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 RAP2B 5912 broad.mit.edu 37 3 152880927 152880962 + In_Frame_Del DEL AACAAAGCCTCGGTAGACGAGCTATTTGCCGAGATC AACAAAGCCTCGGTAGACGAGCTATTTGCCGAGATC - rs138892831 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr3:152880927_152880962delAACAAAGCCTCGGTAGACGAGCTATTTGCCGAGATC ENST00000323534.2 + 1 899_934 c.445_480delAACAAAGCCTCGGTAGACGAGCTATTTGCCGAGATC c.(445-480)aacaaagcctcggtagacgagctatttgccgagatcdel p.NKASVDELFAEI149del RP11-529G21.2_ENST00000487827.1_RNA NM_002886.2 NP_002877.2 P61225 RAP2B_HUMAN RAP2B, member of RAS oncogene family 7 LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11) GTCGGCCAAAAACAAAGCCTCGGTAGACGAGCTATTTGCCGAGATCGTGCGGCAGA 0.661000 0 SO:0001651 inframe_deletion ENST00000323534.2 0 1 hg19 CCDS3170.1 TCGA-H6-8124-01A-11D-2396-08 RAP2B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356707.1 1 0 0 11 84 0 22 0 9.777806e-01 0 53 0 22 2 0 0 0 0 0 0 1 0.999897 35 107 0 22 2 0 0 0 0 0 0 -18.580870 1 1 0 0 1 0 0 0 2.171377 0 0.700000 1.770000 0.700000 0.330000 1.800000e-01 0.540000 0.330000 0.351870 0.330000 0 2.500000e-01 4.400000e-01 LRPAP1 4043 broad.mit.edu 37 4 3516576 3516582 + Frame_Shift_Del DEL AGCTTCT AGCTTCT - TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 AGCTTCT - AGCTTCT AGCTTCT Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr4:3516576_3516582delAGCTTCT ENST00000500728.2 - 7 1054_1060 c.908_914delAGAAGCT c.(907-915)gagaagctgfs p.EKL303fs LRPAP1_ENST00000296325.5_5'UTR NM_002337.3 NP_002328.1 P30533 AMRP_HUMAN low density lipoprotein receptor-related protein associated protein 1 14 TGCGTGCCTCAGCTTCTCGTGCGCAAT 0.614000 0 SO:0001589 frameshift_variant ENST00000500728.2 1 1 hg19 CCDS3371.1 TCGA-H6-8124-01A-11D-2396-08 LRPAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206659.4 1 0 0 212 811 0 294 1 1 26 487 0 294 2 0 0 0 0 0 0 1 1.000000 264 850 0 294 2 0 0 0 0 0 0 -3.884088 1 1 0 0 1 1 2 3 2.239288 0 0.700000 1.770000 0.704142 0.590000 5.200000e-01 1.000000 0.600000 0.613255 0.590000 0 5.600000e-01 6.400000e-01 ADCY1 107 broad.mit.edu 37 7 45614538 45614540 + In_Frame_Del DEL CTT CTT - TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr7:45614538_45614540delCTT ENST00000297323.7 + 1 418_420 c.396_398delCTT c.(394-399)accttc>acc p.F133del ADCY1_ENST00000432715.1_5'UTR NM_021116.2 NP_066939.1 Q08828 ADCY1_HUMAN adenylate cyclase 1 (brain) 71 Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171) TCAGCCTCACCTTCGCGCTGCTC 0.719000 0 SO:0001651 inframe_deletion ENST00000297323.7 1 1 hg19 CCDS34631.1 TCGA-H6-8124-01A-11D-2396-08 ADCY1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340055.2 1 0 0 87 280 0 83 0 0 0 83 0 0 0 0 0 0 1 1.000000 118 290 2 86 22 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 2.170941 0 0.700000 1.770000 0.700000 0.670000 5.500000e-01 0.800000 0.680000 0.680578 0.670000 0 6.100000e-01 7.400000e-01 ADD3 120 broad.mit.edu 37 10 111876161 111876161 + Missense_Mutation SNP A A G TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr10:111876161A>G ENST00000356080.4 + 4 846 c.479A>G c.(478-480)tAt>tGt p.Y160C ADD3_ENST00000497125.1_3'UTR|ADD3_ENST00000360162.3_Missense_Mutation_p.Y160C|ADD3_ENST00000277900.8_Missense_Mutation_p.Y160C NM_016824.3 NP_058432.1 Q9UEY8 ADDG_HUMAN adducin 3 (gamma) 29 Breast(234;0.052)|Lung NSC(174;0.223) GCAAATACCTATATCTCAGTG 0.403000 0 SO:0001583 missense ENST00000356080.4 1 1 hg19 CCDS7561.1 . . . . . . . . . . A 16.40 3.111684 0.56398 . . ENSG00000148700 ENST00000360162;ENST00000356080;ENST00000277900 T;T;T 0.21734 1.99;1.99;1.99 5.47 5.47 0.80525 Class II aldolase/adducin, N-terminal (3); 0.000000 0.85682 D 0.000000 T 0.33323 0.0859 L 0.35341 1.055 0.80722 D 1 D;B 0.89917 1.0;0.451 D;B 0.91635 0.999;0.363 T 0.05162 -1.0902 10 0.51188 T 0.08 -6.7683 10.76 0.46259 0.8583:0.0:0.0:0.1417 . 160;160 Q9UEY8;Q9UEY8-2 ADDG_HUMAN;. C 160 ENSP00000353286:Y160C;ENSP00000348381:Y160C;ENSP00000277900:Y160C ENSP00000277900:Y160C Y + 2 0 ADD3 111866151 1.000000 0.71417 0.712000 0.30502 0.858000 0.48976 7.338000 0.79269 2.083000 0.62718 0.460000 0.39030 TAT TCGA-H6-8124-01A-11D-2396-08 ADD3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050289.1 1 0 1 122 98 0 20 1 1 88 37 0 20 2 0 0 0 0 0 2 1 1.000000 119 96 0 20 2 0 0 0 0 20 2 -20.000000 1 1 121412 1 29 1 0 1 1 1.526225 1 0.700000 1.770000 0.550562 0.990000 9.000000e-01 1.000000 1.000000 0.985790 0.990000 1 9.500000e-01 1 PRTFDC1 56952 broad.mit.edu 37 10 25138811 25138811 + Missense_Mutation SNP C C A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr10:25138811C>A ENST00000320152.6 - 9 668 c.640G>T c.(640-642)Gtc>Ttc p.V214F PRTFDC1_ENST00000376378.1_Missense_Mutation_p.R188L NM_020200.5 NP_064585.1 Q9NRG1 PRDC1_HUMAN phosphoribosyl transferase domain containing 1 9 TCATTGATGACGCATATGTGC 0.378000 0 SO:0001583 missense ENST00000320152.6 1 1 hg19 CCDS7145.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 21.3|21.3 4.124299|4.124299 0.77436|0.77436 .|. .|. ENSG00000099256|ENSG00000099256 ENST00000358336;ENST00000376378|ENST00000320152 D|D 0.99841|0.99232 -7.09|-5.6 5.55|5.55 2.64|2.64 0.31445|0.31445 .|. .|0.058217 .|0.64402 .|D .|0.000002 D|D 0.99524|0.99524 0.9830|0.9830 H|H 0.97983|0.97983 4.12|4.12 0.80722|0.80722 D|D 1|1 B|D 0.13145|0.65815 0.007|0.995 B|D 0.17098|0.67548 0.017|0.952 D|D 0.98786|0.98786 1.0734|1.0734 9|10 0.54805|0.87932 T|D 0.06|0 .|. 7.9935|7.9935 0.30254|0.30254 0.1307:0.7315:0.0:0.1378|0.1307:0.7315:0.0:0.1378 .|. 188|214 Q9NRG1-2|Q9NRG1 .|PRDC1_HUMAN L|F 188|214 ENSP00000365558:R188L|ENSP00000318602:V214F ENSP00000351096:R188L|ENSP00000318602:V214F R|V -|- 2|1 0|0 PRTFDC1|PRTFDC1 25178817|25178817 0.897000|0.897000 0.30589|0.30589 0.858000|0.858000 0.33744|0.33744 0.984000|0.984000 0.73092|0.73092 1.561000|1.561000 0.36342|0.36342 0.270000|0.270000 0.21984|0.21984 0.563000|0.563000 0.77884|0.77884 CGT|GTC TCGA-H6-8124-01A-11D-2396-08 PRTFDC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047243.2 1 0 1 187 217 0 33 1 1 52 20 0 33 2 0 0 0 0 0 2 1 1.000000 182 216 0 31 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 0 1 1 1.520219 1 0.700000 1.770000 0.557522 0.880000 7.900000e-01 0.980000 0.890000 0.894992 0.880000 1 8.400000e-01 9.400000e-01 MAP4K2 5871 broad.mit.edu 37 11 64564293 64564293 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr11:64564293G>A ENST00000294066.2 - 21 1571 c.1480C>T c.(1480-1482)Cct>Tct p.P494S MAP4K2_ENST00000377350.3_Missense_Mutation_p.P486S NM_004579.3 NP_004570.2 Q12851 M4K2_HUMAN mitogen-activated protein kinase kinase kinase kinase 2 8 CGAGTAACAGGGTGAATCCAG 0.637000 0 SO:0001583 missense ENST00000294066.2 1 1 hg19 CCDS8082.1 . . . . . . . . . . G 22.9 4.346951 0.82022 . . ENSG00000168067 ENST00000294066;ENST00000377350 T;T 0.05996 3.36;3.36 4.51 4.51 0.55191 Citron-like (3); 0.000000 0.85682 D 0.000000 T 0.21062 0.0507 M 0.64997 1.995 0.58432 D 0.999994 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.998 T 0.00223 -1.1903 10 0.59425 D 0.04 . 13.1403 0.59430 0.0:0.0:1.0:0.0 . 486;494 Q86VU3;Q12851 .;M4K2_HUMAN S 494;486 ENSP00000294066:P494S;ENSP00000366567:P486S ENSP00000294066:P494S P - 1 0 MAP4K2 64320869 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 8.359000 0.90093 2.247000 0.74100 0.558000 0.71614 CCT TCGA-H6-8124-01A-11D-2396-08 MAP4K2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000105239.1 1 0 1 112 232 0 74 1 9.987351e-01 9 15 0 74 2 0 0 0 0 0 2 1 1.000000 108 227 0 72 2 0 0 0 0 74 2 -10.968850 1 1 0 0 1 0 0 0 2.145534 0 0.700000 1.770000 0.697885 0.910000 7.800000e-01 1.000000 1.000000 0.919661 0.910000 1 8.400000e-01 9.900000e-01 ARHGEF17 9828 broad.mit.edu 37 11 73076866 73076866 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr11:73076866C>T ENST00000263674.3 + 20 6219 c.5869C>T c.(5869-5871)Cgg>Tgg p.R1957W NM_014786.3 NP_055601.2 Q96PE2 ARHGH_HUMAN Rho guanine nucleotide exchange factor (GEF) 17 32 CAGCTGCCCACGGGCACCACT 0.652000 0 SO:0001583 missense ENST00000263674.3 1 1 hg19 CCDS8221.1 . . . . . . . . . . C 14.71 2.617632 0.46736 . . ENSG00000110237 ENST00000263674 T 0.36340 1.26 5.28 4.36 0.52297 WD40 repeat-like-containing domain (1); 0.133526 0.50627 D 0.000118 T 0.48874 0.1524 L 0.53249 1.67 0.19300 N 0.999979 D 0.89917 1.0 D 0.64687 0.928 T 0.34976 -0.9807 10 0.52906 T 0.07 -20.421 8.7897 0.34843 0.4108:0.4532:0.1361:0.0 . 1957 Q96PE2 ARHGH_HUMAN W 1957 ENSP00000263674:R1957W ENSP00000263674:R1957W R + 1 2 ARHGEF17 72754514 0.256000 0.24012 0.269000 0.24586 0.573000 0.36030 1.436000 0.34980 1.442000 0.47568 0.655000 0.94253 CGG TCGA-H6-8124-01A-11D-2396-08 ARHGEF17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397365.1 1 0 1 99 215 0 92 1 1 11 64 0 92 2 0 0 0 0 0 2 1 1.000000 98 213 0 92 2 0 0 0 0 92 2 -20.000000 1 1 0 0 1 1 2 3 2.215795 0 0.700000 1.770000 0.702085 0.900000 7.500000e-01 1.000000 1.000000 0.905737 0.900000 1 8.200000e-01 9.900000e-01 MAML2 84441 broad.mit.edu 37 11 95724867 95724867 + Silent SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr11:95724867G>A ENST00000524717.1 - 3 3444 c.2160C>T c.(2158-2160)ggC>ggT p.G720G NM_032427.1 NP_115803.1 Q8IZL2 MAML2_HUMAN mastermind-like 2 (Drosophila) CRTC3/MAML2(26)|CRTC1/MAML2(516) 43 Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837) CTGTGTTCTGGCCTACCACAG 0.428000 T MECT1, CRTC3 salivary gland mucoepidermoid Dom yes 11 11q22-q23 84441 mastermind-like 2 (Drosophila) E 0 SO:0001819 synonymous_variant ENST00000524717.1 1 1 hg19 CCDS44714.1 TCGA-H6-8124-01A-11D-2396-08 MAML2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395540.1 1 0 1 136 256 0 45 1 1 24 40 0 45 2 0 0 0 0 0 2 1 1.000000 131 265 0 46 2 0 0 0 0 45 2 -20.000000 1 1 120808 3 41 1 1 2 3 2.215795 0 0.700000 1.770000 0.702085 0.990000 8.600000e-01 1.000000 1.000000 0.972284 0.990000 1 9.200000e-01 1 ARHGDIB 397 broad.mit.edu 37 12 15095522 15095522 + Silent SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr12:15095522G>A ENST00000228945.4 - 6 684 c.540C>T c.(538-540)gaC>gaT p.D180D ARHGDIB_ENST00000541546.1_Silent_p.D180D|ARHGDIB_ENST00000539131.1_5'UTR|ARHGDIB_ENST00000541644.1_Silent_p.D180D NM_001175.4 NP_001166.3 P52566 GDIR2_HUMAN Rho GDP dissociation inhibitor (GDI) beta 15 GCTTGTCATCGTCGGTGAAGA 0.567000 0 SO:0001819 synonymous_variant ENST00000228945.4 1 1 hg19 CCDS8671.1 . . . . . . . . . . G 8.275 0.814158 0.16537 . . ENSG00000111348 ENST00000536592 . . . 4.73 -9.03 0.00737 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -23.6554 19.0707 0.93134 0.8544:0.0:0.1456:0.0 . . . . X 174 . . R - 1 2 ARHGDIB 14986789 0.273000 0.24181 0.064000 0.19789 0.971000 0.66376 -0.294000 0.08309 -2.089000 0.00860 -0.145000 0.13849 CGA TCGA-H6-8124-01A-11D-2396-08 ARHGDIB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400871.1 1 0 1 556 213 0 159 1 1 419 194 0 159 2 0 0 0 0 0 2 1 1.000000 549 211 0 156 2 0 0 0 0 159 2 -20.000000 1 1 121412 11 47 1 0 2 2 2.354604 1 0.700000 1.770000 0.700000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V 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 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V 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-H6-8124-01A-11D-2396-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 61 27 0 15 1 9.999999e-01 17 3 0 15 2 1 1 207 129 0 435 2 1 1.000000 61 27 0 15 2 1 1 5456 2557 0 15 2 -20.000000 1 1 0 0 1 0 2 2 2.354604 1 0.700000 1.770000 0.700000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 LRP1 4035 broad.mit.edu 37 12 57573330 57573330 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr12:57573330G>A ENST00000243077.3 + 29 5423 c.4957G>A c.(4957-4959)Gtc>Atc p.V1653I NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 184 Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) GGAGACAGTCGTCTCTGCAGG 0.632000 0 SO:0001583 missense ENST00000243077.3 1 1 hg19 CCDS8932.1 2 9.157509157509158E-4 0 0.0 0 0.0 2 0.0034965034965034965 0 0.0 G 12.57 1.977557 0.34848 . . ENSG00000123384 ENST00000243077 D 0.95554 -3.74 4.8 4.8 0.61643 Six-bladed beta-propeller, TolB-like (1); 0.000000 0.64402 D 0.000014 D 0.93579 0.7950 N 0.10664 0.02 0.80722 D 1 D 0.76494 0.999 D 0.79784 0.993 D 0.90619 0.4558 10 0.10111 T 0.7 . 16.7799 0.85560 0.0:0.0:1.0:0.0 . 1653 Q07954 LRP1_HUMAN I 1653 ENSP00000243077:V1653I ENSP00000243077:V1653I V + 1 0 LRP1 55859597 1.000000 0.71417 0.993000 0.49108 0.657000 0.38888 6.500000 0.73687 2.480000 0.83734 0.655000 0.94253 GTC TCGA-H6-8124-01A-11D-2396-08 LRP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412772.2 1 0 1 72 251 0 60 1 1 26 159 0 60 2 0 0 0 0 0 2 1 1.000000 72 247 0 60 2 0 0 0 0 60 2 -20.000000 1 1 121404 13 40 1 1 4 5 3.965701 1 0.700000 1.770000 0.831176 0.990000 9.200000e-01 1.000000 1.000000 0.994890 0.990000 1 9.900000e-01 1 DUSP6 1848 broad.mit.edu 37 12 89743153 89743153 + Missense_Mutation SNP C C A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr12:89743153C>A ENST00000279488.7 - 3 2255 c.1024G>T c.(1024-1026)Gac>Tac p.D342Y DUSP6_ENST00000308385.6_Missense_Mutation_p.D196Y|DUSP6_ENST00000547291.1_Missense_Mutation_p.D217Y|DUSP6_ENST00000547140.1_5'Flank NM_001946.2 NP_001937.2 Q16828 DUS6_HUMAN dual specificity phosphatase 6 16 CTCTCGAAGTCCAGCAGCTGA 0.478000 Colon(132;3456 5224) 0 SO:0001583 missense ENST00000279488.7 1 1 hg19 CCDS9033.1 . . . . . . . . . . C 22.8 4.333073 0.81801 . . ENSG00000139318 ENST00000279488;ENST00000308385;ENST00000547291 D;D;D 0.86030 -2.06;-2.06;-2.06 5.98 5.98 0.97165 Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2); 0.000000 0.85682 D 0.000000 D 0.93874 0.8040 M 0.87038 2.855 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.99 D 0.93919 0.7204 10 0.87932 D 0 . 20.4581 0.99154 0.0:1.0:0.0:0.0 . 196;342 Q16828-2;Q16828 .;DUS6_HUMAN Y 342;196;217 ENSP00000279488:D342Y;ENSP00000307835:D196Y;ENSP00000449838:D217Y ENSP00000279488:D342Y D - 1 0 DUSP6 88267284 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.745000 0.85046 2.835000 0.97688 0.650000 0.86243 GAC TCGA-H6-8124-01A-11D-2396-08 DUSP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406534.2 1 0 1 269 227 0 96 1 1 566 67 0 96 2 0 0 0 0 0 2 1 1.000000 268 223 0 96 2 0 0 0 0 96 2 -20.000000 1 1 0 0 1 0 1 1 1.563407 1 0.700000 1.770000 0.538462 0.970000 9.000000e-01 1.000000 0.990000 0.971408 0.970000 1 9.400000e-01 1 N4BP2L2 10443 broad.mit.edu 37 13 33110585 33110585 + Missense_Mutation SNP T T C TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr13:33110585T>C ENST00000267068.3 - 2 744 c.580A>G c.(580-582)Aaa>Gaa p.K194E N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.K194E|N4BP2L2_ENST00000399396.3_Intron NM_014887.2 NP_055702.1 Q92802 N42L2_HUMAN NEDD4 binding protein 2-like 2 16 Lung SC(185;0.0262) TCAGATTCTTTACAACTGTTC 0.299000 0 SO:0001583 missense ENST00000267068.3 1 1 hg19 CCDS9346.1 . . . . . . . . . . T 10.41 1.342658 0.24339 . . ENSG00000244754 ENST00000446957;ENST00000505213;ENST00000267068 T;T;T 0.44083 0.93;0.93;0.93 5.58 2.06 0.26882 . . . . . T 0.36358 0.0964 L 0.53249 1.67 0.09310 N 0.999997 B;B 0.21071 0.051;0.024 B;B 0.16722 0.016;0.007 T 0.34675 -0.9819 9 0.72032 D 0.01 -18.8345 7.1289 0.25488 0.0:0.1463:0.2835:0.5702 . 194;194 D6R968;Q92802 .;N42L2_HUMAN E 194 ENSP00000394239:K194E;ENSP00000423362:K194E;ENSP00000267068:K194E ENSP00000267068:K194E K - 1 0 N4BP2L2 32008585 0.013000 0.17824 0.763000 0.31416 0.398000 0.30690 0.010000 0.13242 0.405000 0.25532 0.460000 0.39030 AAA TCGA-H6-8124-01A-11D-2396-08 N4BP2L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044421.1 1 0 1 147 250 0 19 1 1 48 44 0 19 2 0 0 0 0 0 2 1 1.000000 145 249 0 19 2 0 0 0 0 19 2 -20.000000 1 1 0 0 1 1 2 3 2.261976 0 0.700000 1.770000 0.706170 0.990000 9.400000e-01 1.000000 1.000000 0.995890 0.990000 1 9.900000e-01 1 SOHLH2 54937 broad.mit.edu 37 13 36744857 36744857 + Silent SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr13:36744857C>T ENST00000379881.3 - 10 1156 c.1068G>A c.(1066-1068)gcG>gcA p.A356A SOHLH2_ENST00000554962.1_Silent_p.A433A|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.A433A NM_017826.2 NP_060296.2 Q9NX45 SOLH2_HUMAN spermatogenesis and oogenesis specific basic helix-loop-helix 2 26 Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) TCAGAGACAGCGCTGCACTGG 0.388000 0 SO:0001819 synonymous_variant ENST00000379881.3 1 1 hg19 CCDS9355.1 TCGA-H6-8124-01A-11D-2396-08 SOHLH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044477.2 0 0 1 301 495 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 299 490 0 84 2 0 0 0 0 85 2 -20.000000 1 1 121412 2 40 1 1 2 3 2.261976 0 0.700000 1.770000 0.706170 0.990000 9.900000e-01 1.000000 1.000000 0.999664 0.990000 1 9.900000e-01 1 COX8C 341947 broad.mit.edu 37 14 93813699 93813699 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr14:93813699G>A ENST00000342144.2 + 1 163 c.85G>A c.(85-87)Gcc>Acc p.A29T UNC79_ENST00000256339.4_Intron NM_182971.2 NP_892016.1 Q7Z4L0 COX8C_HUMAN cytochrome c oxidase subunit VIIIC 5 all_cancers(154;0.083) TCCCCGCTTCGCCCACTCGGG 0.756000 GBM(134;630 1800 8342 13106 15419) 0 SO:0001583 missense ENST00000342144.2 0 1 hg19 CCDS9910.1 . . . . . . . . . . G 7.584 0.669319 0.14776 . . ENSG00000187581 ENST00000342144 . . . 2.6 -2.3 0.06785 . . . . . T 0.26448 0.0646 . . . 0.09310 N 1 B 0.15719 0.014 B 0.16289 0.015 T 0.26430 -1.0103 7 0.62326 D 0.03 . 3.5519 0.07850 0.4705:0.2318:0.2978:0.0 . 29 Q7Z4L0 COX8C_HUMAN T 29 . ENSP00000340568:A29T A + 1 0 COX8C 92883452 0.000000 0.05858 0.001000 0.08648 0.002000 0.02628 -1.535000 0.02210 -0.438000 0.07232 -0.361000 0.07541 GCC TCGA-H6-8124-01A-11D-2396-08 COX8C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412769.1 0 0 0 6 147 0 33 0 0 0 0 33 2 0 0 0 0 0 2 1 0.927728 6 112 0 31 2 0 0 0 0 33 2 -9.237671 1 1 116578 2 32 1 0 0 0 2.150613 0 0.700000 1.770000 0.697885 0.110000 4.000000e-02 0.230000 0.110000 0.127769 0.110000 0 7.000000e-02 1.700000e-01 MYH13 8735 broad.mit.edu 37 17 10212619 10212619 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr17:10212619G>A ENST00000418404.3 - 34 5264 c.5101C>T c.(5101-5103)Cgg>Tgg p.R1701W RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.R1701W Q9UKX3 MYH13_HUMAN myosin, heavy chain 13, skeletal muscle 108 CTGCGGGTCCGCTCCGTCTGT 0.657000 0 SO:0001583 missense ENST00000418404.3 1 0 hg19 CCDS45613.1 . . . . . . . . . . G 17.91 3.504479 0.64410 . . ENSG00000006788 ENST00000252172 D 0.85013 -1.93 4.45 -3.48 0.04739 Myosin tail (1); . . . . D 0.94958 0.8369 H 0.98525 4.255 0.31829 N 0.624973 D 0.89917 1.0 D 0.91635 0.999 D 0.94056 0.7322 9 0.87932 D 0 . 16.6484 0.85182 0.0:0.0:0.3441:0.6559 . 1701 Q9UKX3 MYH13_HUMAN W 1701 ENSP00000252172:R1701W ENSP00000252172:R1701W R - 1 2 MYH13 10153344 0.078000 0.21339 0.985000 0.45067 0.779000 0.44077 -0.555000 0.05999 -0.297000 0.08934 -0.182000 0.12963 CGG TCGA-H6-8124-01A-11D-2396-08 MYH13-003 KNOWN alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000442255.1 1 0 1 74 146 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 1.000000 73 144 0 66 2 0 0 0 0 67 2 -2.239613 0 1 0 0 1 0 0 0 2.142607 0 0.700000 1.770000 0.695740 0.940000 7.700000e-01 1.000000 1.000000 0.933538 0.940000 1 8.500000e-01 1 TP53 7157 broad.mit.edu 37 17 7577568 7577568 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr17:7577568C>T ENST00000269305.4 - 7 902 c.713G>A c.(712-714)tGt>tAt p.C238Y TP53_ENST00000445888.2_Missense_Mutation_p.C238Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C238Y|TP53_ENST00000420246.2_Missense_Mutation_p.C238Y|TP53_ENST00000359597.4_Missense_Mutation_p.C238Y|TP53_ENST00000413465.2_Missense_Mutation_p.C238Y NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.C238Y(65)|p.C238F(46)|p.C238S(9)|p.0?(8)|p.?(5)|p.C145F(5)|p.C145Y(5)|p.M237_N239delMCN(4)|p.C238fs*21(1)|p.M237fs*1(1)|p.M144_N146delMCN(1)|p.C238del(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.H233fs*6(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)|p.N239_C242del(1)|p.C145S(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGAACTGTTACACATGTAGTT 0.572000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 158 Substitution - Missense(131)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(4) GRCh37 CM034930 TP53 M SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 22.7 4.327056 0.81690 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99964 -9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96 4.09 4.09 0.47781 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99972 0.9991 M 0.92970 3.365 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0 D 0.95847 0.8871 10 0.87932 D 0 -18.536 14.6088 0.68501 0.0:1.0:0.0:0.0 . 238;238;145;238;238;238 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. Y 238;238;238;238;238;238;227;145;106;145 ENSP00000410739:C238Y;ENSP00000352610:C238Y;ENSP00000269305:C238Y;ENSP00000398846:C238Y;ENSP00000391127:C238Y;ENSP00000391478:C238Y;ENSP00000425104:C106Y;ENSP00000423862:C145Y ENSP00000269305:C238Y C - 2 0 TP53 7518293 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.556000 0.82233 2.564000 0.86499 0.462000 0.41574 TGT TCGA-H6-8124-01A-11D-2396-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 144 103 0 96 1 1 54 31 0 96 2 1 1 176 175 0 986 2 1 1.000000 141 100 0 94 2 0 0 0 0 96 2 -20.000000 1 1 121412 3 28 1 0 1 1 1.314500 1 0.700000 1.770000 0.538462 0.970000 9.000000e-01 1.000000 0.990000 0.976208 0.970000 1 9.400000e-01 1 SLC1A6 6511 broad.mit.edu 37 19 15083616 15083616 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr19:15083616C>T ENST00000221742.3 - 1 114 c.107G>A c.(106-108)cGc>cAc p.R36H SLC1A6_ENST00000598504.1_Missense_Mutation_p.R36H|SLC1A6_ENST00000430939.2_Silent_p.A40A|SLC1A6_ENST00000544886.2_Missense_Mutation_p.R36H|SLC1A6_ENST00000600144.1_Missense_Mutation_p.R36H NM_005071.1 NP_005062.1 P48664 EAA4_HUMAN solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6 42 CAGGCGCGTGCGCAGTGCTCT 0.677000 0 SO:0001583 missense ENST00000221742.3 0 1 hg19 CCDS12321.1 . . . . . . . . . . C 16.19 3.053905 0.55218 0.0 1.16E-4 ENSG00000105143 ENST00000221742;ENST00000544886;ENST00000542610 T;T 0.56776 0.44;1.18 4.46 4.46 0.54185 . 0.153858 0.50627 D 0.000114 T 0.53077 0.1774 N 0.24115 0.695 0.43390 D 0.995506 D;D;D 0.76494 0.999;0.999;0.998 P;P;P 0.60236 0.871;0.871;0.769 T 0.53408 -0.8443 10 0.44086 T 0.13 -13.3673 12.4519 0.55681 0.0:1.0:0.0:0.0 . 36;37;36 Q8N753;Q59GB0;P48664 .;.;EAA4_HUMAN H 36;36;37 ENSP00000221742:R36H;ENSP00000446175:R36H ENSP00000221742:R36H R - 2 0 SLC1A6 14944616 1.000000 0.71417 1.000000 0.80357 0.263000 0.26337 3.133000 0.50531 2.306000 0.77630 0.313000 0.20887 CGC TCGA-H6-8124-01A-11D-2396-08 SLC1A6-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466283.1 0 0 0 4 107 1 34 0 0 0 1 34 2 0 0 0 0 0 2 0 0.030501 4 106 1 34 12 0 0 0 1 34 2 -7.628079 1 1 121192 8 37 1 0 1 1 1.405512 1 0.700000 1.770000 0.548193 0.070000 2.000000e-02 0.160000 0.070000 0.083323 0.070000 0 4.000000e-02 1.200000e-01 MYO9B 4650 broad.mit.edu 37 19 17213029 17213029 + Missense_Mutation SNP C C A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr19:17213029C>A ENST00000594824.1 + 2 649 c.502C>A c.(502-504)Cac>Aac p.H168N CTD-2528A14.5_ENST00000597045.1_RNA|MYO9B_ENST00000397274.2_Missense_Mutation_p.H168N|MYO9B_ENST00000593411.1_3'UTR|MYO9B_ENST00000595618.1_Missense_Mutation_p.H168N Q13459 MYO9B_HUMAN myosin IXB 39 GAACCTCAAGCACCGCTTCCT 0.572000 0 SO:0001583 missense ENST00000594824.1 1 1 hg19 . . . . . . . . . . C 1.069 -0.670350 0.03403 . . ENSG00000099331 ENST00000397274 D 0.86956 -2.19 5.62 4.59 0.56863 Myosin head, motor domain (2); 0.714976 0.12174 N 0.492731 T 0.71634 0.3363 N 0.05467 -0.045 0.09310 N 0.999999 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.09377 0.001;0.001;0.004 T 0.57183 -0.7855 10 0.14656 T 0.56 . 7.2307 0.26040 0.0:0.7392:0.0:0.2608 . 168;168;174 Q13459;B0I1T6;Q4LE74 MYO9B_HUMAN;.;. N 168 ENSP00000380444:H168N ENSP00000380444:H168N H + 1 0 MYO9B 17074029 0.006000 0.16342 0.261000 0.24466 0.994000 0.84299 0.110000 0.15437 1.376000 0.46267 0.655000 0.94253 CAC TCGA-H6-8124-01A-11D-2396-08 MYO9B-002 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000463236.1 1 0 1 328 323 0 212 1 1 13 26 0 212 2 0 0 0 0 0 2 1 1.000000 323 316 0 210 2 0 0 0 0 212 2 -20.000000 1 1 0 0 1 0 1 1 1.405512 1 0.700000 1.770000 0.548193 0.940000 8.700000e-01 1.000000 1.000000 0.952117 0.940000 1 9.100000e-01 9.900000e-01 ZNF585A 199704 broad.mit.edu 37 19 37644488 37644488 + Missense_Mutation SNP T T C TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr19:37644488T>C ENST00000356958.4 - 5 571 c.313A>G c.(313-315)Aat>Gat p.N105D ZNF585A_ENST00000355533.2_Missense_Mutation_p.N50D|ZNF585A_ENST00000292841.5_Missense_Mutation_p.N50D|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.N50D Q6P3V2 Z585A_HUMAN zinc finger protein 585A 42 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) CTACATTGATTATGGTCCCAT 0.323000 0 SO:0001583 missense ENST00000356958.4 1 1 hg19 . . . . . . . . . . T 13.10 2.136367 0.37728 . . ENSG00000196967 ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533 T;T;T;T 0.27402 3.3;3.34;3.34;1.67 3.76 2.71 0.32032 . 1.711460 0.03779 U 0.261004 T 0.24470 0.0593 L 0.31804 0.96 0.09310 N 1 B 0.20164 0.042 B 0.24006 0.05 T 0.22312 -1.0220 10 0.27082 T 0.32 . 5.4867 0.16753 0.0:0.1002:0.1734:0.7264 . 105 Q6P3V2 Z585A_HUMAN D 105;50;50;50 ENSP00000349440:N105D;ENSP00000292841:N50D;ENSP00000375998:N50D;ENSP00000347724:N50D ENSP00000292841:N50D N - 1 0 ZNF585A 42336328 0.000000 0.05858 0.179000 0.23059 0.102000 0.19082 -0.109000 0.10840 0.567000 0.29293 0.533000 0.62120 AAT TCGA-H6-8124-01A-11D-2396-08 ZNF585A-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000457980.2 1 0 1 630 600 0 61 1 7.046121e-01 3 1 0 61 2 0 0 0 0 0 2 1 1.000000 624 600 0 59 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 1 2 3 2.772088 1 0.700000 1.770000 0.766264 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 FCGBP 8857 broad.mit.edu 37 19 40363276 40363276 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr19:40363276C>T ENST00000221347.6 - 32 14801 c.14794G>A c.(14794-14796)Gag>Aag p.E4932K NM_003890.2 NP_003881.2 Q9Y6R7 FCGBP_HUMAN Fc fragment of IgG binding protein 165 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) GCCACAGCCTCGCCGTCCACG 0.652000 0 SO:0001583 missense ENST00000221347.6 1 1 hg19 CCDS12546.1 . . . . . . . . . . C 11.28 1.591238 0.28357 . . ENSG00000090920 ENST00000221347 T 0.58210 0.35 5.05 4.0 0.46444 von Willebrand factor, type D domain (3); 0.000000 0.64402 U 0.000001 T 0.58595 0.2133 L 0.48642 1.525 0.09310 N 1 D 0.89917 1.0 D 0.78314 0.991 T 0.50482 -0.8823 10 0.06891 T 0.86 . 11.216 0.48827 0.0:0.8151:0.1849:0.0 . 4932 Q9Y6R7 FCGBP_HUMAN K 4932 ENSP00000221347:E4932K ENSP00000221347:E4932K E - 1 0 FCGBP 45055116 0.037000 0.19845 0.071000 0.20095 0.946000 0.59487 3.060000 0.49955 1.326000 0.45319 0.313000 0.20887 GAG TCGA-H6-8124-01A-11D-2396-08 FCGBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462507.1 1 0 1 116 106 0 36 1 1 11 66 0 36 2 0 0 0 0 0 2 1 1.000000 116 103 0 35 2 0 0 0 0 36 2 -20.000000 1 1 120874 1 30 1 1 2 3 2.772088 1 0.700000 1.770000 0.766264 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 IGSF8 93185 broad.mit.edu 37 1 160063798 160063798 + Missense_Mutation SNP A A C TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr1:160063798A>C ENST00000368086.1 - 3 822 c.606T>G c.(604-606)ttT>ttG p.F202L IGSF8_ENST00000460351.1_5'UTR|IGSF8_ENST00000314485.7_Missense_Mutation_p.F202L Q969P0 IGSF8_HUMAN immunoglobulin superfamily, member 8 33 all_cancers(52;1.11e-16)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246) CAGATCGCCCAAAGGACACTG 0.637000 0 SO:0001583 missense ENST00000368086.1 1 1 hg19 CCDS1195.1 . . . . . . . . . . A 17.08 3.297471 0.60086 . . ENSG00000162729 ENST00000314485;ENST00000368086;ENST00000358475;ENST00000448417 T;T;T 0.21932 1.98;1.98;1.98 3.88 -1.42 0.08913 Immunoglobulin subtype (1);Immunoglobulin-like fold (1); 0.156351 0.41938 D 0.000796 T 0.14356 0.0347 L 0.29908 0.895 0.48830 D 0.999713 D 0.76494 0.999 D 0.80764 0.994 T 0.14420 -1.0473 10 0.72032 D 0.01 -3.709 5.1525 0.15017 0.4767:0.1584:0.3649:0.0 . 202 Q969P0 IGSF8_HUMAN L 202 ENSP00000316664:F202L;ENSP00000357065:F202L;ENSP00000397464:F202L ENSP00000316664:F202L F - 3 2 IGSF8 158330422 0.968000 0.33430 0.906000 0.35671 0.836000 0.47400 0.137000 0.15995 -0.375000 0.07955 -0.438000 0.05819 TTT TCGA-H6-8124-01A-11D-2396-08 IGSF8-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060636.1 1 0 1 192 414 0 163 1 1 59 67 0 163 2 0 0 0 0 0 2 1 1.000000 186 410 0 161 2 0 0 0 0 163 2 -20.000000 1 1 0 0 1 0 0 0 2.144885 0 0.700000 1.770000 0.697885 0.890000 7.900000e-01 1.000000 0.890000 0.899220 0.890000 1 8.400000e-01 9.500000e-01 KLHDC8A 55220 broad.mit.edu 37 1 205312365 205312365 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr1:205312365G>A ENST00000367156.3 - 5 1184 c.368C>T c.(367-369)aCg>aTg p.T123M KLHDC8A_ENST00000367155.3_Missense_Mutation_p.T123M|KLHDC8A_ENST00000537168.1_Intron|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.T123M|KLHDC8A_ENST00000460687.1_Intron|KLHDC8A_ENST00000606529.1_5'Flank NM_001271863.1 NP_001258792.1 Q8IYD2 KLD8A_HUMAN kelch domain containing 8A 14 Breast(84;0.23) BRCA - Breast invasive adenocarcinoma(75;0.117) GCCTTTGGCCGTGACAGAAAT 0.592000 0 SO:0001583 missense ENST00000367156.3 1 1 hg19 CCDS30985.1 . . . . . . . . . . G 17.73 3.461883 0.63513 . . ENSG00000162873 ENST00000367155;ENST00000367156;ENST00000539253 T;T;T 0.67865 -0.29;-0.29;-0.29 5.65 5.65 0.86999 Kelch-type beta propeller (1); 0.147910 0.64402 D 0.000012 T 0.67813 0.2933 L 0.59436 1.845 0.53688 D 0.999975 D 0.56287 0.975 B 0.43225 0.412 T 0.72931 -0.4142 10 0.66056 D 0.02 -13.9286 19.3222 0.94246 0.0:0.0:1.0:0.0 . 123 Q8IYD2 KLD8A_HUMAN M 123 ENSP00000356123:T123M;ENSP00000356124:T123M;ENSP00000442229:T123M ENSP00000356123:T123M T - 2 0 KLHDC8A 203578988 1.000000 0.71417 0.996000 0.52242 0.996000 0.88848 5.523000 0.67099 2.646000 0.89796 0.655000 0.94253 ACG TCGA-H6-8124-01A-11D-2396-08 KLHDC8A-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090397.1 1 0 1 271 517 1 187 0 5.601188e-01 0 5 1 187 2 0 0 0 0 0 2 1 1.000000 266 512 1 186 15 0 0 0 1 187 2 -20.000000 1 1 0 0 1 1 2 3 2.235718 0 0.700000 1.770000 0.704142 0.990000 8.900000e-01 1.000000 1.000000 0.979284 0.990000 1 9.400000e-01 1 PANK4 55229 broad.mit.edu 37 1 2444410 2444410 + Silent SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr1:2444410C>T ENST00000378466.3 - 13 1656 c.1644G>A c.(1642-1644)ctG>ctA p.L548L PANK4_ENST00000435556.3_Silent_p.L509L NM_018216.1 NP_060686.1 Q9NVE7 PANK4_HUMAN pantothenate kinase 4 23 all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634) all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123) CCTCCCAGCCCAGCGCGTCCA 0.677000 0 SO:0001819 synonymous_variant ENST00000378466.3 1 1 hg19 CCDS42.1 TCGA-H6-8124-01A-11D-2396-08 PANK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000002082.1 1 0 1 330 640 0 294 1 9.999485e-01 6 25 0 294 2 0 0 0 0 0 2 1 1.000000 326 626 0 289 2 0 0 0 0 294 2 -20.000000 1 1 0 0 1 1 2 3 2.188926 0 0.700000 1.770000 0.701046 0.970000 8.800000e-01 1.000000 1.000000 0.967722 0.970000 1 9.200000e-01 1 AJAP1 55966 broad.mit.edu 37 1 4772528 4772528 + Missense_Mutation SNP G G A rs138033447 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr1:4772528G>A ENST00000378191.4 + 2 979 c.598G>A c.(598-600)Gtt>Att p.V200I AJAP1_ENST00000378190.3_Missense_Mutation_p.V200I NM_018836.3 NP_061324.1 Q9UKB5 AJAP1_HUMAN adherens junctions associated protein 1 24 all_cancers(77;0.071)|Ovarian(185;0.0721) all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215) ATTTCCGGGCGTTTACGGCCC 0.652000 0 SO:0001583 missense ENST00000378191.4 1 1 hg19 CCDS54.1 . . . . . . . . . . G 0.001 -3.194097 0.00026 2.27E-4 0.0 ENSG00000196581 ENST00000378190;ENST00000378191 T;T 0.40225 1.04;1.04 5.04 -10.1 0.00402 . 1.402030 0.05157 N 0.497146 T 0.11239 0.0274 N 0.02539 -0.55 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.09122 -1.0689 10 0.02654 T 1 3.1249 2.9387 0.05823 0.0974:0.3502:0.3527:0.1997 . 200 Q9UKB5 AJAP1_HUMAN I 200 ENSP00000367432:V200I;ENSP00000367433:V200I ENSP00000367432:V200I V + 1 0 AJAP1 4672388 0.000000 0.05858 0.000000 0.03702 0.200000 0.23975 -3.993000 0.00318 -6.103000 0.00006 -0.657000 0.03884 GTT TCGA-H6-8124-01A-11D-2396-08 AJAP1-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000001542.3 1 0 1 55 88 0 42 0 0 0 1 0 42 2 0 0 0 0 0 2 1 1.000000 55 84 0 42 2 0 0 0 0 42 2 -20.000000 1 1 121344 1 29 1 1 2 3 2.188926 0 0.700000 1.770000 0.701046 0.990000 8.700000e-01 1.000000 1.000000 0.988793 0.990000 1 9.800000e-01 1 DEPDC1 55635 broad.mit.edu 37 1 68952619 68952619 + Splice_Site SNP C C A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr1:68952619C>A ENST00000456315.2 - 6 884 c.e6+1 DEPDC1_ENST00000370966.5_Splice_Site NM_001114120.1 NP_001107592.1 Q5TB30 DEP1A_HUMAN DEP domain containing 1 13 ATTTAACTTACAATTTGCTAG 0.328000 0 SO:0001630 splice_region_variant ENST00000456315.2 1 1 hg19 CCDS44159.1 . . . . . . . . . . C 21.8 4.196068 0.78902 . . ENSG00000024526 ENST00000456315;ENST00000370966;ENST00000370964 . . . 5.38 5.38 0.77491 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.1258 0.93384 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . DEPDC1 68725207 1.000000 0.71417 1.000000 0.80357 0.900000 0.52787 6.994000 0.76251 2.534000 0.85438 0.585000 0.79938 . TCGA-H6-8124-01A-11D-2396-08 DEPDC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000025514.2 1 0 1 123 280 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 1.000000 116 263 0 27 2 0 0 0 0 39 2 -20.000000 1 1 0 0 1 1 2 3 2.225223 0 0.700000 1.770000 0.704142 0.880000 7.500000e-01 1.000000 0.880000 0.888090 0.880000 1 8.100000e-01 9.600000e-01 XKR7 343702 broad.mit.edu 37 20 30584387 30584387 + Silent SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr20:30584387C>T ENST00000562532.2 + 3 1041 c.867C>T c.(865-867)gaC>gaT p.D289D NM_001011718.1 NP_001011718.1 Q5GH72 XKR7_HUMAN XK, Kell blood group complex subunit-related family, member 7 34 Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347) ACTCGCGGGACGACAAGCGGC 0.701000 0 SO:0001819 synonymous_variant ENST00000562532.2 1 1 hg19 CCDS33459.1 TCGA-H6-8124-01A-11D-2396-08 XKR7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078597.3 1 0 0 73 198 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 1.000000 72 193 0 71 2 0 0 0 0 72 2 -20.000000 1 1 0 0 1 0 0 0 2.158459 0 0.700000 1.770000 0.697885 0.760000 6.100000e-01 0.910000 0.770000 0.767773 0.760000 0 6.800000e-01 8.400000e-01 PXDN 7837 broad.mit.edu 37 2 1670184 1670184 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr2:1670184C>T ENST00000252804.4 - 10 1143 c.1093G>A c.(1093-1095)Gcc>Acc p.A365T PXDN_ENST00000483018.1_5'UTR NM_012293.1 NP_036425.1 Q92626 PXDN_HUMAN peroxidasin homolog (Drosophila) 112 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) TGGCCTGTGGCGCTGCACTCC 0.587000 0 SO:0001583 missense ENST00000252804.4 1 1 hg19 CCDS46221.1 . . . . . . . . . . C 18.27 3.587546 0.66105 . . ENSG00000130508 ENST00000252804 T 0.68331 -0.32 5.09 4.21 0.49690 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.176187 0.49916 N 0.000139 T 0.73976 0.3656 M 0.67625 2.065 0.46542 D 0.999097 D;B 0.64830 0.994;0.127 P;B 0.59761 0.863;0.178 T 0.75243 -0.3386 10 0.87932 D 0 -31.0361 7.7167 0.28708 0.1612:0.756:0.0:0.0828 . 365;365 Q92626-2;Q92626 .;PXDN_HUMAN T 365 ENSP00000252804:A365T ENSP00000252804:A365T A - 1 0 PXDN 1649191 1.000000 0.71417 0.987000 0.45799 0.734000 0.41952 4.819000 0.62664 1.140000 0.42260 0.655000 0.94253 GCC TCGA-H6-8124-01A-11D-2396-08 PXDN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322505.1 1 0 1 17 101 0 52 0 9.991124e-01 0 74 0 52 2 0 0 0 0 0 2 1 0.999970 17 98 0 49 2 0 0 0 0 52 2 -20.000000 1 1 0 0 1 0 1 1 1.893316 1 0.700000 1.770000 0.648300 0.350000 2.100000e-01 0.520000 0.350000 0.363904 0.350000 0 2.700000e-01 4.400000e-01 PLCD4 84812 broad.mit.edu 37 2 219500518 219500518 + Splice_Site SNP G G C TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr2:219500518G>C ENST00000450993.2 + 14 2235 c.e14-1 PLCD4_ENST00000417849.1_Splice_Site|RP11-548H3.1_ENST00000607946.1_RNA|PLCD4_ENST00000432688.1_Splice_Site NM_032726.3 NP_116115.1 Q9BRC7 PLCD4_HUMAN phospholipase C, delta 4 23 Renal(207;0.0915) CCTGACTACAGGTGATCAGCG 0.532000 0 SO:0001630 splice_region_variant ENST00000450993.2 1 1 hg19 CCDS46516.1 . . . . . . . . . . G 19.16 3.774719 0.70107 . . ENSG00000115556 ENST00000450993;ENST00000417849;ENST00000432688 . . . 4.85 4.85 0.62838 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 18.1177 0.89561 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . PLCD4 219208762 1.000000 0.71417 1.000000 0.80357 0.814000 0.46013 9.601000 0.98297 2.676000 0.91093 0.655000 0.94253 . TCGA-H6-8124-01A-11D-2396-08 PLCD4-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336876.1 1 0 1 48 54 0 23 1 7.685852e-01 2 3 0 23 2 0 0 0 0 0 2 1 1.000000 47 53 0 23 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 0 1 1 1.853026 1 0.700000 1.770000 0.643917 0.990000 8.900000e-01 1.000000 1.000000 0.992078 0.990000 1 9.900000e-01 1 TOPBP1 11073 broad.mit.edu 37 3 133327737 133327737 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr3:133327737G>A ENST00000260810.5 - 26 4374 c.4243C>T c.(4243-4245)Ctt>Ttt p.L1415F NM_007027.3 NP_008958.2 Q92547 TOPB1_HUMAN topoisomerase (DNA) II binding protein 1 40 CCTGACTGAAGAAGGCGTTTG 0.368000 Other conserved DNA damage response genes Ovarian(21;193 658 4424 15423 17362) 0 SO:0001583 missense ENST00000260810.5 1 1 hg19 CCDS46919.1 . . . . . . . . . . G 27.3 4.819176 0.90873 . . ENSG00000163781 ENST00000260810 T 0.28069 1.63 5.57 5.57 0.84162 . 0.000000 0.85682 D 0.000000 T 0.60741 0.2292 M 0.81497 2.545 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.62358 -0.6871 10 0.52906 T 0.07 . 19.5504 0.95315 0.0:0.0:1.0:0.0 . 1415 Q92547 TOPB1_HUMAN F 1415 ENSP00000260810:L1415F ENSP00000260810:L1415F L - 1 0 TOPBP1 134810427 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 8.006000 0.88564 2.612000 0.88384 0.655000 0.94253 CTT TCGA-H6-8124-01A-11D-2396-08 TOPBP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357254.1 1 0 1 86 178 0 12 1 1 29 33 0 12 2 0 0 0 0 0 2 1 1.000000 87 176 0 11 2 0 0 0 0 12 2 -20.000000 1 1 0 0 1 0 0 0 2.171377 0 0.700000 1.770000 0.700000 0.920000 7.600000e-01 1.000000 1.000000 0.923053 0.920000 1 8.400000e-01 1 CELSR3 1951 broad.mit.edu 37 3 48699138 48699138 + Silent SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr3:48699138C>T ENST00000164024.4 - 1 1210 c.930G>A c.(928-930)gcG>gcA p.A310A RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Silent_p.A310A NM_001407.2 NP_001398.2 Q9NYQ7 CELR3_HUMAN cadherin, EGF LAG seven-pass G-type receptor 3 p.A310A(1) 83 GTGCCCGGTTCGCCGAGGTTA 0.706000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000164024.4 1 1 hg19 CCDS2775.1 TCGA-H6-8124-01A-11D-2396-08 CELSR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257523.1 1 0 1 101 503 1 180 0 2.675188e-01 0 6 1 180 2 1 9.999669e-01 18 57 0 50 2 1 1.000000 100 499 1 178 13 0 0 0 1 180 2 -3.027413 1 1 0 0 1 0 0 0 2.171377 0 0.700000 1.770000 0.700000 0.470000 3.900000e-01 0.560000 0.480000 0.480554 0.470000 0 4.300000e-01 5.200000e-01 ZFYVE28 57732 broad.mit.edu 37 4 2306490 2306490 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr4:2306490G>A ENST00000290974.2 - 8 1916 c.1577C>T c.(1576-1578)tCc>tTc p.S526F ZFYVE28_ENST00000515312.1_Missense_Mutation_p.S456F|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.S496F|RP11-478C1.7_ENST00000510632.1_RNA NM_020972.2 NP_066023.2 Q9HCC9 LST2_HUMAN zinc finger, FYVE domain containing 28 31 AGAGTCCAGGGAAGTGGGCGA 0.667000 0 SO:0001583 missense ENST00000290974.2 1 1 hg19 CCDS33942.1 . . . . . . . . . . G 14.05 2.420143 0.42918 . . ENSG00000159733 ENST00000290974;ENST00000511071;ENST00000515312 T;T;T 0.60424 0.21;0.19;0.21 4.21 3.37 0.38596 . 0.815729 0.11518 N 0.556019 T 0.51601 0.1684 L 0.50333 1.59 0.09310 N 1 B;P 0.45902 0.004;0.868 B;B 0.43052 0.007;0.406 T 0.46359 -0.9197 10 0.72032 D 0.01 . 6.0708 0.19887 0.1057:0.2096:0.6846:0.0 . 496;526 Q9HCC9-2;Q9HCC9 .;LST2_HUMAN F 526;496;456 ENSP00000290974:S526F;ENSP00000425706:S496F;ENSP00000426299:S456F ENSP00000290974:S526F S - 2 0 ZFYVE28 2276288 0.032000 0.19561 0.001000 0.08648 0.011000 0.07611 2.501000 0.45389 0.997000 0.38969 0.306000 0.20318 TCC TCGA-H6-8124-01A-11D-2396-08 ZFYVE28-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000360078.1 1 0 1 163 382 0 138 1 4.710303e-01 2 3 0 138 2 0 0 0 0 0 2 1 1.000000 161 378 0 137 2 0 0 0 0 138 2 -20.000000 1 1 0 0 1 1 2 3 2.239288 0 0.700000 1.770000 0.704142 0.860000 7.500000e-01 1.000000 0.860000 0.871507 0.860000 1 8.000000e-01 9.300000e-01 GRID2 2895 broad.mit.edu 37 4 94006305 94006305 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr4:94006305G>A ENST00000282020.4 + 3 662 c.404G>A c.(403-405)cGg>cAg p.R135Q GRID2_ENST00000505687.1_3'UTR|GRID2_ENST00000510992.1_Intron NM_001510.2 NP_001501.2 O43424 GRID2_HUMAN glutamate receptor, ionotropic, delta 2 100 Hepatocellular(203;0.114)|all_hematologic(202;0.177) GGACTCACCCGGAGCAACAGG 0.537000 0 SO:0001583 missense ENST00000282020.4 1 1 hg19 CCDS3637.1 . . . . . . . . . . G 19.21 3.783512 0.70222 . . ENSG00000152208 ENST00000282020 D 0.85955 -2.05 5.23 5.23 0.72850 Extracellular ligand-binding receptor (1); 0.168825 0.50627 D 0.000117 T 0.75324 0.3834 N 0.14661 0.345 0.80722 D 1 P;P 0.46987 0.888;0.888 B;B 0.40009 0.185;0.316 T 0.75351 -0.3348 10 0.25106 T 0.35 . 19.1731 0.93588 0.0:0.0:1.0:0.0 . 135;76 O43424;B4DYB9 GRID2_HUMAN;. Q 135 ENSP00000282020:R135Q ENSP00000282020:R135Q R + 2 0 GRID2 94225328 1.000000 0.71417 0.999000 0.59377 0.991000 0.79684 3.748000 0.55142 2.613000 0.88420 0.655000 0.94253 CGG TCGA-H6-8124-01A-11D-2396-08 GRID2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253588.2 0 0 1 222 445 1 100 0 0 0 1 100 2 0 0 0 0 0 2 1 1.000000 221 437 1 100 21 0 0 0 1 100 2 -18.194470 1 1 0 0 1 1 2 3 2.239288 0 0.700000 1.770000 0.704142 0.960000 8.500000e-01 1.000000 1.000000 0.958031 0.960000 1 9.000000e-01 1 IL12B 3593 broad.mit.edu 37 5 158750144 158750144 + Silent SNP G G A rs142017503 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr5:158750144G>A ENST00000231228.2 - 3 737 c.282C>T c.(280-282)ggC>ggT p.G94G NM_002187.2 NP_002178.2 P29460 IL12B_HUMAN interleukin 12B 11 Renal(175;0.00196) Medulloblastoma(196;0.0354)|all_neural(177;0.138) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) TTAGAACCTCGCCTCCTTTGT 0.478000 0 SO:0001819 synonymous_variant ENST00000231228.2 1 1 hg19 CCDS4346.1 TCGA-H6-8124-01A-11D-2396-08 IL12B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252652.2 1 0 1 120 226 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 1.000000 119 223 0 41 2 0 0 0 0 43 2 -20.000000 1 1 121410 2 37 1 1 2 3 2.204364 0 0.700000 1.770000 0.701046 0.980000 8.400000e-01 1.000000 1.000000 0.968476 0.980000 1 9.100000e-01 1 DLL1 28514 broad.mit.edu 37 6 170597430 170597430 + Silent SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr6:170597430G>A ENST00000366756.3 - 4 900 c.567C>T c.(565-567)tcC>tcT p.S189S FAM120B_ENST00000540480.1_5'Flank NM_005618.3 NP_005609.3 O00548 DLL1_HUMAN delta-like 1 (Drosophila) 33 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) GGCAGAAAACGGAGCAGCCCT 0.632000 0 SO:0001819 synonymous_variant ENST00000366756.3 1 1 hg19 CCDS5313.1 TCGA-H6-8124-01A-11D-2396-08 DLL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043254.1 1 0 1 147 167 0 117 1 9.999420e-01 7 14 0 117 2 0 0 0 0 0 2 1 1.000000 145 166 0 116 2 0 0 0 0 117 2 -20.000000 1 1 0 0 1 0 1 1 1.509146 1 0.700000 1.770000 0.540933 0.860000 7.600000e-01 0.970000 0.870000 0.871460 0.860000 1 8.100000e-01 9.200000e-01 CUX1 1523 broad.mit.edu 37 7 101870648 101870648 + Splice_Site SNP A A C TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 A C A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr7:101870648A>C ENST00000292535.7 + 21 3170 c.3132A>C c.(3130-3132)gaA>gaC p.E1044D CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Splice_Site_p.E942D|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Splice_Site_p.E1055D|CUX1_ENST00000549414.2_Splice_Site_p.E1022D|CUX1_ENST00000550008.2_Splice_Site_p.E988D|CUX1_ENST00000556210.1_Splice_Site_p.E886D NM_181552.3 NP_853530.2 P39880 CUX1_HUMAN cut-like homeobox 1 70 TAATTACAGAAAGCACTCCAA 0.512000 0 SO:0001630 splice_region_variant ENST00000292535.7 1 0 hg19 CCDS5721.1 . . . . . . . . . . A 14.04 2.417793 0.42918 . . ENSG00000257923 ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210 T;T;T;T;T;T 0.60797 0.18;0.17;0.17;0.16;0.17;0.16 5.67 0.0822 0.14428 . 0.111571 0.64402 D 0.000015 T 0.37972 0.1023 L 0.43152 1.355 0.53688 D 0.999971 B;B 0.06786 0.001;0.0 B;B 0.09377 0.003;0.004 T 0.07654 -1.0761 10 0.21540 T 0.41 . 2.1663 0.03838 0.5209:0.1682:0.2064:0.1045 . 1044;1055 P39880;P39880-3 CUX1_HUMAN;. D 1055;1044;1022;988;942;886 ENSP00000353401:E1055D;ENSP00000292535:E1044D;ENSP00000446630:E1022D;ENSP00000447373:E988D;ENSP00000450125:E942D;ENSP00000451558:E886D ENSP00000292535:E1044D E + 3 2 CUX1 101657368 1.000000 0.71417 1.000000 0.80357 0.956000 0.61745 1.791000 0.38744 0.402000 0.25451 0.533000 0.62120 GAA TCGA-H6-8124-01A-11D-2396-08 CUX1-004 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000347535.1 1 0 1 862 1733 0 218 0 9.997194e-01 0 27 0 218 2 0 0 0 0 0 2 1 1.000000 856 1718 0 218 2 0 0 0 0 218 2 -20.000000 1 1 0 0 1 0.700000 1.770000 0 0 POM121L12 285877 broad.mit.edu 37 7 53103972 53103972 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr7:53103972G>A ENST00000408890.4 + 1 624 c.608G>A c.(607-609)aGc>aAc p.S203N NM_182595.3 NP_872401.3 Q8N7R1 P1L12_HUMAN POM121 transmembrane nucleoporin-like 12 61 GTCTCAGACAGCAAGGGTGGC 0.667000 0 SO:0001583 missense ENST00000408890.4 1 1 hg19 CCDS43584.1 . . . . . . . . . . G 10.09 1.253636 0.22965 . . ENSG00000221900 ENST00000408890 T 0.11604 2.76 1.68 0.545 0.17190 . . . . . T 0.04770 0.0129 N 0.20986 0.625 0.09310 N 1 P 0.50710 0.938 B 0.37451 0.25 T 0.31475 -0.9942 9 0.11182 T 0.66 . 4.9354 0.13937 0.0:0.0:0.5027:0.4973 . 203 Q8N7R1 P1L12_HUMAN N 203 ENSP00000386133:S203N ENSP00000386133:S203N S + 2 0 POM121L12 53071466 0.001000 0.12720 0.003000 0.11579 0.080000 0.17528 0.642000 0.24735 0.131000 0.18576 0.561000 0.74099 AGC TCGA-H6-8124-01A-11D-2396-08 POM121L12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342656.1 1 0 0 221 406 0 173 0 0 0 0 173 2 0 0 0 0 0 2 1 1.000000 217 397 0 171 2 0 0 0 0 173 2 -20.000000 1 1 120902 1 32 1 0 0 0 2.170941 0 0.700000 1.770000 0.700000 0.990000 8.900000e-01 1.000000 1.000000 0.981761 0.990000 1 9.400000e-01 1 ADAM22 53616 broad.mit.edu 37 7 87564445 87564445 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr7:87564445G>A ENST00000265727.7 + 2 269 c.190G>A c.(190-192)Gaa>Aaa p.E64K ADAM22_ENST00000439864.1_Missense_Mutation_p.E64K|ADAM22_ENST00000398201.4_Missense_Mutation_p.E64K|ADAM22_ENST00000315984.7_Missense_Mutation_p.E64K|ADAM22_ENST00000398209.3_Missense_Mutation_p.E64K|ADAM22_ENST00000398204.4_Missense_Mutation_p.E64K Q9P0K1 ADA22_HUMAN ADAM metallopeptidase domain 22 53 Esophageal squamous(14;0.00202) STAD - Stomach adenocarcinoma(171;0.215) CGGCGAAGACGAAAGTCGGCA 0.687000 0 SO:0001583 missense ENST00000265727.7 1 1 hg19 CCDS47637.1 . . . . . . . . . . G 21.2 4.114188 0.77210 . . ENSG00000008277 ENST00000398204;ENST00000439864;ENST00000412441;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203 T;T;T;T;T;T;T;T 0.17528 4.45;3.6;2.27;4.45;4.45;4.46;4.46;4.44 4.94 1.94 0.25998 . 0.154004 0.43416 N 0.000575 T 0.30198 0.0757 L 0.55213 1.73 0.24151 N 0.995698 D;D;D;P;P;D 0.76494 0.99;0.979;0.983;0.639;0.94;0.999 P;P;P;B;P;D 0.69142 0.869;0.761;0.846;0.245;0.535;0.962 T 0.02179 -1.1200 10 0.59425 D 0.04 . 8.3943 0.32548 0.0851:0.2937:0.6211:0.0 . 116;64;64;64;64;64 E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2;E7EPF1;D6W5P7 .;.;ADA22_HUMAN;.;.;. K 64;64;64;64;64;64;64;31 ENSP00000381262:E64K;ENSP00000391334:E64K;ENSP00000413899:E64K;ENSP00000381260:E64K;ENSP00000265727:E64K;ENSP00000315900:E64K;ENSP00000381267:E64K;ENSP00000381261:E31K ENSP00000265727:E64K E + 1 0 ADAM22 87402381 1.000000 0.71417 0.909000 0.35828 0.748000 0.42578 1.511000 0.35801 0.779000 0.33543 0.655000 0.94253 GAA TCGA-H6-8124-01A-11D-2396-08 ADAM22-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000268370.2 1 0 0 94 331 0 66 0 6.851146e-01 0 10 0 66 2 0 0 0 0 0 2 1 1.000000 92 328 0 66 2 0 0 0 0 66 2 -20.000000 1 1 0 0 1 0.700000 1.770000 0 0 ADCK5 203054 broad.mit.edu 37 8 145616829 145616829 + Missense_Mutation SNP G G A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr8:145616829G>A ENST00000308860.6 + 8 892 c.848G>A c.(847-849)cGc>cAc p.R283H ADCK5_ENST00000526231.2_3'UTR|MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_5'Flank NM_174922.3 NP_777582.4 Q3MIX3 ADCK5_HUMAN aarF domain containing kinase 5 8 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055) AATGAGGGCCGCAACGCAGAG 0.677000 0 SO:0001583 missense ENST00000308860.6 0 1 hg19 CCDS34965.1 . . . . . . . . . . G 9.295 1.051513 0.19827 2.31E-4 0.0 ENSG00000173137 ENST00000308860 T 0.54071 0.59 5.17 3.38 0.38709 ABC-1 (1);Protein kinase-like domain (1); 0.207878 0.39020 N 0.001489 T 0.42154 0.1190 L 0.41710 1.295 0.80722 D 1 B 0.21688 0.059 B 0.21546 0.035 T 0.25363 -1.0134 10 0.48119 T 0.1 -20.9067 9.5897 0.39539 0.1731:0.0:0.8269:0.0 . 283 Q3MIX3 ADCK5_HUMAN H 283 ENSP00000310547:R283H ENSP00000310547:R283H R + 2 0 ADCK5 145587637 0.929000 0.31497 0.509000 0.27700 0.016000 0.09150 1.319000 0.33655 0.589000 0.29677 -0.258000 0.10820 CGC TCGA-H6-8124-01A-11D-2396-08 ADCK5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382556.2 0 0 0 3 42 0 10 0 4.349692e-01 0 17 0 10 2 0 0 0 0 0 2 1 0.812618 3 42 0 10 2 0 0 0 0 10 2 -7.795558 1 1 117324 1 16 1 1 2 3 2.208213 0 0.700000 1.770000 0.702085 0.220000 6.000000e-02 0.550000 0.200000 0.250019 0.220000 0 1.200000e-01 3.600000e-01 HR 55806 broad.mit.edu 37 8 21986391 21986391 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr8:21986391C>T ENST00000381418.4 - 2 1773 c.293G>A c.(292-294)cGc>cAc p.R98H HR_ENST00000312841.8_Missense_Mutation_p.R98H|HR_ENST00000518377.1_5'Flank NM_005144.4 NP_005135.2 O43593 HAIR_HUMAN hair growth associated 27 Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116) CTCCTTCCAGCGCAGTCCCTC 0.652000 0 SO:0001583 missense ENST00000381418.4 1 1 hg19 CCDS6022.1 . . . . . . . . . . C 13.80 2.344423 0.41498 . . ENSG00000168453 ENST00000381418;ENST00000312841 T;T 0.74106 -0.8;-0.81 4.72 2.85 0.33270 . 0.160475 0.29692 N 0.011458 T 0.59459 0.2195 L 0.34521 1.04 0.27888 N 0.939439 B;B;B 0.18741 0.023;0.03;0.017 B;B;B 0.14578 0.004;0.011;0.005 T 0.52852 -0.8520 10 0.51188 T 0.08 -7.088 6.2548 0.20867 0.0:0.7605:0.0:0.2395 . 98;98;98 A6NCE3;O43593-2;O43593 .;.;HAIR_HUMAN H 98 ENSP00000370826:R98H;ENSP00000326765:R98H ENSP00000326765:R98H R - 2 0 HR 22042336 0.048000 0.20356 0.996000 0.52242 0.905000 0.53344 -0.070000 0.11523 0.549000 0.28973 -0.258000 0.10820 CGC TCGA-H6-8124-01A-11D-2396-08 HR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214213.1 1 0 1 32 299 0 100 1 2.230885e-01 2 7 0 100 2 0 0 0 0 0 2 1 1.000000 32 291 0 99 2 0 0 0 0 100 2 -20.000000 1 1 121402 1 27 1 1 2 3 2.208213 0 0.700000 1.770000 0.702085 0.270000 1.900000e-01 0.400000 0.280000 0.291762 0.270000 0 2.300000e-01 3.300000e-01 CLU 1191 broad.mit.edu 37 8 27463908 27463908 + Missense_Mutation SNP C C T TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr8:27463908C>T ENST00000316403.10 - 4 785 c.380G>A c.(379-381)cGc>cAc p.R127H CLU_ENST00000546343.1_Missense_Mutation_p.R138H|CLU_ENST00000405140.3_Missense_Mutation_p.R127H|CLU_ENST00000523500.1_Missense_Mutation_p.R127H|CLU_ENST00000560366.1_Missense_Mutation_p.R179H P10909 CLUS_HUMAN clusterin 21 Ovarian(32;2.61e-05) TCTGCAGACGCGTGCGTAGAA 0.572000 0 SO:0001583 missense ENST00000316403.10 0 1 hg19 CCDS47832.1 . . . . . . . . . . C 19.17 3.775112 0.70107 . . ENSG00000120885 ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000523589;ENST00000520796;ENST00000519742;ENST00000520491;ENST00000522413 T;T;T;T;T;T;T;T 0.27402 1.67;1.67;1.67;1.67;1.67;1.67;1.67;1.67 5.52 2.27 0.28462 Clusterin, N-terminal (1); 0.111708 0.52532 D 0.000064 T 0.40322 0.1112 M 0.78637 2.42 0.09310 N 1 D;D;D 0.58620 0.979;0.979;0.983 P;P;P 0.51974 0.558;0.558;0.686 T 0.29088 -1.0023 10 0.87932 D 0 -8.8843 5.2716 0.15628 0.0:0.5819:0.1628:0.2554 . 179;138;127 P10909-2;P10909-5;P10909 .;.;CLUS_HUMAN H 179;138;127;127;127;127;127;127;127 ENSP00000446413:R138H;ENSP00000385419:R127H;ENSP00000429620:R127H;ENSP00000431070:R127H;ENSP00000429336:R127H;ENSP00000431026:R127H;ENSP00000429881:R127H;ENSP00000428779:R127H ENSP00000315130:R179H R - 2 0 CLU 27519825 0.005000 0.15991 0.034000 0.17996 0.973000 0.67179 1.095000 0.30964 0.687000 0.31509 0.655000 0.94253 CGC TCGA-H6-8124-01A-11D-2396-08 CLU-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219953.3 0 0 0 9 628 0 134 1 9.998469e-01 6 1227 0 134 2 0 0 0 0 0 2 1 0.993969 9 621 0 131 2 0 0 0 0 134 2 -2.924029 1 0 121412 6 39 1 1 2 3 2.208213 0 0.700000 1.770000 0.702085 0.030000 0 0.080000 0.040000 0.054634 0.030000 0 2.000000e-02 6.000000e-02 TGFBR1 7046 broad.mit.edu 37 9 101911535 101911535 + Missense_Mutation SNP G G A rs113605875 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chr9:101911535G>A ENST00000374994.4 + 9 1577 c.1460G>A c.(1459-1461)cGg>cAg p.R487Q TGFBR1_ENST00000552516.1_Missense_Mutation_p.R491Q|TGFBR1_ENST00000374990.2_Missense_Mutation_p.R410Q|TGFBR1_ENST00000550253.1_Missense_Mutation_p.R418Q NM_004612.2 NP_004603.1 P36897 TGFR1_HUMAN transforming growth factor, beta receptor 1 27 Acute lymphoblastic leukemia(62;0.0559) ACAGCATTGCGGATTAAGAAA 0.373000 0 GRCh37 CM050757|CM063198 TGFBR1 M rs113605875 SO:0001583 missense ENST00000374994.4 0 1 hg19 CCDS6738.1 . . . . . . . . . . G 28.3 4.907570 0.92107 . . ENSG00000106799 ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000550253 D;D;D;D 0.92495 -3.05;-3.05;-3.05;-3.05 5.66 5.66 0.87406 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 D 0.95201 0.8444 L 0.55103 1.725 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.916;0.999 D 0.95213 0.8327 10 0.87932 D 0 . 18.8853 0.92375 0.0:0.0:1.0:0.0 . 410;487 P36897-3;P36897 .;TGFR1_HUMAN Q 487;449;410;491;418 ENSP00000364133:R487Q;ENSP00000364129:R410Q;ENSP00000447297:R491Q;ENSP00000450052:R418Q ENSP00000364129:R410Q R + 2 0 TGFBR1 100951356 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.869000 0.99810 2.827000 0.97445 0.655000 0.94253 CGG TCGA-H6-8124-01A-11D-2396-08 TGFBR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053390.3 1 0 0 8 176 0 24 1 7.031618e-01 2 52 0 24 2 1 9.957717e-01 16 341 1 782 4 1 0.989853 8 176 0 24 2 0 0 0 0 24 2 -2.909994 1 1 0 0 1 0 1 1 1.411584 1 0.700000 1.770000 0.538462 0.080000 3.000000e-02 0.150000 0.080000 0.089437 0.080000 0 5.000000e-02 1.200000e-01 FLNA 2316 broad.mit.edu 37 X 153587767 153587767 + Missense_Mutation SNP C C A TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chrX:153587767C>A ENST00000369850.3 - 25 4386 c.4150G>T c.(4150-4152)Ggc>Tgc p.G1384C FLNA_ENST00000369856.3_5'Flank|FLNA_ENST00000422373.1_Missense_Mutation_p.G1384C|FLNA_ENST00000344736.4_Missense_Mutation_p.G1384C|FLNA_ENST00000360319.4_Missense_Mutation_p.G1384C NM_001110556.1 NP_001104026.1 P21333 FLNA_HUMAN filamin A, alpha 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) CCGCCCGTGCCAGCTCCCCTG 0.647000 0 SO:0001583 missense ENST00000369850.3 1 1 hg19 CCDS48194.1 . . . . . . . . . . C 22.3 4.277760 0.80692 . . ENSG00000196924 ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736 D;D;D;D 0.95035 -3.59;-3.59;-3.59;-3.59 5.36 5.36 0.76844 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 D 0.98353 0.9453 H 0.97051 3.93 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.99811 1.1041 10 0.87932 D 0 . 18.1702 0.89743 0.0:1.0:0.0:0.0 . 1384;1384 P21333-2;P21333 .;FLNA_HUMAN C 1384;1357;1384;1384;1384 ENSP00000353467:G1384C;ENSP00000416926:G1384C;ENSP00000358866:G1384C;ENSP00000358863:G1384C ENSP00000358863:G1384C G - 1 0 FLNA 153240961 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.788000 0.85771 2.229000 0.72834 0.600000 0.82982 GGC TCGA-H6-8124-01A-11D-2396-08 FLNA-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058942.3 1 0 1 560 1080 0 532 1 1 2 882 0 532 2 0 0 0 0 0 2 1 1.000000 551 1061 0 529 2 0 0 0 0 532 2 -20.000000 1 1 0 0 1 0 1 1 0.700000 1.770000 0.700000 0.970000 9.000000e-01 1.000000 1.000000 0.970993 0.970000 1 9.300000e-01 1 ARAF 369 broad.mit.edu 37 X 47426043 47426043 + Missense_Mutation SNP G G A rs66933407 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chrX:47426043G>A ENST00000377045.4 + 7 757 c.563G>A c.(562-564)cGc>cAc p.R188H ARAF_ENST00000290277.6_Intron NM_001256196.1|NM_001654.4 NP_001243125.1|NP_001645.1 P10398 ARAF_HUMAN A-Raf proto-oncogene, serine/threonine kinase p.R188H(1) 29 Adenosine triphosphate(DB00171) GGCAGCCCCCGCACCCAGCAC 0.622000 1 Substitution - Missense(1) SO:0001583 missense ENST00000377045.4 1 1 hg19 CCDS35232.1 . . . . . . . . . . G 0.030 -1.341094 0.01277 . . ENSG00000078061 ENST00000377045 T 0.74421 -0.84 5.37 2.02 0.26589 . 1.428110 0.03652 N 0.241251 T 0.59729 0.2215 N 0.22421 0.69 0.09310 N 0.999999 P;B 0.34629 0.46;0.0 B;B 0.26517 0.07;0.001 T 0.47209 -0.9135 10 0.29301 T 0.29 . 8.5422 0.33399 0.1819:0.0:0.6845:0.1336 . 188;54 P10398;B4DV85 ARAF_HUMAN;. H 188 ENSP00000366244:R188H ENSP00000366244:R188H R + 2 0 ARAF 47310987 0.896000 0.30565 0.181000 0.23098 0.004000 0.04260 2.153000 0.42282 0.100000 0.17581 -1.195000 0.01675 CGC TCGA-H6-8124-01A-11D-2396-08 ARAF-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056418.1 1 0 1 72 102 0 34 0 1 0 160 0 34 2 0 0 0 0 0 2 1 1.000000 71 98 0 34 2 0 0 0 0 34 2 -20.000000 1 1 120406 6 32 1 0 1 1 0.700000 1.770000 0.700000 0.990000 9.700000e-01 1.000000 1.000000 0.998334 0.990000 1 9.900000e-01 1 CLCN5 1184 broad.mit.edu 37 X 49854844 49854844 + Missense_Mutation SNP G G A rs138935720 TCGA-H6-8124-01A-11D-2396-08 TCGA-H6-8124-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 575ab748-dec0-42a8-85a6-1e337f07b129 3952ea3a-0fab-4436-a3ec-3bbd1c7e24a2 g.chrX:49854844G>A ENST00000307367.2 + 10 1897 c.1606G>A c.(1606-1608)Gtg>Atg p.V536M CLCN5_ENST00000376108.3_Missense_Mutation_p.V536M|CLCN5_ENST00000376088.3_Missense_Mutation_p.V606M|CLCN5_ENST00000376091.3_Missense_Mutation_p.V606M P51795 CLCN5_HUMAN chloride channel, voltage-sensitive 5 30 Ovarian(276;0.236) AGAATACATCGTGCCTCTGAT 0.502000 0 SO:0001583 missense ENST00000307367.2 1 1 hg19 CCDS14328.1 . . . . . . . . . . G 24.8 4.566129 0.86439 . . ENSG00000171365 ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367 D;D;D;D 0.94793 -3.52;-3.52;-3.52;-3.52 5.79 5.79 0.91817 Chloride channel, core (2); 0.000000 0.85682 D 0.000000 D 0.97692 0.9243 M 0.88704 2.975 0.80722 D 1 D;D 0.89917 0.997;1.0 D;D 0.83275 0.921;0.996 D 0.98214 1.0474 10 0.62326 D 0.03 -0.1014 17.6718 0.88220 0.0:0.0:1.0:0.0 . 536;606 P51795;P51795-2 CLCN5_HUMAN;. M 606;438;606;536;536 ENSP00000365256:V606M;ENSP00000365259:V606M;ENSP00000365276:V536M;ENSP00000304257:V536M ENSP00000304257:V536M V + 1 0 CLCN5 49741584 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 9.705000 0.98719 2.445000 0.82738 0.600000 0.82982 GTG TCGA-H6-8124-01A-11D-2396-08 CLCN5-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056544.1 1 0 1 396 719 0 157 0 6.903426e-01 0 6 0 157 2 0 0 0 0 0 2 1 1.000000 394 708 0 155 2 0 0 0 0 157 2 -20.000000 1 1 121410 4 41 1 0 1 1 0.700000 1.770000 0.700000 0.990000 9.200000e-01 1.000000 1.000000 0.989902 0.990000 1 9.600000e-01 1