682 D 0.000000 D 0.90995 0.7168 M 0.92077 3.27 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.995;1.0 D 0.92661 0.6141 10 0.87932 D 0 . 17.3795 0.87401 0.0:1.0:0.0:0.0 . 288;288 Q53GL5;P48735 .;IDHP_HUMAN L 288;158;236 ENSP00000331897:R288L;ENSP00000438457:R158L;ENSP00000446147:R236L ENSP00000331897:R288L R - 2 0 IDH2 88431452 1.000000 0.71417 1.000000 0.80357 0.401000 0.30781 7.786000 0.85741 2.709000 0.92574 0.491000 0.48974 CGG TCGA-IB-AAUO-01A-12D-A38G-08 IDH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313426.1 0 0 0 6 235 0 113 1 9.815272e-01 10 281 0 113 2 0 0 0 0 0 2 1 0.964155 6 232 0 113 2 0 0 0 0 113 2 -3.142651 1 1 0 0 1 1 2 3 2.061161 0 0.380000 1.860000 0.381176 0.130000 0.050000 0.280000 0.130000 0.150883 0.130000 0 0.090000 0.210000 WWP2 11060 broad.mit.edu 37 16 69969883 69969883 + Nonsense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr16:69969883G>A ENST00000359154.2 + 18 2071 c.1970G>A c.(1969-1971)tGg>tAg p.W657* MIR140_ENST00000385282.1_RNA|WWP2_ENST00000542271.1_Nonsense_Mutation_p.W541*|WWP2_ENST00000356003.2_Nonsense_Mutation_p.W657*|WWP2_ENST00000568684.1_Nonsense_Mutation_p.W218*|WWP2_ENST00000448661.1_Nonsense_Mutation_p.W657*|WWP2_ENST00000544162.1_3'UTR NM_001270454.1|NM_007014.4 NP_001257383.1|NP_008945.2 O00308 WWP2_HUMAN WW domain containing E3 ubiquitin protein ligase 2 42 TCCATTGTCTGGATCAAGTGA 0.542000 0 SO:0001587 stop_gained ENST00000359154.2 0 1 hg19 CCDS10885.1 . . . . . . . . . . G 39 7.554393 0.98355 . . ENSG00000198373 ENST00000359154;ENST00000545099;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271 . . . 5.7 5.7 0.88788 . 0.105878 0.64402 D 0.000001 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . . 19.843 0.96697 0.0:0.0:1.0:0.0 . . . . X 657;218;657;657;544;541 . . W + 2 0 WWP2 68527384 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 9.869000 0.99810 2.679000 0.91253 0.655000 0.94253 TGG TCGA-IB-AAUO-01A-12D-A38G-08 WWP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268954.1 1 0 0 82 348 0 157 1 9.988206e-01 7 38 0 157 2 1 1 85 333 0 358 2 1 1.000000 82 344 0 152 2 0 0 0 0 157 2 -2.865302 1 1 0 0 1 1 2 3 2.056115 0 0.380000 1.860000 0.381176 0.990000 0.810000 1.000000 1.000000 0.964804 0.990000 1 0.900000 1.000000 ADAMTS18 170692 broad.mit.edu 37 16 77317969 77317969 + Splice_Site SNP C C G TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr16:77317969C>G ENST00000282849.5 - 23 3969 c.e23-1 RP11-538I12.3_ENST00000561672.1_RNA NM_199355.2 NP_955387.1 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 18 118 GATGGATCCTCTAAAATAAGA 0.398000 0 SO:0001630 splice_region_variant ENST00000282849.5 1 1 hg19 CCDS10926.1 . . . . . . . . . . C 19.80 3.894540 0.72639 . . ENSG00000140873 ENST00000282849 . . . 5.93 5.93 0.95920 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.3291 0.94278 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . ADAMTS18 75875470 1.000000 0.71417 0.997000 0.53966 0.888000 0.51559 7.188000 0.77739 2.814000 0.96858 0.655000 0.94253 . TCGA-IB-AAUO-01A-12D-A38G-08 ADAMTS18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269037.1 1 0 0 35 238 0 117 0 0 0 0 117 2 0 0 0 0 0 2 1 1.000000 35 236 0 117 2 0 0 0 0 117 2 -2.842164 1 1 121408 1 30 1 1 2 3 2.056115 0 0.380000 1.860000 0.381176 0.670000 0.480000 0.910000 0.670000 0.686066 0.670000 0 0.570000 0.790000 PRPF8 10594 broad.mit.edu 37 17 1564593 1564593 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:1564593C>T ENST00000572621.1 - 26 4575 c.4310G>A c.(4309-4311)cGt>cAt p.R1437H PRPF8_ENST00000304992.6_Missense_Mutation_p.R1437H Q6P2Q9 PRP8_HUMAN pre-mRNA processing factor 8 77 AGTTCTGACACGCCAGCCCTT 0.483000 0 SO:0001583 missense ENST00000572621.1 1 0 hg19 CCDS11010.1 . . . . . . . . . . c 29.7 5.028120 0.93518 . . ENSG00000174231 ENST00000304992 D 0.85484 -1.99 6.17 6.17 0.99709 . 0.000000 0.85682 D 0.000000 D 0.94971 0.8373 M 0.93283 3.4 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.95043 0.8180 10 0.87932 D 0 . 20.8794 0.99867 0.0:1.0:0.0:0.0 . 1437 Q6P2Q9 PRP8_HUMAN H 1437 ENSP00000304350:R1437H ENSP00000304350:R1437H R - 2 0 PRPF8 1511343 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.792000 0.85828 2.941000 0.99782 0.655000 0.94253 CGT TCGA-IB-AAUO-01A-12D-A38G-08 PRPF8-002 NOVEL alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438412.2 0 0 1 87 473 2 239 0 9.811253e-01 0 47 2 239 3 0 0 0 0 0 2 1 1.000000 87 465 2 239 13 0 0 0 2 239 2 -20.000000 1 0 0 0 1 0 1 1 2.050195 0 0.380000 1.860000 0.378820 0.810000 0.660000 0.970000 0.820000 0.819632 0.810000 0 0.730000 0.900000 SLC47A1 55244 broad.mit.edu 37 17 19458922 19458922 + Missense_Mutation SNP A A G TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:19458922A>G ENST00000270570.4 + 8 744 c.658A>G c.(658-660)Aac>Gac p.N220D SLC47A1_ENST00000395585.1_Missense_Mutation_p.N220D|SNORA59B_ENST00000458926.1_RNA|SLC47A1_ENST00000542886.1_Missense_Mutation_p.K187R|SLC47A1_ENST00000457293.1_Missense_Mutation_p.N220D|SLC47A1_ENST00000575023.1_Intron|SLC47A1_ENST00000436810.2_Missense_Mutation_p.N197D|SLC47A1_ENST00000571335.1_Intron NM_018242.2 NP_060712.2 Q96FL8 S47A1_HUMAN solute carrier family 47 (multidrug and toxin extrusion), member 1 23 all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345) Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877) TGCACTGGCAAACTTGATTTC 0.527000 0 SO:0001583 missense ENST00000270570.4 1 1 hg19 CCDS11209.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 14.34|14.34 2.506537|2.506537 0.44558|0.44558 .|. .|. ENSG00000142494|ENSG00000142494 ENST00000542886|ENST00000436810;ENST00000270570;ENST00000457293;ENST00000395585 .|T;T;T;T .|0.32272 .|1.51;1.46;1.46;1.46 5.34|5.34 5.34|5.34 0.76211|0.76211 .|. .|0.082064 .|0.85682 .|D .|0.000000 T|T 0.50257|0.50257 0.1605|0.1605 H|H 0.95260|0.95260 3.645|3.645 0.32301|0.32301 N|N 0.565074|0.565074 .|B;B;B .|0.33238 .|0.403;0.059;0.04 .|B;B;B .|0.34873 .|0.191;0.067;0.078 T|T 0.69109|0.69109 -0.5232|-0.5232 6|10 0.14656|0.66056 T|D 0.56|0.02 -5.1336|-5.1336 14.5405|14.5405 0.67990|0.67990 1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0 .|. .|197;220;220 .|E7EX57;Q96FL8;Q96FL8-3 .|.;S47A1_HUMAN;. R|D 187|197;220;220;220 .|ENSP00000407155:N197D;ENSP00000270570:N220D;ENSP00000415586:N220D;ENSP00000378951:N220D ENSP00000440435:K187R|ENSP00000270570:N220D K|N +|+ 2|1 0|0 SLC47A1|SLC47A1 19399514|19399514 1.000000|1.000000 0.71417|0.71417 0.729000|0.729000 0.30791|0.30791 0.302000|0.302000 0.27658|0.27658 6.624000|6.624000 0.74243|0.74243 2.036000|2.036000 0.60181|0.60181 0.529000|0.529000 0.55759|0.55759 AAA|AAC TCGA-IB-AAUO-01A-12D-A38G-08 SLC47A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132250.1 1 0 1 71 200 0 134 0 0 0 0 134 2 0 0 0 0 0 2 1 1.000000 69 195 0 130 2 0 0 0 0 134 2 -20.000000 1 1 0 0 1 0 1 1 1.676844 1 0.380000 1.860000 0.234568 0.950000 0.820000 1.000000 0.990000 0.948216 0.950000 1 0.890000 0.990000 KRT24 192666 broad.mit.edu 37 17 38857493 38857493 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:38857493G>A ENST00000264651.2 - 3 810 c.754C>T c.(754-756)Cgg>Tgg p.R252W NM_019016.2 NP_061889.2 Q2M2I5 K1C24_HUMAN keratin 24 29 Breast(137;0.00526) AGGACTTTCCGCAGGCCATTG 0.547000 GBM(61;380 1051 14702 23642 31441) 0 SO:0001583 missense ENST00000264651.2 1 1 hg19 CCDS11372.1 . . . . . . . . . . G 13.59 2.282977 0.40394 . . ENSG00000167916 ENST00000264651 D 0.92545 -3.06 5.82 1.51 0.23008 Filament (1); . . . . D 0.97145 0.9067 H 0.96175 3.78 0.38355 D 0.944446 D 0.89917 1.0 D 0.78314 0.991 D 0.98696 1.0698 9 0.87932 D 0 . 15.8909 0.79296 0.0:0.0:0.5363:0.4637 . 252 Q2M2I5 K1C24_HUMAN W 252 ENSP00000264651:R252W ENSP00000264651:R252W R - 1 2 KRT24 36111019 0.000000 0.05858 0.001000 0.08648 0.108000 0.19459 0.336000 0.19823 0.078000 0.16900 -1.227000 0.01581 CGG TCGA-IB-AAUO-01A-12D-A38G-08 KRT24-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257217.1 0 0 0 11 268 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 0.998221 11 262 0 83 2 0 0 0 0 86 2 -3.186940 1 1 0 0 1 1 2 3 2.100635 0 0.380000 1.860000 0.388138 0.220000 0.110000 1.000000 0.210000 0.269596 0.220000 0 0.160000 0.310000 VPS25 84313 broad.mit.edu 37 17 40925498 40925498 + Missense_Mutation SNP C C A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:40925498C>A ENST00000253794.2 + 1 45 c.5C>A c.(4-6)gCg>gAg p.A2E NM_032353.2 NP_115729.1 Q9BRG1 VPS25_HUMAN vacuolar protein sorting 25 homolog (S. cerevisiae) 5 Breast(137;0.00104) ACTACGATGGCGATGAGTTTC 0.612000 0 SO:0001583 missense ENST00000253794.2 1 1 hg19 CCDS11438.1 . . . . . . . . . . C 17.88 3.496557 0.64186 . . ENSG00000131475 ENST00000253794 T 0.47869 0.83 4.95 4.95 0.65309 . 0.067954 0.56097 D 0.000024 T 0.35799 0.0944 N 0.24115 0.695 0.48341 D 0.999631 B 0.11235 0.004 B 0.11329 0.006 T 0.19811 -1.0294 10 0.62326 D 0.03 -16.8888 13.689 0.62533 0.0:1.0:0.0:0.0 . 2 Q9BRG1 VPS25_HUMAN E 2 ENSP00000253794:A2E ENSP00000253794:A2E A + 2 0 VPS25 38179024 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 2.300000 0.43620 2.292000 0.77174 0.491000 0.48974 GCG TCGA-IB-AAUO-01A-12D-A38G-08 VPS25-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452383.1 1 0 1 89 554 0 251 1 9.999971e-01 27 86 0 251 2 0 0 0 0 0 2 1 1.000000 86 547 0 249 2 0 0 0 0 251 2 -20.000000 1 1 121412 1 27 1 1 2 3 2.100635 0 0.380000 1.860000 0.388138 0.740000 0.600000 1.000000 0.740000 0.756694 0.740000 0 0.660000 0.830000 BRCA1 672 broad.mit.edu 37 17 41245612 41245612 + Missense_Mutation SNP T T C TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:41245612T>C ENST00000357654.3 - 10 2054 c.1936A>G c.(1936-1938)Agc>Ggc p.S646G BRCA1_ENST00000346315.3_Missense_Mutation_p.S646G|BRCA1_ENST00000493795.1_Missense_Mutation_p.S599G|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S646G|BRCA1_ENST00000309486.4_Missense_Mutation_p.S350G|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.S646G|BRCA1_ENST00000491747.2_Intron NM_007294.3 NP_009225.1 P38398 BRCA1_HUMAN breast cancer 1, early onset 120 Breast(137;0.000717) TCTTCACTGCTAGAACAACTA 0.408000 D, Mis, N, F, S ovarian breast, ovarian Homologous recombination Hereditary Breast-Ovarian Cancer, BRCA1 type TCGA Ovarian(2;0.000030) yes Rec yes Hereditary breast/ovarian cancer 17 17q21 672 familial breast/ovarian cancer gene 1 E 0 SO:0001583 missense Familial Cancer Database ENST00000357654.3 1 1 hg19 CCDS11453.1 . . . . . . . . . . T 14.99 2.701528 0.48307 . . ENSG00000012048 ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795;ENST00000470026;ENST00000477152 D;D;D;D;D;D;D;D 0.99032 -3.64;-3.72;-3.69;-3.57;-3.66;-3.78;-3.99;-5.35 5.15 5.15 0.70609 . 0.000000 0.64402 D 0.000002 D 0.99318 0.9761 M 0.93594 3.435 0.32644 N 0.52031 D;D;P;P;D;P 0.89917 1.0;1.0;0.751;0.849;0.984;0.808 D;D;B;P;P;P 0.71414 0.973;0.973;0.318;0.561;0.799;0.614 D 0.99886 1.1122 10 0.72032 D 0.01 -12.2956 9.02 0.36193 0.0:0.0823:0.0:0.9177 . 646;605;646;646;646;646 E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2 .;.;.;.;BRCA1_HUMAN;. G 646;646;646;646;350;646;599;646;620 ENSP00000350283:S646G;ENSP00000326002:S646G;ENSP00000246907:S646G;ENSP00000310938:S350G;ENSP00000418960:S646G;ENSP00000418775:S599G;ENSP00000419274:S646G;ENSP00000419988:S620G ENSP00000310938:S350G S - 1 0 BRCA1 38499138 1.000000 0.71417 0.987000 0.45799 0.844000 0.47949 3.457000 0.53007 2.170000 0.68504 0.459000 0.35465 AGC TCGA-IB-AAUO-01A-12D-A38G-08 BRCA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348798.2 1 0 1 57 514 0 203 0 0 0 1 0 203 2 1 1 28 295 0 240 2 1 1.000000 56 503 0 202 2 0 0 0 0 203 2 -17.872030 1 1 0 0 1 1 2 3 2.100635 0 0.380000 1.860000 0.388138 0.530000 0.400000 1.000000 0.540000 0.564082 0.530000 0 0.460000 0.620000 EFTUD2 9343 broad.mit.edu 37 17 42928694 42928694 + Missense_Mutation SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:42928694G>T ENST00000426333.2 - 28 3164 c.2867C>A c.(2866-2868)cCt>cAt p.P956H EFTUD2_ENST00000591382.1_Missense_Mutation_p.P956H|EFTUD2_ENST00000402521.3_Missense_Mutation_p.P921H|EFTUD2_ENST00000592576.1_Missense_Mutation_p.P946H NM_001142605.1|NM_001258354.1|NM_004247.3 NP_001136077.1|NP_001245283.1|NP_004238.3 Q15029 U5S1_HUMAN elongation factor Tu GTP binding domain containing 2 32 Prostate(33;0.109) CAGCAACATAGGATCATCGAA 0.522000 Ovarian(10;65 485 10258 29980 30707) 0 SO:0001583 missense ENST00000426333.2 1 1 hg19 CCDS11489.1 . . . . . . . . . . G 33 5.195069 0.94960 . . ENSG00000108883 ENST00000426333;ENST00000262414;ENST00000402521 T;T 0.71103 -0.53;-0.54 5.64 5.64 0.86602 . 0.000000 0.85682 D 0.000000 D 0.86293 0.5898 M 0.87758 2.905 0.80722 D 1 D;D 0.71674 0.998;0.998 D;D 0.65773 0.938;0.938 D 0.87972 0.2737 10 0.72032 D 0.01 -13.7718 19.7014 0.96054 0.0:0.0:1.0:0.0 . 946;956 B4DMC0;Q15029 .;U5S1_HUMAN H 956;946;921 ENSP00000392094:P956H;ENSP00000385873:P921H ENSP00000262414:P946H P - 2 0 EFTUD2 40284220 1.000000 0.71417 1.000000 0.80357 0.969000 0.65631 9.277000 0.95755 2.660000 0.90430 0.563000 0.77884 CCT TCGA-IB-AAUO-01A-12D-A38G-08 EFTUD2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448672.1 1 0 1 85 520 0 234 1 1 70 262 0 234 2 0 0 0 0 0 2 1 1.000000 85 504 0 231 2 0 0 0 0 234 2 -3.318829 1 1 0 0 1 1 2 3 2.100635 0 0.380000 1.860000 0.388138 0.750000 0.600000 1.000000 0.750000 0.767346 0.750000 0 0.670000 0.850000 LPO 4025 broad.mit.edu 37 17 56345237 56345237 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:56345237C>T ENST00000262290.4 + 13 2337 c.2021C>T c.(2020-2022)aCc>aTc p.T674I LPO_ENST00000543544.1_Missense_Mutation_p.T615I|LPO_ENST00000582328.1_Missense_Mutation_p.T591I|LPO_ENST00000421678.2_Missense_Mutation_p.T591I NM_006151.2 NP_006142.1 P22079 PERL_HUMAN lactoperoxidase 30 TGTGACAACACCCGCATCACC 0.557000 0 SO:0001583 missense ENST00000262290.4 1 1 hg19 CCDS32689.1 . . . . . . . . . . C 29.3 4.992253 0.93167 . . ENSG00000167419 ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576 T;T;T 0.71817 -0.6;-0.6;-0.6 5.5 5.5 0.81552 . 0.046101 0.85682 D 0.000000 D 0.86994 0.6067 M 0.88640 2.97 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.998;1.0 D 0.89017 0.3432 10 0.72032 D 0.01 -33.3127 17.9786 0.89133 0.0:1.0:0.0:0.0 . 591;674 E7EMJ3;P22079 .;PERL_HUMAN I 674;591;615;419 ENSP00000262290:T674I;ENSP00000400245:T591I;ENSP00000445344:T615I ENSP00000262290:T674I T + 2 0 LPO 53700236 1.000000 0.71417 1.000000 0.80357 0.977000 0.68977 7.267000 0.78462 2.591000 0.87537 0.655000 0.94253 ACC TCGA-IB-AAUO-01A-12D-A38G-08 LPO-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000443961.1 1 0 1 68 284 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 1.000000 66 279 0 147 2 0 0 0 0 148 2 -20.000000 1 1 0 0 1 1 2 3 2.114584 0 0.380000 1.860000 0.389283 0.990000 0.820000 1.000000 1.000000 0.973526 0.990000 1 0.920000 1.000000 WSCD1 23302 broad.mit.edu 37 17 6023840 6023840 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:6023840G>A ENST00000574946.1 + 9 1977 c.1587G>A c.(1585-1587)cgG>cgA p.R529R WSCD1_ENST00000573634.1_Silent_p.R413R|WSCD1_ENST00000539421.1_Silent_p.R529R|WSCD1_ENST00000317744.5_Silent_p.R529R|WSCD1_ENST00000574232.1_Silent_p.R529R Q658N2 WSCD1_HUMAN WSC domain containing 1 35 GCAGCTTCCGGCGGCGCGGCC 0.647000 0 SO:0001819 synonymous_variant ENST00000574946.1 1 1 hg19 CCDS32538.1 TCGA-IB-AAUO-01A-12D-A38G-08 WSCD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438965.4 1 0 1 65 173 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 1.000000 64 166 0 98 2 0 0 0 0 102 2 -20.000000 1 1 0 0 1 0 1 1 1.701426 1 0.380000 1.860000 0.246933 0.990000 0.870000 1.000000 1.000000 0.982674 0.990000 1 0.950000 1.000000 ENPP7 339221 broad.mit.edu 37 17 77709028 77709028 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr17:77709028G>A ENST00000328313.5 + 3 807 c.586G>A c.(586-588)Ggg>Agg p.G196R NM_178543.3 NP_848638.3 ectonucleotide pyrophosphatase/phosphodiesterase 7 34 OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224) ACTCTACTTCGGGGAGCCGGA 0.627000 0 SO:0001583 missense ENST00000328313.5 1 1 hg19 CCDS11763.1 . . . . . . . . . . G 16.64 3.179033 0.57692 . . ENSG00000182156 ENST00000328313 T 0.71698 -0.59 4.75 3.76 0.43208 Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1); 0.058821 0.64402 D 0.000002 T 0.72350 0.3449 L 0.60845 1.875 0.80722 D 1 D 0.58620 0.983 P 0.49451 0.611 T 0.72950 -0.4136 10 0.42905 T 0.14 -33.0178 14.1159 0.65154 0.0:0.0:0.8483:0.1517 . 196 Q6UWV6 ENPP7_HUMAN R 196 ENSP00000332656:G196R ENSP00000332656:G196R G + 1 0 ENPP7 75323623 1.000000 0.71417 0.978000 0.43139 0.346000 0.29079 7.909000 0.87444 0.962000 0.38057 0.591000 0.81541 GGG TCGA-IB-AAUO-01A-12D-A38G-08 ENPP7-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437038.1 0 0 0 5 159 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 0.934398 5 155 0 65 2 0 0 0 0 66 2 -3.522876 1 1 0 0 1 1 2 3 2.114584 0 0.380000 1.860000 0.389283 0.180000 0.060000 1.000000 0.160000 0.243320 0.180000 0 0.110000 0.290000 SERPINB10 5273 broad.mit.edu 37 18 61602106 61602106 + Missense_Mutation SNP A A C TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr18:61602106A>C ENST00000238508.3 + 8 883 c.824A>C c.(823-825)gAg>gCg p.E275A AC009802.1_ENST00000599868.1_Intron NM_005024.1 NP_005015.1 P48595 SPB10_HUMAN serpin peptidase inhibitor, clade B (ovalbumin), member 10 24 Esophageal squamous(42;0.131) AAGCTGAATGAGTGGACCAGT 0.438000 0 SO:0001583 missense ENST00000238508.3 1 1 hg19 CCDS11990.1 . . . . . . . . . . A 4.321 0.059004 0.08339 . . ENSG00000242550 ENST00000238508 D 0.84589 -1.87 5.53 3.07 0.35406 Serpin domain (3); 0.291996 0.37623 N 0.002012 T 0.75649 0.3878 L 0.43701 1.375 0.36153 D 0.847574 B 0.28419 0.211 B 0.28465 0.09 T 0.66976 -0.5787 10 0.12766 T 0.61 . 7.9103 0.29787 0.7907:0.1376:0.0717:0.0 . 275 P48595 SPB10_HUMAN A 275 ENSP00000238508:E275A ENSP00000238508:E275A E + 2 0 SERPINB10 59753086 0.078000 0.21339 0.629000 0.29254 0.699000 0.40488 1.977000 0.40589 0.446000 0.26666 0.533000 0.62120 GAG TCGA-IB-AAUO-01A-12D-A38G-08 SERPINB10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000134012.3 1 0 1 52 239 0 120 0 0 0 0 120 2 0 0 0 0 0 2 1 1.000000 51 232 0 120 2 0 0 0 0 120 2 -20.000000 1 1 0 0 1 0 0 0 2.047911 0 0.380000 1.860000 0.377635 0.930000 0.710000 1.000000 1.000000 0.918748 0.930000 1 0.820000 1.000000 ZNF653 115950 broad.mit.edu 37 19 11596490 11596490 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr19:11596490C>T ENST00000293771.5 - 7 1687 c.1551G>A c.(1549-1551)cgG>cgA p.R517R CTC-398G3.6_ENST00000585656.1_Intron NM_138783.3 NP_620138.2 Q96CK0 ZN653_HUMAN zinc finger protein 653 17 TGATCATGTGCCGCCGCAGGT 0.592000 Pancreas(83;980 1446 4542 6441 43352) 0 SO:0001819 synonymous_variant ENST00000293771.5 0 1 hg19 CCDS12261.1 TCGA-IB-AAUO-01A-12D-A38G-08 ZNF653-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458836.2 0 0 0 6 299 0 133 0 2.334933e-01 0 40 0 133 2 0 0 0 0 0 2 1 0.961623 5 290 0 133 2 0 0 0 0 133 2 -2.527964 1 1 0 0 1 1 2 3 2.086690 0 0.380000 1.860000 0.385835 0.110000 0.040000 1.000000 0.100000 0.153914 0.110000 0 0.070000 0.170000 DAPK3 1613 broad.mit.edu 37 19 3964300 3964300 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr19:3964300C>T ENST00000545797.2 - 4 738 c.495G>A c.(493-495)gcG>gcA p.A165A MIR637_ENST00000385000.1_RNA|DAPK3_ENST00000301264.3_Silent_p.A165A O43293 DAPK3_HUMAN death-associated protein kinase 3 21 Hepatocellular(1079;0.137) CGATCTTGTGCGCGATGCCGA 0.622000 0 SO:0001819 synonymous_variant ENST00000545797.2 0 1 hg19 CCDS12116.1 TCGA-IB-AAUO-01A-12D-A38G-08 DAPK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457817.2 0 0 0 4 170 0 49 0 9.785343e-01 1 325 0 49 2 0 0 0 0 0 2 1 0.884336 4 165 0 46 2 0 0 0 0 49 2 -2.691923 1 1 121392 6 30 1 1 2 3 2.086690 0 0.380000 1.860000 0.385835 0.130000 0.040000 1.000000 0.120000 0.181860 0.130000 0 0.080000 0.230000 PSG3 5671 broad.mit.edu 37 19 43237204 43237204 + Silent SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr19:43237204G>T ENST00000327495.5 - 3 625 c.441C>A c.(439-441)ccC>ccA p.P147P PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Silent_p.P147P NM_021016.3 NP_066296.2 Q16557 PSG3_HUMAN pregnancy specific beta-1-glycoprotein 3 36 Prostate(69;0.00682) TGGAGGGCTTGGGAGTCTCCA 0.522000 0 SO:0001819 synonymous_variant ENST00000327495.5 1 1 hg19 CCDS12611.1 TCGA-IB-AAUO-01A-12D-A38G-08 PSG3-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321423.2 1 0 0 151 699 0 380 0 0 0 0 380 2 0 0 0 0 0 2 1 1.000000 141 676 0 417 2 0 0 0 0 380 2 -2.689206 1 1 0 0 1 1 2 3 2.077877 0 0.380000 1.860000 0.384676 0.940000 0.800000 1.000000 1.000000 0.937454 0.940000 1 0.870000 1.000000 ZNF667 63934 broad.mit.edu 37 19 56953041 56953041 + Silent SNP T T C TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr19:56953041T>C ENST00000504904.3 - 7 2042 c.1323A>G c.(1321-1323)aaA>aaG p.K441K ZNF667_ENST00000292069.6_Silent_p.K441K|ZNF667_ENST00000342634.3_Silent_p.K569K|ZNF667_ENST00000591790.1_3'UTR Q5HYK9 ZN667_HUMAN zinc finger protein 667 38 Colorectal(82;0.000256)|Ovarian(87;0.243) ATTTGAAAGGTTTCTCTTCAG 0.338000 0 SO:0001819 synonymous_variant ENST00000504904.3 1 1 hg19 CCDS12944.1 TCGA-IB-AAUO-01A-12D-A38G-08 ZNF667-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458394.1 0 0 0 12 429 0 164 0 0 0 0 164 2 0 0 0 0 0 2 1 0.999026 12 420 0 163 2 0 0 0 0 164 2 -3.468115 1 1 0 0 1 1 2 3 2.081337 0 0.380000 1.860000 0.384676 0.140000 0.070000 1.000000 0.140000 0.179382 0.140000 0 0.100000 0.200000 MBD3L1 85509 broad.mit.edu 37 19 8953738 8953738 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr19:8953738G>A ENST00000595891.1 + 3 615 c.384G>A c.(382-384)gcG>gcA p.A128A MBD3L1_ENST00000305625.2_Silent_p.A128A Q8WWY6 MB3L1_HUMAN methyl-CpG binding domain protein 3-like 1 12 CTTCAGATGCGGTGGAGATAA 0.522000 0 SO:0001819 synonymous_variant ENST00000595891.1 1 1 hg19 CCDS12209.1 TCGA-IB-AAUO-01A-12D-A38G-08 MBD3L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459973.1 0 0 1 21 122 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 0.999998 21 119 0 44 2 0 0 0 0 44 2 -3.169665 1 1 121412 1 29 1 1 2 3 2.086690 0 0.380000 1.860000 0.385835 0.790000 0.510000 1.000000 1.000000 0.796399 0.790000 0 0.640000 0.980000 MUC16 94025 broad.mit.edu 37 19 9074660 9074660 + Silent SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr19:9074660G>T ENST00000397910.4 - 3 12989 c.12786C>A c.(12784-12786)atC>atA p.I4262I NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TATGGCCTGGGATAGGAGAAT 0.468000 0 SO:0001819 synonymous_variant ENST00000397910.4 0 1 hg19 CCDS54212.1 TCGA-IB-AAUO-01A-12D-A38G-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 0 0 0 7 258 0 114 0 0 0 1 0 114 2 0 0 0 0 0 2 1 0.979368 7 252 0 113 2 0 0 0 0 114 2 -7.963883 1 1 0 0 1 1 2 3 2.086690 0 0.380000 1.860000 0.385835 0.140000 0.060000 1.000000 0.140000 0.190207 0.140000 0 0.090000 0.220000 ADAMTSL4 54507 broad.mit.edu 37 1 150530955 150530955 + Missense_Mutation SNP G G A rs138636937 TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr1:150530955G>A ENST00000369038.2 + 13 2590 c.2389G>A c.(2389-2391)Gtg>Atg p.V797M ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.V820M|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.V797M|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.V797M Q6UY14 ATL4_HUMAN ADAMTS-like 4 32 all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206) TCAGTGCTCCGTGCGGTGCGG 0.647000 0 SO:0001583 missense ENST00000369038.2 1 1 hg19 CCDS955.1 . . . . . . . . . . G 17.96 3.516530 0.64634 0.0 1.16E-4 ENSG00000143382 ENST00000369041;ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038 T;T;T;T 0.64991 -0.13;-0.13;-0.13;-0.13 4.91 4.91 0.64330 . . . . . T 0.79924 0.4530 M 0.90198 3.095 0.58432 D 0.999993 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.85130 0.997;0.996;0.997;0.992 D 0.83613 0.0135 9 0.66056 D 0.02 . 15.633 0.76926 0.0:0.0:1.0:0.0 . 758;820;797;797 B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2 .;.;ATL4_HUMAN;. M 797;797;335;820;797 ENSP00000358037:V797M;ENSP00000271643:V797M;ENSP00000358035:V820M;ENSP00000358034:V797M ENSP00000271643:V797M V + 1 0 ADAMTSL4 148797579 1.000000 0.71417 0.776000 0.31678 0.216000 0.24613 9.034000 0.93747 2.549000 0.85964 0.462000 0.41574 GTG TCGA-IB-AAUO-01A-12D-A38G-08 ADAMTSL4-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084395.4 1 0 1 37 117 0 68 1 9.996079e-01 16 26 0 68 2 0 0 0 0 0 2 1 1.000000 36 109 0 67 2 0 0 0 0 68 2 -20.000000 1 1 121388 7 37 1 0 0 0 2.041409 0 0.380000 1.860000 0.377635 0.990000 0.920000 1.000000 1.000000 0.995769 0.990000 1 0.990000 1.000000 CLCNKB 1188 broad.mit.edu 37 1 16374889 16374889 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr1:16374889C>T ENST00000375679.4 + 6 661 c.550C>T c.(550-552)Cgc>Tgc p.R184C CLCNKB_ENST00000375667.3_5'Flank NM_000085.4 NP_000076.2 P51801 CLCKB_HUMAN chloride channel, voltage-sensitive Kb 21 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) GGGCCGTGTGCGCACCACGAC 0.662000 0 SO:0001583 missense ENST00000375679.4 0 1 hg19 CCDS168.1 . . . . . . . . . . c 18.37 3.608384 0.66558 . . ENSG00000184908 ENST00000375679;ENST00000331579 D 0.92911 -3.13 4.68 3.69 0.42338 Chloride channel, core (2); 0.349083 0.30649 N 0.009166 D 0.86456 0.5937 L 0.38649 1.16 0.80722 D 1 B 0.20052 0.041 B 0.21151 0.033 D 0.84245 0.0474 10 0.87932 D 0 . 8.4362 0.32789 0.2762:0.5817:0.1421:0.0 . 184 P51801 CLCKB_HUMAN C 184 ENSP00000364831:R184C ENSP00000332055:R184C R + 1 0 CLCNKB 16247476 1.000000 0.71417 0.627000 0.29227 0.928000 0.56348 2.311000 0.43717 2.139000 0.66308 0.655000 0.94253 CGC TCGA-IB-AAUO-01A-12D-A38G-08 CLCNKB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026331.1 0 0 0 4 143 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 0.883130 4 138 0 96 2 0 0 0 0 84 2 -2.811024 1 1 0 0 1 0 1 1 1.708494 1 0.380000 1.860000 0.236359 0.120000 0.040000 0.270000 0.110000 0.140263 0.120000 0 0.070000 0.200000 TDRD5 163589 broad.mit.edu 37 1 179604922 179604922 + Missense_Mutation SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr1:179604922G>T ENST00000367614.1 + 9 1779 c.1420G>T c.(1420-1422)Ggg>Tgg p.G474W TDRD5_ENST00000294848.8_Missense_Mutation_p.G474W|TDRD5_ENST00000444136.1_Missense_Mutation_p.G474W NM_001199091.1 NP_001186020.1 Q8NAT2 TDRD5_HUMAN tudor domain containing 5 77 TTCCCTCATAGGGGTCTTTGT 0.463000 0 SO:0001583 missense ENST00000367614.1 1 1 hg19 CCDS1332.1 . . . . . . . . . . G 20.9 4.058568 0.76074 . . ENSG00000162782 ENST00000367614;ENST00000294848;ENST00000444136 T;T;T 0.09723 2.95;2.95;2.95 4.94 4.94 0.65067 Maternal tudor protein (1); 0.299142 0.33272 N 0.005083 T 0.28797 0.0714 L 0.52011 1.625 0.46203 D 0.998927 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.01309 -1.1389 10 0.72032 D 0.01 -19.4684 16.7233 0.85415 0.0:0.0:1.0:0.0 . 474;474 Q8NAT2-1;Q8NAT2 .;TDRD5_HUMAN W 474 ENSP00000356586:G474W;ENSP00000294848:G474W;ENSP00000406052:G474W ENSP00000294848:G474W G + 1 0 TDRD5 177871545 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 6.639000 0.74314 2.279000 0.76181 0.585000 0.79938 GGG TCGA-IB-AAUO-01A-12D-A38G-08 TDRD5-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000085295.1 1 0 1 33 247 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 1.000000 32 242 0 107 2 0 0 0 0 107 2 -2.879535 1 1 0 0 1 1 2 3 2.057212 0 0.380000 1.860000 0.381176 0.620000 0.440000 0.840000 0.620000 0.632074 0.620000 0 0.520000 0.730000 PLXNA2 5362 broad.mit.edu 37 1 208276511 208276511 + Missense_Mutation SNP A A G TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr1:208276511A>G ENST00000367033.3 - 5 2345 c.1588T>C c.(1588-1590)Tgg>Cgg p.W530R NM_025179.3 NP_079455.3 O75051 PLXA2_HUMAN plexin A2 80 AGGGCACACCAGCCACAGTGA 0.547000 0 SO:0001583 missense ENST00000367033.3 1 1 hg19 CCDS31013.1 . . . . . . . . . . A 21.9 4.220286 0.79464 . . ENSG00000076356 ENST00000367033 D 0.92249 -3.0 4.8 4.8 0.61643 . 0.000000 0.85682 D 0.000000 D 0.97263 0.9105 H 0.95917 3.74 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 D 0.98485 1.0607 10 0.87932 D 0 . 14.5136 0.67804 1.0:0.0:0.0:0.0 . 530 O75051 PLXA2_HUMAN R 530 ENSP00000356000:W530R ENSP00000356000:W530R W - 1 0 PLXNA2 206343134 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 8.798000 0.91888 2.025000 0.59659 0.533000 0.62120 TGG TCGA-IB-AAUO-01A-12D-A38G-08 PLXNA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000088932.6 1 0 1 18 77 0 41 1 6.513763e-01 6 5 0 41 2 0 0 0 0 0 2 1 0.999988 17 75 0 41 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 1 2 3 2.063294 0 0.380000 1.860000 0.381176 0.990000 0.630000 1.000000 1.000000 0.925065 0.990000 1 0.800000 1.000000 EXTL1 2134 broad.mit.edu 37 1 26359784 26359784 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr1:26359784G>A ENST00000374280.3 + 8 2363 c.1496G>A c.(1495-1497)cGc>cAc p.R499H NM_004455.2 NP_004446.2 Q92935 EXTL1_HUMAN exostosin-like glycosyltransferase 1 23 Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298) CTCGATGCCCGCAGCAGTCTT 0.597000 0 SO:0001583 missense ENST00000374280.3 0 1 hg19 CCDS271.1 . . . . . . . . . . G 14.20 2.464549 0.43736 2.27E-4 0.0 ENSG00000158008 ENST00000374280 T 0.75704 -0.96 5.06 3.93 0.45458 EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1); 0.323633 0.33092 N 0.005297 T 0.36496 0.0969 N 0.00237 -1.79 0.27362 N 0.955932 B 0.09022 0.002 B 0.09377 0.004 T 0.37686 -0.9695 10 0.51188 T 0.08 -12.2433 7.0466 0.25048 0.8869:0.0:0.1131:0.0 . 499 Q92935 EXTL1_HUMAN H 499 ENSP00000363398:R499H ENSP00000363398:R499H R + 2 0 EXTL1 26232371 1.000000 0.71417 0.991000 0.47740 0.940000 0.58332 6.140000 0.71738 0.950000 0.37743 0.561000 0.74099 CGC TCGA-IB-AAUO-01A-12D-A38G-08 EXTL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000019749.1 0 0 0 4 157 0 87 0 3.271530e-03 0 3 0 87 2 0 0 0 0 0 2 1 0.889902 4 156 0 87 2 0 0 0 0 87 2 -3.108916 1 1 121412 3 38 1 0 1 1 1.713541 1 0.380000 1.860000 0.234568 0.110000 0.030000 0.250000 0.100000 0.128130 0.110000 0 0.060000 0.180000 OPRD1 4985 broad.mit.edu 37 1 29185499 29185499 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr1:29185499C>T ENST00000234961.2 + 2 503 c.261C>T c.(259-261)taC>taT p.Y87Y NM_000911.3 NP_000902.3 P41143 OPRD_HUMAN opioid receptor, delta 1 15 Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123) Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193) CCAACATCTACATCTTCAACC 0.493000 0 SO:0001819 synonymous_variant ENST00000234961.2 0 1 hg19 CCDS329.1 TCGA-IB-AAUO-01A-12D-A38G-08 OPRD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000010330.1 0 0 0 9 405 0 189 0 0 0 0 189 2 0 0 0 0 0 2 1 0.993805 9 397 0 186 2 0 0 0 0 189 2 -3.115331 1 1 0 0 1 0 1 1 1.713541 1 0.380000 1.860000 0.234568 0.090000 0.040000 0.170000 0.090000 0.101666 0.090000 0 0.060000 0.130000 PATZ1 23598 broad.mit.edu 37 22 31740473 31740473 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr22:31740473C>T ENST00000266269.5 - 1 1745 c.1116G>A c.(1114-1116)cgG>cgA p.R372R PATZ1_ENST00000215919.3_Silent_p.R372R|AC005003.1_ENST00000504184.2_5'Flank|PATZ1_ENST00000405309.3_Silent_p.R372R|PATZ1_ENST00000351933.4_Silent_p.R372R NM_014323.2 NP_055138.2 Q9HBE1 PATZ1_HUMAN POZ (BTB) and AT hook containing zinc finger 1 p.R372R(2) EWSR1/PATZ1(2) 12 ACAGCTTGTGCCGGTTAAGAT 0.582000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000266269.5 0 1 hg19 CCDS13894.1 TCGA-IB-AAUO-01A-12D-A38G-08 PATZ1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321932.1 0 0 0 5 317 0 143 0 3.387003e-01 0 66 0 143 2 0 0 0 0 0 2 1 0.935946 5 313 0 141 2 0 0 0 0 143 2 -1.974263 0 1 121412 1 32 1 0 1 1 1.836368 1 0.380000 1.860000 0.295695 0.070000 0.020000 0.160000 0.070000 0.085161 0.070000 0 0.040000 0.120000 IL1RL2 8808 broad.mit.edu 37 2 102851439 102851439 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:102851439C>T ENST00000264257.2 + 11 1506 c.1380C>T c.(1378-1380)ggC>ggT p.G460G IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000441515.2_Silent_p.G342G|IL1RL2_ENST00000539491.1_Silent_p.G460G NM_003854.2 NP_003845.2 Q9HB29 ILRL2_HUMAN interleukin 1 receptor-like 2 26 TGGGCTTTGGCCTGTTGAAGA 0.488000 0 SO:0001819 synonymous_variant ENST00000264257.2 0 1 hg19 CCDS2056.1 TCGA-IB-AAUO-01A-12D-A38G-08 IL1RL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253290.1 0 0 0 5 251 0 108 0 3.564281e-03 0 4 0 108 2 0 0 0 0 0 2 1 0.934211 5 246 0 107 2 0 0 0 0 108 2 -2.633924 1 1 0 0 1 1 2 3 2.055032 0 0.380000 1.860000 0.381176 0.110000 0.030000 0.240000 0.100000 0.121860 0.110000 0 0.060000 0.170000 GREB1 9687 broad.mit.edu 37 2 11780565 11780565 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:11780565G>A ENST00000381486.2 + 33 6135 c.5835G>A c.(5833-5835)acG>acA p.T1945T GREB1_ENST00000234142.5_Silent_p.T1945T|GREB1_ENST00000396123.1_Silent_p.T943T NM_014668.3 NP_055483.2 Q4ZG55 GREB1_HUMAN growth regulation by estrogen in breast cancer 1 30 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) TTTTTCTGACGGGACGACACA 0.607000 Ovarian(39;850 945 2785 23371 33093) 0 SO:0001819 synonymous_variant ENST00000381486.2 1 1 hg19 CCDS42655.1 TCGA-IB-AAUO-01A-12D-A38G-08 GREB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000280490.1 1 0 0 29 301 0 125 0 0 0 1 0 125 2 0 0 0 0 0 2 1 1.000000 29 296 0 125 2 0 0 0 0 125 2 -2.429492 0 1 120886 14 45 1 0 1 1 2.052975 0 0.380000 1.860000 0.375252 0.450000 0.310000 0.630000 0.450000 0.469598 0.450000 0 0.380000 0.550000 ZDBF2 57683 broad.mit.edu 37 2 207171284 207171284 + Missense_Mutation SNP G G T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:207171284G>T ENST00000374423.3 + 5 2418 c.2032G>T c.(2032-2034)Gac>Tac p.D678Y NM_020923.1 NP_065974.1 Q9HCK1 ZDBF2_HUMAN zinc finger, DBF-type containing 2 95 TCAATTAGCTGACCAGTCTCA 0.428000 0 SO:0001583 missense ENST00000374423.3 1 1 hg19 CCDS46501.1 . . . . . . . . . . G 13.61 2.287181 0.40494 . . ENSG00000204186 ENST00000374423 T 0.54675 0.56 4.24 3.33 0.38152 . 0.943578 0.08666 N 0.911684 T 0.57330 0.2046 L 0.34521 1.04 0.09310 N 1 D 0.69078 0.997 P 0.58577 0.841 T 0.47156 -0.9139 10 0.66056 D 0.02 . 9.9562 0.41668 0.0:0.2064:0.7936:0.0 . 678 Q9HCK1 ZDBF2_HUMAN Y 678 ENSP00000363545:D678Y ENSP00000363545:D678Y D + 1 0 ZDBF2 206879529 0.012000 0.17670 0.014000 0.15608 0.007000 0.05969 1.571000 0.36450 1.318000 0.45170 0.655000 0.94253 GAC TCGA-IB-AAUO-01A-12D-A38G-08 ZDBF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336458.1 1 0 1 30 158 0 54 0 2.733535e-02 0 2 0 54 2 0 0 0 0 0 2 1 1.000000 29 155 0 53 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.055032 0 0.380000 1.860000 0.381176 0.840000 0.590000 1.000000 1.000000 0.841017 0.840000 0 0.700000 0.990000 ASB18 401036 broad.mit.edu 37 2 237172977 237172977 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:237172977C>T ENST00000409749.3 - 1 11 c.12G>A c.(10-12)tcG>tcA p.S4S AC079135.1_ENST00000415226.1_RNA NM_212556.2 NP_997721.2 Q6ZVZ8 ASB18_HUMAN ankyrin repeat and SOCS box containing 18 6 all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815) GAAGGTAATCCGAGTTGGACA 0.493000 0 SO:0001819 synonymous_variant ENST00000409749.3 0 1 hg19 CCDS46548.1 TCGA-IB-AAUO-01A-12D-A38G-08 ASB18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329436.1 0 0 0 5 215 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 0.936751 5 213 0 83 2 0 0 0 0 83 2 -2.769569 1 1 120908 1 37 1 1 2 3 2.084111 0 0.380000 1.860000 0.385835 0.130000 0.040000 1.000000 0.120000 0.175124 0.130000 0 0.080000 0.210000 PREPL 9581 broad.mit.edu 37 2 44586652 44586652 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:44586652C>T ENST00000409936.1 - 2 640 c.203G>A c.(202-204)cGg>cAg p.R68Q CAMKMT_ENST00000403853.3_5'Flank|PREPL_ENST00000410081.1_Missense_Mutation_p.R68Q|PREPL_ENST00000540817.1_Intron|PREPL_ENST00000260648.6_Missense_Mutation_p.R68Q|PREPL_ENST00000541738.1_Intron|CAMKMT_ENST00000402247.1_5'Flank|PREPL_ENST00000378520.3_Missense_Mutation_p.R68Q|CAMKMT_ENST00000407131.1_5'Flank|PREPL_ENST00000409411.1_Intron|PREPL_ENST00000409957.1_Intron|PREPL_ENST00000409272.1_Missense_Mutation_p.R68Q|PREPL_ENST00000378511.3_Missense_Mutation_p.R68Q|CAMKMT_ENST00000378494.3_5'Flank NM_001171606.1 NP_001165077.1 Q4J6C6 PPCEL_HUMAN prolyl endopeptidase-like 33 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) TGAGAAGCTCCGACTTGGGAT 0.308000 0 SO:0001583 missense ENST00000409936.1 1 1 hg19 CCDS33190.1 . . . . . . . . . . C 23.3 4.400937 0.83120 . . ENSG00000138078 ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511;ENST00000438314 . . . 5.27 4.38 0.52667 . 0.251803 0.28409 N 0.015459 T 0.48370 0.1496 N 0.08118 0 0.80722 D 1 D;D;D 0.89917 0.999;0.999;1.0 D;D;P 0.77557 0.975;0.99;0.846 T 0.42085 -0.9472 9 0.30854 T 0.27 -13.6207 10.0499 0.42210 0.0:0.907:0.0:0.093 . 68;68;68 Q4J6C6-3;Q4J6C6-2;Q4J6C6 .;.;PPCEL_HUMAN Q 68 . ENSP00000260648:R68Q R - 2 0 PREPL 44440156 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 1.885000 0.39678 2.735000 0.93741 0.655000 0.94253 CGG TCGA-IB-AAUO-01A-12D-A38G-08 PREPL-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000327900.1 1 0 1 110 575 0 254 0 4.378813e-01 0 9 0 254 2 0 0 0 0 0 2 1 1.000000 108 565 0 253 2 0 0 0 0 254 2 -2.808899 1 1 121412 1 34 1 1 2 3 2.055032 0 0.380000 1.860000 0.381176 0.840000 0.700000 1.000000 0.840000 0.849203 0.840000 0 0.770000 0.920000 BCL11A 53335 broad.mit.edu 37 2 60688929 60688929 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:60688929G>A ENST00000335712.6 - 4 1345 c.1118C>T c.(1117-1119)cCg>cTg p.P373L BCL11A_ENST00000538214.1_Missense_Mutation_p.P339L|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.P339L|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.P373L NM_022893.3 NP_075044.2 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A (zinc finger protein) 59 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) GGACTTGACCGGGGGCTGGGA 0.627000 T IGH@ B-CLL Dom yes 2 2p13 53335 B-cell CLL/lymphoma 11A L 0 SO:0001583 missense ENST00000335712.6 1 1 hg19 CCDS1862.1 . . . . . . . . . . G 11.92 1.783620 0.31593 . . ENSG00000119866 ENST00000356842;ENST00000378117;ENST00000538214;ENST00000335712;ENST00000358510 T;T;T;T 0.10288 2.89;3.11;3.12;3.03 5.74 4.84 0.62591 . 0.186906 0.46442 D 0.000293 T 0.16471 0.0396 M 0.61703 1.905 0.80722 D 1 B;D;B;P 0.56746 0.334;0.977;0.226;0.652 B;B;B;B 0.43194 0.063;0.411;0.017;0.044 T 0.02126 -1.1209 10 0.54805 T 0.06 -1.7699 16.5742 0.84633 0.0:0.1305:0.8695:0.0 . 339;339;373;373 F5H2Y4;Q9H165-6;Q9H165;D9YZV9 .;.;BC11A_HUMAN;. L 373;409;339;373;339 ENSP00000349300:P373L;ENSP00000438303:P339L;ENSP00000338774:P373L;ENSP00000351307:P339L ENSP00000338774:P373L P - 2 0 BCL11A 60542433 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.309000 0.65774 1.392000 0.46585 0.655000 0.94253 CCG TCGA-IB-AAUO-01A-12D-A38G-08 BCL11A-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000251579.2 1 0 1 47 222 1 99 0 0 0 1 99 2 0 0 0 0 0 2 1 1.000000 44 208 1 96 11 0 0 0 1 99 2 -2.492123 0 1 121362 1 32 1 1 2 3 2.055032 0 0.380000 1.860000 0.381176 0.910000 0.690000 1.000000 1.000000 0.906756 0.910000 1 0.800000 1.000000 DYSF 8291 broad.mit.edu 37 2 71742844 71742844 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:71742844C>T ENST00000258104.3 + 7 1032 c.755C>T c.(754-756)aCg>aTg p.T252M DYSF_ENST00000429174.2_Missense_Mutation_p.T252M|DYSF_ENST00000410020.3_Missense_Mutation_p.T284M|DYSF_ENST00000413539.2_Missense_Mutation_p.T283M|DYSF_ENST00000409762.1_Missense_Mutation_p.T283M|DYSF_ENST00000409651.1_Missense_Mutation_p.T284M|DYSF_ENST00000409744.1_Missense_Mutation_p.T253M|DYSF_ENST00000409582.3_Missense_Mutation_p.T283M|DYSF_ENST00000409366.1_Missense_Mutation_p.T253M|DYSF_ENST00000394120.2_Missense_Mutation_p.T253M|DYSF_ENST00000410041.1_Missense_Mutation_p.T284M NM_001130976.1|NM_003494.3 NP_001124448.1|NP_003485.1 O75923 DYSF_HUMAN dysferlin 111 ACCAAGCGGACGCGGATCCAC 0.612000 0 SO:0001583 missense ENST00000258104.3 1 1 hg19 CCDS1918.1 . . . . . . . . . . C 19.83 3.899610 0.72754 . . ENSG00000135636 ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041 D;D;D;D;D;D;D;D;D;D;D 0.94966 -3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57 5.0 5.0 0.66597 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.000000 0.85682 D 0.000000 D 0.98086 0.9369 H 0.95470 3.675 0.53688 D 0.99997 D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0 D 0.99274 1.0894 10 0.87932 D 0 -14.9292 16.1703 0.81808 0.0:1.0:0.0:0.0 . 284;284;253;253;284;253;283;252;283;283;252;252;253;252 O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923 .;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN M 283;283;283;252;252;284;253;253;253;284;284 ENSP00000407046:T283M;ENSP00000387137:T283M;ENSP00000386547:T283M;ENSP00000398305:T252M;ENSP00000258104:T252M;ENSP00000386683:T284M;ENSP00000377678:T253M;ENSP00000386285:T253M;ENSP00000386512:T253M;ENSP00000386881:T284M;ENSP00000386617:T284M ENSP00000258104:T252M T + 2 0 DYSF 71596352 1.000000 0.71417 0.934000 0.37439 0.374000 0.29953 7.351000 0.79395 2.475000 0.83589 0.549000 0.68633 ACG TCGA-IB-AAUO-01A-12D-A38G-08 DYSF-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251970.3 1 0 0 11 242 0 112 0 1.331951e-02 0 4 0 112 2 0 0 0 0 0 2 1 0.998292 11 238 0 111 2 0 0 0 0 112 2 -12.760410 1 1 0 0 1 1 2 3 2.055032 0 0.380000 1.860000 0.381176 0.230000 0.120000 0.400000 0.220000 0.246563 0.230000 0 0.170000 0.320000 CTNNA2 1496 broad.mit.edu 37 2 79971679 79971679 + Missense_Mutation SNP T T G TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr2:79971679T>G ENST00000402739.4 + 2 274 c.269T>G c.(268-270)gTg>gGg p.V90G CTNNA2_ENST00000496558.1_Missense_Mutation_p.V90G|CTNNA2_ENST00000466387.1_Missense_Mutation_p.V90G|CTNNA2_ENST00000361291.4_Missense_Mutation_p.V124G|CTNNA2_ENST00000540488.1_Missense_Mutation_p.V90G|CTNNA2_ENST00000541047.1_Missense_Mutation_p.V90G NM_001282597.1 NP_001269526.1 P26232 CTNA2_HUMAN catenin (cadherin-associated protein), alpha 2 78 GAAGAGTTGGTGGCTGCTGTA 0.443000 0 SO:0001583 missense ENST00000402739.4 0 1 hg19 . . . . . . . . . . T 16.78 3.219037 0.58560 . . ENSG00000066032 ENST00000466387;ENST00000496558;ENST00000409971;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488 T;T;T;T;T;T;T 0.37915 1.17;1.17;1.17;1.17;1.17;1.17;1.17 5.5 5.5 0.81552 . 0.140504 0.47852 D 0.000201 T 0.19406 0.0466 N 0.08118 0 0.80722 D 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.06405 0.002;0.001;0.001 T 0.10497 -1.0627 10 0.15066 T 0.55 . 13.5514 0.61734 0.0:0.0:0.0:1.0 . 90;90;90 P26232;P26232-3;P26232-2 CTNA2_HUMAN;.;. G 90;90;90;124;90;90;90 ENSP00000418191:V90G;ENSP00000419295:V90G;ENSP00000387073:V90G;ENSP00000355398:V124G;ENSP00000384638:V90G;ENSP00000444675:V90G;ENSP00000441705:V90G ENSP00000355398:V124G V + 2 0 CTNNA2 79825187 1.000000 0.71417 0.964000 0.40570 0.951000 0.60555 6.280000 0.72626 2.091000 0.63221 0.383000 0.25322 GTG TCGA-IB-AAUO-01A-12D-A38G-08 CTNNA2-003 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000328511.4 0 0 0 5 162 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 0.932324 5 156 0 71 2 0 0 0 0 71 2 -7.333867 1 1 0 0 1 1 2 3 2.055032 0 0.380000 1.860000 0.381176 0.170000 0.060000 0.360000 0.160000 0.185404 0.170000 0 0.100000 0.260000 PHLDB2 90102 broad.mit.edu 37 3 111603672 111603672 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr3:111603672G>A ENST00000431670.2 + 2 1159 c.748G>A c.(748-750)Gga>Aga p.G250R PHLDB2_ENST00000481953.1_Missense_Mutation_p.G250R|PHLDB2_ENST00000393923.3_Missense_Mutation_p.G277R|PHLDB2_ENST00000393925.3_Missense_Mutation_p.G250R|PHLDB2_ENST00000478922.1_Missense_Mutation_p.G250R|PHLDB2_ENST00000477695.1_Missense_Mutation_p.G250R|PHLDB2_ENST00000412622.1_Missense_Mutation_p.G250R NM_001134438.1 NP_001127910.1 Q86SQ0 PHLB2_HUMAN pleckstrin homology-like domain, family B, member 2 55 GAGTCACATGGGAGCCTACAG 0.507000 0 SO:0001583 missense ENST00000431670.2 1 1 hg19 CCDS46886.1 . . . . . . . . . . G 19.37 3.815029 0.70912 . . ENSG00000144824 ENST00000359729;ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000478922;ENST00000477695;ENST00000393925;ENST00000481953 T;T;T;T;T;T 0.57273 0.44;0.62;0.46;0.41;0.62;0.46 5.4 5.4 0.78164 . 0.241259 0.41823 D 0.000803 T 0.67988 0.2952 L 0.51422 1.61 0.48185 D 0.999601 D;D;D;D;D 0.89917 0.999;1.0;1.0;0.998;1.0 D;D;D;D;D 0.97110 0.942;1.0;1.0;0.962;0.995 T 0.69320 -0.5176 10 0.72032 D 0.01 . 16.4564 0.84019 0.0:0.0:1.0:0.0 . 250;250;250;250;277 Q86SQ0;G5E9V3;E9PDY7;Q86SQ0-2;Q86SQ0-3 PHLB2_HUMAN;.;.;.;. R 277;277;250;250;250;250;250;250;250 ENSP00000377500:G277R;ENSP00000405405:G250R;ENSP00000405292:G250R;ENSP00000418296:G250R;ENSP00000377502:G250R;ENSP00000418319:G250R ENSP00000352764:G277R G + 1 0 PHLDB2 113086362 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.291000 0.65667 2.703000 0.92315 0.655000 0.94253 GGA TCGA-IB-AAUO-01A-12D-A38G-08 PHLDB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354337.1 1 0 1 152 269 0 113 1 9.227752e-01 5 5 0 113 2 0 0 0 0 0 2 1 1.000000 150 265 0 112 2 0 0 0 0 113 2 -17.212780 1 1 0 0 1 1 3 4 2.744515 1 0.380000 1.860000 0.530018 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MBD4 8930 broad.mit.edu 37 3 129151965 129151965 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr3:129151965C>T ENST00000249910.1 - 6 1712 c.1537G>A c.(1537-1539)Gca>Aca p.A513T MBD4_ENST00000507208.1_Missense_Mutation_p.A513T|MBD4_ENST00000429544.2_Missense_Mutation_p.A507T|MBD4_ENST00000503197.1_Missense_Mutation_p.A513T|MBD4_ENST00000509587.1_5'Flank|MBD4_ENST00000393278.2_Missense_Mutation_p.A195T NM_003925.1 NP_003916.1 O95243 MBD4_HUMAN methyl-CpG binding domain protein 4 22 ATGGTTTTTGCCCGAAGATCG 0.403000 Base excision repair (BER), DNA glycosylases 0 SO:0001583 missense ENST00000249910.1 0 1 hg19 CCDS3058.1 . . . . . . . . . . C 33 5.273592 0.95459 . . ENSG00000129071 ENST00000429544;ENST00000249910;ENST00000503197;ENST00000393278;ENST00000507208 T;T;T;T;T 0.62498 0.02;0.02;0.02;0.02;0.02 6.14 6.14 0.99180 HhH-GPD domain (1);DNA glycosylase (2); 0.000000 0.85682 D 0.000000 T 0.81293 0.4792 M 0.79123 2.44 0.80722 D 1 D;D;D;D;D 0.89917 0.996;0.994;0.995;1.0;0.998 D;D;D;D;D 0.91635 0.968;0.945;0.945;0.999;0.98 T 0.80353 -0.1418 10 0.56958 D 0.05 -21.0242 20.4701 0.99162 0.0:1.0:0.0:0.0 . 513;195;507;513;513 E9PEE4;Q2MD36;O95243-2;O95243-3;O95243 .;.;.;.;MBD4_HUMAN T 507;513;513;195;513 ENSP00000394080:A507T;ENSP00000249910:A513T;ENSP00000424873:A513T;ENSP00000376959:A195T;ENSP00000422327:A513T ENSP00000249910:A513T A - 1 0 MBD4 130634655 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 7.291000 0.78721 2.937000 0.99478 0.650000 0.86243 GCA TCGA-IB-AAUO-01A-12D-A38G-08 MBD4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000355529.1 0 0 0 7 567 0 153 0 7.789249e-01 1 229 0 153 2 0 0 0 0 0 2 1 0.979063 7 554 0 152 2 0 0 0 0 153 2 -2.231298 0 1 0 0 1 1 3 4 2.765071 1 0.380000 1.860000 0.531368 0.090000 0.020000 1.000000 0.080000 0.203991 0.090000 0 0.050000 0.160000 TRIM42 287015 broad.mit.edu 37 3 140407107 140407107 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr3:140407107G>A ENST00000286349.3 + 3 1774 c.1583G>A c.(1582-1584)gGc>gAc p.G528D NM_152616.4 NP_689829.3 Q8IWZ5 TRI42_HUMAN tripartite motif containing 42 69 CACAGCCTCGGCAACCAGCAC 0.577000 0 SO:0001583 missense ENST00000286349.3 0 1 hg19 CCDS3113.1 . . . . . . . . . . G 6.665 0.491250 0.12702 . . ENSG00000155890 ENST00000286349 T 0.36699 1.24 5.52 -4.17 0.03857 . 0.998540 0.08106 N 0.996959 T 0.15998 0.0385 N 0.24115 0.695 0.09310 N 0.999991 B 0.02656 0.0 B 0.04013 0.001 T 0.30736 -0.9968 10 0.10111 T 0.7 -11.6821 1.9929 0.03450 0.3788:0.1671:0.3411:0.113 . 528 Q8IWZ5 TRI42_HUMAN D 528 ENSP00000286349:G528D ENSP00000286349:G528D G + 2 0 TRIM42 141889797 0.000000 0.05858 0.007000 0.13788 0.846000 0.48090 -0.386000 0.07370 -0.646000 0.05452 0.655000 0.94253 GGC TCGA-IB-AAUO-01A-12D-A38G-08 TRIM42-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359531.2 0 0 0 6 429 1 157 0 0 0 1 157 2 1 9.996380e-01 19 1294 0 892 2 0 0.156637 6 424 1 156 11 0 0 0 1 157 2 -2.975212 1 1 0 0 1 1 3 4 2.765071 1 0.380000 1.860000 0.531368 0.100000 0.030000 1.000000 0.110000 0.216902 0.100000 0 0.060000 0.190000 WDR48 57599 broad.mit.edu 37 3 39118643 39118643 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr3:39118643G>A ENST00000302313.5 + 9 939 c.911G>A c.(910-912)aGa>aAa p.R304K WDR48_ENST00000418020.1_5'UTR|WDR48_ENST00000396258.3_Missense_Mutation_p.R222K|WDR48_ENST00000544962.1_Missense_Mutation_p.R96K NM_020839.2 NP_065890.1 Q8TAF3 WDR48_HUMAN WD repeat domain 48 15 GAGCTTGATAGATCAGCTGAT 0.373000 0 SO:0001583 missense ENST00000302313.5 1 1 hg19 CCDS33738.1 . . . . . . . . . . G 15.83 2.948961 0.53186 . . ENSG00000114742 ENST00000302313;ENST00000544962;ENST00000396258 T;D;T 0.87809 2.28;-2.3;2.25 6.16 6.16 0.99307 WD40 repeat-like-containing domain (1); 0.000000 0.85682 D 0.000000 D 0.88489 0.6450 N 0.22421 0.69 0.80722 D 1 P;B;B;B 0.47910 0.902;0.046;0.003;0.024 P;B;B;B 0.60173 0.87;0.007;0.001;0.002 D 0.84664 0.0708 10 0.22706 T 0.39 -0.2443 20.8598 0.99761 0.0:0.0:1.0:0.0 . 96;222;295;304 Q8TAF3-5;Q8TAF3-4;Q8TAF3-3;Q8TAF3 .;.;.;WDR48_HUMAN K 304;96;222 ENSP00000307491:R304K;ENSP00000445187:R96K;ENSP00000379557:R222K ENSP00000307491:R304K R + 2 0 WDR48 39093647 1.000000 0.71417 0.998000 0.56505 0.985000 0.73830 9.771000 0.98977 2.937000 0.99478 0.650000 0.86243 AGA TCGA-IB-AAUO-01A-12D-A38G-08 WDR48-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342529.1 0 0 1 60 324 1 122 1 5.352718e-01 4 7 1 122 2 0 0 0 0 0 2 1 1.000000 59 318 1 122 12 0 0 0 1 122 2 -20.000000 1 1 0 0 1 1 2 3 2.099036 0 0.380000 1.860000 0.388138 0.830000 0.650000 1.000000 1.000000 0.845776 0.830000 0 0.730000 0.960000 FAT1 2195 broad.mit.edu 37 4 187510153 187510153 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr4:187510153C>T ENST00000441802.2 - 27 13569 c.13360G>A c.(13360-13362)Gaa>Aaa p.E4454K NM_005245.3 NP_005236.2 Q14517 FAT1_HUMAN FAT atypical cadherin 1 p.E4454K(1) 228 TTGCTGAATTCGGGCGGTAAC 0.527000 HNSCC(5;0.00058) Colon(197;1040 2055 4143 4984 49344) 1 Substitution - Missense(1) SO:0001583 missense ENST00000441802.2 1 1 hg19 CCDS47177.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 18.74|18.74 3.688735|3.688735 0.68271|0.68271 0.0|0.0 1.21E-4|1.21E-4 ENSG00000083857|ENSG00000083857 ENST00000441802;ENST00000260147|ENST00000512772;ENST00000507105 T|. 0.41400|. 1.0|. 5.37|5.37 5.37|5.37 0.77165|0.77165 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.74107|0.74107 0.3673|0.3673 M|M 0.63428|0.63428 1.95|1.95 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.80764|. 0.994|. T|T 0.70999|0.70999 -0.4719|-0.4719 10|5 0.42905|. T|. 0.14|. .|. 19.3098|19.3098 0.94182|0.94182 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 4454|. Q14517|. FAT1_HUMAN|. K|Q 4454;4456|233;221 ENSP00000406229:E4454K|. ENSP00000260147:E4456K|. E|R -|- 1|2 0|0 FAT1|FAT1 187747147|187747147 1.000000|1.000000 0.71417|0.71417 0.163000|0.163000 0.22734|0.22734 0.033000|0.033000 0.12548|0.12548 7.111000|7.111000 0.77077|0.77077 2.800000|2.800000 0.96347|0.96347 0.455000|0.455000 0.32223|0.32223 GAA|CGA TCGA-IB-AAUO-01A-12D-A38G-08 FAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360209.3 0 0 0 26 908 0 438 1 9.994895e-01 29 375 0 438 2 0 0 0 0 0 2 1 1.000000 25 883 0 434 2 0 0 0 0 438 2 -2.092925 0 1 120870 1 31 1 0 1 1 1.887815 1 0.380000 1.860000 0.301723 0.120000 0.080000 0.190000 0.130000 0.134470 0.120000 0 0.100000 0.160000 PPARGC1A 10891 broad.mit.edu 37 4 23830129 23830129 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr4:23830129G>A ENST00000264867.2 - 5 770 c.651C>T c.(649-651)aaC>aaT p.N217N PPARGC1A_ENST00000509702.1_5'UTR NM_013261.3 NP_037393.1 Q9UBK2 PRGC1_HUMAN peroxisome proliferator-activated receptor gamma, coactivator 1 alpha 51 Breast(46;0.0503) GAGGGTCATCGTTTGTGGTCA 0.468000 Esophageal Squamous(29;694 744 13796 34866 44181) 0 SO:0001819 synonymous_variant ENST00000264867.2 1 1 hg19 CCDS3429.1 TCGA-IB-AAUO-01A-12D-A38G-08 PPARGC1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214976.1 0 0 0 12 556 0 234 0 0 0 0 234 2 0 0 0 0 0 2 1 0.999008 12 544 0 232 2 0 0 0 0 234 2 -2.701458 1 1 121412 1 41 1 0 1 1 1.801955 1 0.380000 1.860000 0.292641 0.090000 0.040000 0.160000 0.100000 0.104767 0.090000 0 0.070000 0.130000 GRID2 2895 broad.mit.edu 37 4 94376915 94376915 + Nonsense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr4:94376915C>T ENST00000282020.4 + 11 1906 c.1648C>T c.(1648-1650)Cga>Tga p.R550* GRID2_ENST00000510992.1_Nonsense_Mutation_p.R455* NM_001510.2 NP_001501.2 O43424 GRID2_HUMAN glutamate receptor, ionotropic, delta 2 100 Hepatocellular(203;0.114)|all_hematologic(202;0.177) GGTACTACTTCGAAGGGCTGA 0.478000 0 SO:0001587 stop_gained ENST00000282020.4 0 1 hg19 CCDS3637.1 . . . . . . . . . . C 41 9.088102 0.99061 . . ENSG00000152208 ENST00000282020;ENST00000510992 . . . 5.97 5.97 0.96955 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 15.1877 0.73016 0.1408:0.8592:0.0:0.0 . . . . X 550;455 . ENSP00000282020:R550X R + 1 2 GRID2 94595938 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.461000 0.53035 2.836000 0.97738 0.655000 0.94253 CGA TCGA-IB-AAUO-01A-12D-A38G-08 GRID2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253588.2 0 0 0 13 376 0 189 0 0 0 0 189 2 0 0 0 0 0 2 1 0.999468 12 367 0 188 2 0 0 0 0 189 2 -2.960591 1 1 0 0 1 0 1 1 1.819567 1 0.380000 1.860000 0.294171 0.150000 0.080000 0.250000 0.150000 0.164518 0.150000 0 0.110000 0.210000 GRID2 2895 broad.mit.edu 37 4 94547520 94547520 + Missense_Mutation SNP T T G TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr4:94547520T>G ENST00000282020.4 + 14 2552 c.2294T>G c.(2293-2295)gTt>gGt p.V765G GRID2_ENST00000510992.1_Missense_Mutation_p.V670G NM_001510.2 NP_001501.2 O43424 GRID2_HUMAN glutamate receptor, ionotropic, delta 2 100 Hepatocellular(203;0.114)|all_hematologic(202;0.177) GGAAATACTGTTGCTGATCGG 0.388000 0 SO:0001583 missense ENST00000282020.4 1 1 hg19 CCDS3637.1 . . . . . . . . . . T 15.69 2.906796 0.52333 . . ENSG00000152208 ENST00000282020;ENST00000510992 T;T 0.11604 2.76;2.76 5.13 5.13 0.70059 Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2); 0.109275 0.64402 D 0.000006 T 0.11281 0.0275 L 0.34521 1.04 0.80722 D 1 B;B 0.20459 0.045;0.045 B;B 0.21917 0.037;0.037 T 0.05305 -1.0893 10 0.87932 D 0 . 15.2141 0.73250 0.0:0.0:0.0:1.0 . 670;765 E9PH24;O43424 .;GRID2_HUMAN G 765;670 ENSP00000282020:V765G;ENSP00000421257:V670G ENSP00000282020:V765G V + 2 0 GRID2 94766543 1.000000 0.71417 0.996000 0.52242 0.975000 0.68041 4.456000 0.60081 2.055000 0.61198 0.397000 0.26171 GTT TCGA-IB-AAUO-01A-12D-A38G-08 GRID2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253588.2 0 0 0 20 513 1 224 0 0 0 1 1 224 2 0 0 0 0 0 2 1 0.999994 20 502 0 223 2 0 0 0 1 224 2 -3.854210 1 1 0 0 1 0 1 1 1.819567 1 0.380000 1.860000 0.294171 0.170000 0.100000 0.260000 0.170000 0.180657 0.170000 0 0.130000 0.220000 SGCD 6444 broad.mit.edu 37 5 155771593 155771593 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr5:155771593G>A ENST00000435422.3 + 2 582 c.95G>A c.(94-96)cGa>cAa p.R32Q SGCD_ENST00000447401.1_Missense_Mutation_p.R33Q|SGCD_ENST00000517913.1_Missense_Mutation_p.R33Q|SGCD_ENST00000337851.4_Missense_Mutation_p.R33Q NM_001128209.1 NP_001121681.1 Q92629 SGCD_HUMAN sarcoglycan, delta (35kDa dystrophin-associated glycoprotein) 24 Renal(175;0.00488) Medulloblastoma(196;0.0378)|all_neural(177;0.106) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) TGGCGGAAACGATGCCTGTAT 0.483000 0 SO:0001583 missense ENST00000435422.3 1 1 hg19 CCDS47327.1 . . . . . . . . . . G 36 5.719233 0.96839 . . ENSG00000170624 ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401 D;D;D;D 0.95035 -3.59;-3.59;-3.59;-3.59 5.59 5.59 0.84812 . 0.000000 0.85682 D 0.000000 D 0.96981 0.9014 M 0.73962 2.25 0.80722 D 1 D;D;D 0.89917 0.998;0.998;1.0 D;D;D 0.83275 0.992;0.986;0.996 D 0.95484 0.8563 10 0.25751 T 0.34 -9.9405 19.6056 0.95580 0.0:0.0:1.0:0.0 . 32;33;33 Q92629;Q92629-2;Q92629-3 SGCD_HUMAN;.;. Q 33;32;33;33 ENSP00000429378:R33Q;ENSP00000403003:R32Q;ENSP00000338343:R33Q;ENSP00000408324:R33Q ENSP00000338343:R33Q R + 2 0 SGCD 155704171 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.731000 0.98807 2.625000 0.88918 0.655000 0.94253 CGA TCGA-IB-AAUO-01A-12D-A38G-08 SGCD-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000373469.3 1 0 1 40 240 0 95 0 5.781092e-02 0 3 0 95 2 0 0 0 0 0 2 1 1.000000 40 238 0 94 2 0 0 0 0 95 2 -3.322178 1 1 0 0 1 0 1 1 2.049852 0 0.380000 1.860000 0.378820 0.740000 0.550000 0.970000 0.750000 0.758394 0.740000 0 0.640000 0.860000 ADAMTS12 81792 broad.mit.edu 37 5 33596156 33596156 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr5:33596156C>T ENST00000504830.1 - 17 2872 c.2537G>A c.(2536-2538)cGc>cAc p.R846H ADAMTS12_ENST00000352040.3_Missense_Mutation_p.R761H|ADAMTS12_ENST00000504582.1_5'UTR NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 p.R846H(1) 216 GGCAGTTTGGCGGCGGATACC 0.517000 HNSCC(64;0.19) 1 Substitution - Missense(1) SO:0001583 missense ENST00000504830.1 1 1 hg19 CCDS34140.1 . . . . . . . . . . C 20.6 4.010730 0.75046 . . ENSG00000151388 ENST00000504830;ENST00000352040 T;T 0.52983 0.64;0.64 5.77 4.9 0.64082 . 0.196715 0.50627 D 0.000112 T 0.49541 0.1563 L 0.55990 1.75 0.80722 D 1 P;P 0.52577 0.463;0.954 B;P 0.48552 0.067;0.581 T 0.43442 -0.9391 10 0.16420 T 0.52 . 15.3406 0.74293 0.0:0.9327:0.0:0.0673 . 761;846 P58397-3;P58397 .;ATS12_HUMAN H 846;761 ENSP00000422554:R846H;ENSP00000344847:R761H ENSP00000344847:R761H R - 2 0 ADAMTS12 33631913 0.994000 0.37717 0.987000 0.45799 0.998000 0.95712 2.459000 0.45023 1.582000 0.49881 0.585000 0.79938 CGC TCGA-IB-AAUO-01A-12D-A38G-08 ADAMTS12-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367164.2 1 0 1 52 337 0 133 0 1.867269e-02 0 2 0 133 2 0 0 0 0 0 2 1 1.000000 52 329 0 131 2 0 0 0 0 133 2 -3.222046 1 1 121412 2 36 1 0 1 1 2.053532 0 0.380000 1.860000 0.378820 0.690000 0.530000 0.880000 0.700000 0.709020 0.690000 0 0.610000 0.800000 TIAM2 26230 broad.mit.edu 37 6 155451469 155451469 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr6:155451469C>T ENST00000461783.3 + 6 2385 c.1112C>T c.(1111-1113)gCg>gTg p.A371V TIAM2_ENST00000360366.4_Missense_Mutation_p.A371V|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000318981.5_Missense_Mutation_p.A371V|TIAM2_ENST00000456144.1_Missense_Mutation_p.A371V|TIAM2_ENST00000529824.2_Missense_Mutation_p.A371V Q8IVF5 TIAM2_HUMAN T-cell lymphoma invasion and metastasis 2 65 Ovarian(120;0.196) GAGGATACTGCGAAGAAGGAC 0.547000 0 SO:0001583 missense ENST00000461783.3 1 1 hg19 CCDS34558.1 . . . . . . . . . . C 13.07 2.126396 0.37533 . . ENSG00000146426 ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824 T;T;T;T;T;T 0.05382 3.57;3.45;3.51;3.57;3.57;3.51 5.29 5.29 0.74685 . 0.813614 0.11671 N 0.540830 T 0.03608 0.0103 L 0.40543 1.245 0.47407 D 0.999411 B 0.29909 0.261 B 0.19148 0.024 T 0.35276 -0.9795 10 0.59425 D 0.04 . 17.1487 0.86773 0.0:1.0:0.0:0.0 . 371 Q8IVF5 TIAM2_HUMAN V 371;617;371;371;371;371;371 ENSP00000437188:A371V;ENSP00000434901:A371V;ENSP00000407746:A371V;ENSP00000327315:A371V;ENSP00000353528:A371V;ENSP00000433348:A371V ENSP00000327315:A371V A + 2 0 TIAM2 155493161 0.002000 0.14202 0.364000 0.25888 0.430000 0.31655 1.419000 0.34793 2.489000 0.83994 0.655000 0.94253 GCG TCGA-IB-AAUO-01A-12D-A38G-08 TIAM2-005 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000387980.2 0 0 0 12 201 1 91 0 0 0 1 91 2 0 0 0 0 0 2 1 0.713298 11 195 1 91 10 0 0 0 1 91 2 -4.756731 1 1 121412 5 40 1 0 1 1 1.683475 1 0.380000 1.860000 0.234568 0.240000 0.130000 0.390000 0.240000 0.253837 0.240000 0 0.180000 0.320000 HIST1H2BF 8343 broad.mit.edu 37 6 26199947 26199947 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr6:26199947G>A ENST00000359985.1 + 1 200 c.161G>A c.(160-162)gGc>gAc p.G54D HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000377831.5_5'Flank|HIST1H3D_ENST00000356476.2_5'Flank NM_003522.3 NP_003513.1 P62807 H2B1C_HUMAN histone cluster 1, H2bf 17 all_hematologic(11;0.196) CCCGACACCGGCATCTCATCC 0.567000 0 SO:0001583 missense ENST00000359985.1 0 1 hg19 CCDS4592.1 . . . . . . . . . . . 16.80 3.222980 0.58668 . . ENSG00000197846 ENST00000359985 T 0.69435 -0.4 3.89 3.89 0.44902 . 0.000000 0.42172 D 0.000755 T 0.73442 0.3587 . . . 0.41511 D 0.988346 . . . . . . T 0.78807 -0.2059 7 0.87932 D 0 . 15.7145 0.77658 0.0:0.0:1.0:0.0 . . . . D 54 ENSP00000353074:G54D ENSP00000353074:G54D G + 2 0 HIST1H2BF 26307926 1.000000 0.71417 0.996000 0.52242 0.014000 0.08584 9.518000 0.98022 2.102000 0.63906 0.650000 0.86243 GGC TCGA-IB-AAUO-01A-12D-A38G-08 HIST1H2BF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040108.1 0 0 0 7 861 0 446 0 5.811399e-03 0 12 0 446 2 0 0 0 0 0 2 1 0.979120 7 843 0 442 2 0 0 0 0 446 2 -1.773335 0 1 0 0 1 0 1 1 1.735691 1 0.380000 1.860000 0.258905 0.030000 0.010000 0.070000 0.040000 0.040361 0.030000 0 0.020000 0.050000 NCR2 9436 broad.mit.edu 37 6 41318497 41318497 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr6:41318497G>A ENST00000373089.5 + 5 814 c.726G>A c.(724-726)acG>acA p.T242T NCR2_ENST00000373086.3_3'UTR|NCR2_ENST00000373083.4_3'UTR NM_004828.3 NP_004819.2 O95944 NCTR2_HUMAN natural cytotoxicity triggering receptor 2 14 Ovarian(28;0.0327)|Colorectal(47;0.196) aacaggtcacggaccttccct 0.478000 0 SO:0001819 synonymous_variant ENST00000373089.5 0 1 hg19 CCDS4855.1 TCGA-IB-AAUO-01A-12D-A38G-08 NCR2-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000040511.3 0 0 0 7 206 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 0.980475 7 204 0 112 2 0 0 0 0 115 2 -3.239604 1 1 0 0 1 0 1 1 1.719762 1 0.380000 1.860000 0.257218 0.140000 0.060000 0.280000 0.140000 0.161258 0.140000 0 0.100000 0.210000 COQ3 51805 broad.mit.edu 37 6 99831606 99831606 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr6:99831606G>A ENST00000254759.3 - 2 225 c.201C>T c.(199-201)atC>atT p.I67I COQ3_ENST00000369242.1_5'UTR|COQ3_ENST00000479163.1_5'UTR NM_017421.3 NP_059117.3 Q9NZJ6 COQ3_HUMAN coenzyme Q3 methyltransferase 8 all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186) AACAGGAAAAGATCGTCCTGT 0.338000 0 SO:0001819 synonymous_variant ENST00000254759.3 1 1 hg19 CCDS5042.1 TCGA-IB-AAUO-01A-12D-A38G-08 COQ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041602.1 0 0 0 23 726 0 352 0 5.578315e-02 1 11 0 352 2 0 0 0 0 0 2 1 0.999999 23 712 0 353 2 0 0 0 0 352 2 -18.621690 1 1 0 0 1 0 1 1 1.719762 1 0.380000 1.860000 0.257218 0.130000 0.080000 0.200000 0.130000 0.139851 0.130000 0 0.100000 0.170000 CDHR3 222256 broad.mit.edu 37 7 105673026 105673026 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr7:105673026G>A ENST00000317716.9 + 19 2621 c.2541G>A c.(2539-2541)gcG>gcA p.A847A CDHR3_ENST00000478080.1_Silent_p.A759A|CDHR3_ENST00000343407.5_3'UTR|CDHR3_ENST00000542731.1_Silent_p.A847A NM_152750.4 NP_689963.2 Q6ZTQ4 CDHR3_HUMAN cadherin-related family member 3 23 GTGGCAAAGCGTGGGCTGAGG 0.577000 0 SO:0001819 synonymous_variant ENST00000317716.9 1 1 hg19 CCDS47684.1 TCGA-IB-AAUO-01A-12D-A38G-08 CDHR3-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000349025.2 1 0 0 9 163 0 76 0 3.612479e-03 0 2 0 76 2 0 0 0 0 0 2 1 0.994603 9 162 0 75 2 0 0 0 0 76 2 -4.752440 1 1 0 0 1 0 0 0 2.043431 0 0.380000 1.860000 0.377635 0.280000 0.130000 0.480000 0.280000 0.298461 0.280000 0 0.200000 0.380000 FLNC 2318 broad.mit.edu 37 7 128480725 128480725 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr7:128480725G>A ENST00000325888.8 + 10 1934 c.1673G>A c.(1672-1674)cGc>cAc p.R558H FLNC_ENST00000346177.6_Missense_Mutation_p.R558H NM_001458.4 NP_001449.3 Q14315 FLNC_HUMAN filamin C, gamma 128 GCCATCCCTCGCAGGTGAGTA 0.637000 0 SO:0001583 missense ENST00000325888.8 1 1 hg19 CCDS43644.1 . . . . . . . . . . G 18.84 3.708659 0.68615 . . ENSG00000128591 ENST00000325888;ENST00000346177 D;D 0.91894 -2.93;-2.93 5.02 5.02 0.67125 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.059561 0.64402 D 0.000004 D 0.94345 0.8182 L 0.53249 1.67 0.47183 D 0.999344 D;D 0.89917 1.0;0.999 D;D 0.91635 0.999;0.953 D 0.94549 0.7752 10 0.87932 D 0 . 12.2416 0.54546 0.0893:0.0:0.9107:0.0 . 558;558 Q14315-2;Q14315 .;FLNC_HUMAN H 558 ENSP00000327145:R558H;ENSP00000344002:R558H ENSP00000327145:R558H R + 2 0 FLNC 128267961 0.981000 0.34729 1.000000 0.80357 0.037000 0.13140 4.138000 0.58017 2.327000 0.79052 0.491000 0.48974 CGC TCGA-IB-AAUO-01A-12D-A38G-08 FLNC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059948.3 1 0 1 44 345 0 158 0 1.350540e-02 1 1 0 158 2 0 0 0 0 0 2 1 1.000000 41 336 0 158 2 0 0 0 0 158 2 -16.205010 1 1 121074 5 41 1 0 0 0 2.043431 0 0.380000 1.860000 0.377635 0.590000 0.430000 0.760000 0.590000 0.600882 0.590000 0 0.510000 0.680000 MRPS33 51650 broad.mit.edu 37 7 140710243 140710243 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr7:140710243G>A ENST00000393008.3 - 2 346 c.191C>T c.(190-192)aCg>aTg p.T64M MRPS33_ENST00000467334.1_Missense_Mutation_p.T54M|MRPS33_ENST00000324787.5_Missense_Mutation_p.T64M|MRPS33_ENST00000472343.1_5'Flank|MRPS33_ENST00000496958.1_Missense_Mutation_p.T64M|MRPS33_ENST00000469351.1_Missense_Mutation_p.T64M NM_016071.3 NP_057155.1 Q9Y291 RT33_HUMAN mitochondrial ribosomal protein S33 4 Melanoma(164;0.00956) AAATCGGAGCGTCTGCATGAG 0.413000 0 SO:0001583 missense ENST00000393008.3 1 1 hg19 CCDS5864.1 . . . . . . . . . . G 9.817 1.184686 0.21870 0.0 2.33E-4 ENSG00000090263 ENST00000544013;ENST00000393008;ENST00000324787;ENST00000496958;ENST00000469351;ENST00000467334 . . . 5.1 -4.84 0.03151 . 0.517024 0.23549 N 0.046999 T 0.20780 0.0500 N 0.16368 0.405 0.09310 N 0.999996 D 0.69078 0.997 P 0.56514 0.8 T 0.25363 -1.0134 9 0.28530 T 0.3 -2.3832 5.3 0.15773 0.4111:0.0:0.2195:0.3694 . 64 Q9Y291 RT33_HUMAN M 64;64;64;64;64;54 . ENSP00000320567:T64M T - 2 0 MRPS33 140356712 0.093000 0.21703 0.010000 0.14722 0.057000 0.15508 0.429000 0.21412 -0.574000 0.05990 0.467000 0.42956 ACG TCGA-IB-AAUO-01A-12D-A38G-08 MRPS33-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348878.1 1 0 1 61 309 0 124 1 1 56 151 0 124 2 0 0 0 0 0 2 1 1.000000 61 301 0 124 2 0 0 0 0 124 2 -20.000000 1 1 121412 11 43 1 0 0 0 2.043431 0 0.380000 1.860000 0.377635 0.860000 0.670000 1.000000 1.000000 0.864594 0.860000 1 0.760000 0.970000 LIMK1 3984 broad.mit.edu 37 7 73511508 73511508 + Silent SNP C C A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr7:73511508C>A ENST00000336180.2 + 4 441 c.390C>A c.(388-390)tcC>tcA p.S130S LIMK1_ENST00000418310.1_Silent_p.S160S|LIMK1_ENST00000538333.3_Silent_p.S96S|LIMK1_ENST00000491052.1_3'UTR NM_002314.3 NP_002305.1 P53667 LIMK1_HUMAN LIM domain kinase 1 21 Lung NSC(55;0.137) Dabrafenib(DB08912) TGGAGCACTCCAAGCTGTACT 0.617000 0 SO:0001819 synonymous_variant ENST00000336180.2 1 0 hg19 CCDS5563.1 TCGA-IB-AAUO-01A-12D-A38G-08 LIMK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252335.2 1 0 0 4 86 0 40 0 6.813097e-01 0 49 0 40 2 0 0 0 0 0 2 1 0.883922 3 84 0 40 2 0 0 0 0 40 2 -7.787154 1 0 0 0 1 0 0 0 2.043431 0 0.380000 1.860000 0.377635 0.250000 0.080000 0.530000 0.230000 0.279792 0.250000 0 0.150000 0.390000 ZHX2 22882 broad.mit.edu 37 8 123965170 123965170 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr8:123965170G>A ENST00000314393.4 + 3 2255 c.1420G>A c.(1420-1422)Gag>Aag p.E474K NM_014943.3 NP_055758.1 Q9Y6X8 ZHX2_HUMAN zinc fingers and homeoboxes 2 45 Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105) STAD - Stomach adenocarcinoma(47;0.00527) CCGGCTCATCGAGGTGACTGG 0.557000 Esophageal Squamous(94;1056 1388 11767 13799 49639) 0 SO:0001583 missense ENST00000314393.4 0 1 hg19 CCDS6336.1 . . . . . . . . . . G 11.86 1.765980 0.31228 2.27E-4 0.0 ENSG00000178764 ENST00000314393 D 0.95949 -3.86 5.94 5.07 0.68467 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.102570 0.64402 D 0.000003 D 0.90106 0.6909 N 0.21448 0.665 0.80722 D 1 B 0.24043 0.096 B 0.20577 0.03 D 0.86463 0.1780 10 0.09843 T 0.71 -24.8951 15.4187 0.74995 0.0667:0.0:0.9333:0.0 . 474 Q9Y6X8 ZHX2_HUMAN K 474 ENSP00000314709:E474K ENSP00000314709:E474K E + 1 0 ZHX2 124034351 1.000000 0.71417 1.000000 0.80357 0.468000 0.32798 7.641000 0.83368 1.531000 0.49152 0.561000 0.74099 GAG TCGA-IB-AAUO-01A-12D-A38G-08 ZHX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381709.1 0 0 0 6 176 0 69 0 1.405705e-01 0 17 0 69 2 0 0 0 0 0 2 1 0.961326 5 170 0 68 2 0 0 0 0 69 2 -7.954317 1 1 121412 2 36 1 0 0 0 2.045321 0 0.380000 1.860000 0.377635 0.180000 0.070000 0.350000 0.170000 0.197672 0.180000 0 0.120000 0.270000 BAI1 575 broad.mit.edu 37 8 143618425 143618425 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr8:143618425C>T ENST00000517894.1 + 26 4542 c.3648C>T c.(3646-3648)aaC>aaT p.N1216N BAI1_ENST00000323289.5_Silent_p.N1216N O14514 BAI1_HUMAN brain-specific angiogenesis inhibitor 1 57 all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155) CCTTCCAGAACGGCCACGCCC 0.692000 0 SO:0001819 synonymous_variant ENST00000517894.1 0 1 hg19 TCGA-IB-AAUO-01A-12D-A38G-08 BAI1-001 KNOWN non_canonical_conserved|not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000379963.3 0 0 0 4 47 0 25 0 0 1 0 0 25 2 0 0 0 0 0 2 1 0.888377 4 46 0 25 2 0 0 0 0 25 2 -8.885540 1 1 120508 2 22 1 0 0 0 2.045321 0 0.380000 1.860000 0.377635 0.440000 0.150000 0.900000 0.400000 0.477273 0.440000 0 0.270000 0.670000 COL5A1 1289 broad.mit.edu 37 9 137709638 137709638 + Silent SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr9:137709638C>T ENST00000371817.3 + 54 4605 c.4191C>T c.(4189-4191)ccC>ccT p.P1397P NM_000093.3|NM_001278074.1 NP_000084.3|NP_001265003.1 P20908 CO5A1_HUMAN collagen, type V, alpha 1 115 Myeloproliferative disorder(178;0.0341) CCCCAGGCCCCGCAGGCCCCG 0.657000 0 SO:0001819 synonymous_variant ENST00000371817.3 1 1 hg19 CCDS6982.1 TCGA-IB-AAUO-01A-12D-A38G-08 COL5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054954.2 1 0 1 11 46 0 24 1 9.999994e-01 15 144 0 24 2 0 0 0 0 0 2 1 0.998775 11 45 0 24 2 0 0 0 0 24 2 -19.894380 1 1 0 0 1 0 1 1 2.053346 0 0.380000 1.860000 0.378820 0.990000 0.560000 1.000000 1.000000 0.913558 0.990000 1 0.760000 1.000000 SNAPC4 6621 broad.mit.edu 37 9 139289824 139289824 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr9:139289824C>T ENST00000298532.2 - 4 765 c.397G>A c.(397-399)Ggc>Agc p.G133S NM_003086.2 NP_003077.2 small nuclear RNA activating complex, polypeptide 4, 190kDa 33 Myeloproliferative disorder(178;0.0511) AGGCTTTTGCCATCTTTCACC 0.567000 0 SO:0001583 missense ENST00000298532.2 1 1 hg19 CCDS6998.1 . . . . . . . . . . C 6.565 0.472500 0.12461 . . ENSG00000165684 ENST00000298532 T 0.28255 1.62 5.35 -2.81 0.05805 . 1.072810 0.07153 N 0.849409 T 0.25791 0.0628 L 0.48362 1.52 0.09310 N 0.999994 B 0.28378 0.209 B 0.22880 0.042 T 0.25012 -1.0144 10 0.52906 T 0.07 -3.3704 10.5123 0.44868 0.0:0.4466:0.0:0.5534 . 133 Q5SXM2 SNPC4_HUMAN S 133 ENSP00000298532:G133S ENSP00000298532:G133S G - 1 0 SNAPC4 138409645 0.003000 0.15002 0.000000 0.03702 0.004000 0.04260 -0.062000 0.11674 -0.992000 0.03472 -1.074000 0.02243 GGC TCGA-IB-AAUO-01A-12D-A38G-08 SNAPC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055071.1 0 0 0 9 275 0 103 0 6.684777e-02 0 12 0 103 2 0 0 0 0 0 2 1 0.993849 9 269 0 103 2 0 0 0 0 103 2 -3.002049 1 1 121380 1 29 1 0 1 1 2.053346 0 0.380000 1.860000 0.378820 0.170000 0.080000 0.300000 0.160000 0.182619 0.170000 0 0.120000 0.240000 ARID3C 138715 broad.mit.edu 37 9 34622033 34622033 + Silent SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr9:34622033G>A ENST00000378909.2 - 6 1214 c.1122C>T c.(1120-1122)aaC>aaT p.N374N DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000477738.2_5'Flank|DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank|DCTN3_ENST00000378913.2_5'Flank NM_001017363.1 NP_001017363.1 A6NKF2 ARI3C_HUMAN AT rich interactive domain 3C (BRIGHT-like) 14 all_epithelial(49;0.102) STAD - Stomach adenocarcinoma(86;0.178) AGACCACCCCGTTGATCTCTA 0.552000 0 SO:0001819 synonymous_variant ENST00000378909.2 1 1 hg19 CCDS35006.1 TCGA-IB-AAUO-01A-12D-A38G-08 ARID3C-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348265.1 1 0 1 42 302 0 126 0 0 0 0 126 2 0 0 0 0 0 2 1 1.000000 42 293 0 125 2 0 0 0 0 126 2 -3.221920 1 1 121412 3 41 1 0 0 0 2.022799 0 0.380000 1.860000 0.370431 0.630000 0.460000 0.820000 0.630000 0.640969 0.630000 0 0.540000 0.730000 TRPM6 140803 broad.mit.edu 37 9 77390934 77390934 + Missense_Mutation SNP G G A TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chr9:77390934G>A ENST00000360774.1 - 24 3505 c.3268C>T c.(3268-3270)Cgc>Tgc p.R1090C TRPM6_ENST00000451710.3_Missense_Mutation_p.R1090C|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.R1090C|TRPM6_ENST00000361255.3_Missense_Mutation_p.R1085C|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1085C NM_017662.4 NP_060132.3 Q9BX84 TRPM6_HUMAN transient receptor potential cation channel, subfamily M, member 6 126 ATGATGTAGCGATAGCGGTTG 0.493000 0 SO:0001583 missense ENST00000360774.1 1 1 hg19 CCDS6647.1 . . . . . . . . . . G 32 5.120843 0.94385 . . ENSG00000119121 ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641 T;T;T;T;T 0.55588 0.6;0.6;0.6;0.6;0.51 5.76 5.76 0.90799 . 0.046412 0.85682 D 0.000000 T 0.72779 0.3503 M 0.72894 2.215 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.67900 0.932;0.931;0.954 T 0.74426 -0.3669 10 0.87932 D 0 . 19.9561 0.97218 0.0:0.0:1.0:0.0 . 1090;1085;1085 Q9BX84;Q9BX84-3;Q9BX84-2 TRPM6_HUMAN;.;. C 1090;1090;1085;1085;1090;753;753 ENSP00000354006:R1090C;ENSP00000407341:R1090C;ENSP00000396672:R1085C;ENSP00000354962:R1085C;ENSP00000366060:R1090C ENSP00000309693:R753C R - 1 0 TRPM6 76580754 1.000000 0.71417 1.000000 0.80357 0.885000 0.51271 7.827000 0.86722 2.725000 0.93324 0.591000 0.81541 CGC TCGA-IB-AAUO-01A-12D-A38G-08 TRPM6-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000052693.1 0 0 0 12 424 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 0.999078 12 419 0 143 2 0 0 0 0 147 2 -2.818145 1 1 0 0 1 0 0 0 2.022799 0 0.380000 1.860000 0.370431 0.140000 0.070000 0.240000 0.140000 0.153237 0.140000 0 0.100000 0.190000 DMD 1756 broad.mit.edu 37 X 32663260 32663260 + Missense_Mutation SNP C C T TCGA-IB-AAUO-01A-12D-A38G-08 TCGA-IB-AAUO-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx fea1f02f-d937-4ce1-99cc-b1253242f1cf 84813019-93c1-4f1c-8103-a43c6b33b120 g.chrX:32663260C>T ENST00000357033.4 - 10 1176 c.970G>A c.(970-972)Gct>Act p.A324T DMD_ENST00000288447.4_Missense_Mutation_p.A316T|DMD_ENST00000378677.2_Missense_Mutation_p.A320T NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2 NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1 P11532 DMD_HUMAN dystrophin 77 all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203) TCTTCAGGAGCTTCCAAATGC 0.348000 0 SO:0001583 missense ENST00000357033.4 0 1 hg19 CCDS14233.1 . . . . . . . . . . C 3.513 -0.099324 0.07010 . . ENSG00000198947 ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447 T;T;T 0.72615 0.16;0.16;-0.67 5.67 2.85 0.33270 . 0.197530 0.24231 U 0.040342 T 0.40815 0.1132 N 0.05078 -0.115 0.80722 D 1 B;B;B;B;B 0.10296 0.0;0.0;0.002;0.003;0.001 B;B;B;B;B 0.10450 0.0;0.0;0.005;0.002;0.002 T 0.32188 -0.9916 10 0.02654 T 1 . 7.4854 0.27429 0.0:0.574:0.0:0.426 . 320;316;316;324;320 B1AK23;Q4G0X0;P11532-4;P11532;E9PDN5 .;.;.;DMD_HUMAN;. T 316;320;324;324;201;316 ENSP00000367948:A320T;ENSP00000354923:A324T;ENSP00000288447:A316T ENSP00000288447:A316T A - 1 0 DMD 32573181 0.963000 0.33076 1.000000 0.80357 0.984000 0.73092 -0.020000 0.12525 0.611000 0.30052 0.600000 0.82982 GCT TCGA-IB-AAUO-01A-12D-A38G-08 DMD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056182.2 0 0 0 8 439 1 205 0 0 0 1 205 2 0 0 0 0 0 2 0 0.387457 8 430 1 202 10 0 0 0 1 205 2 -7.139841 1 1 0 0 1 0 1 1 0.380000 1.860000 0.380000 0.090000 0.040000 0.180000 0.100000 0.105095 0.090000 0 0.060000 0.140000