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 INF2 64423 broad.mit.edu 37 14 105180688 105180689 + Frame_Shift_Ins INS - - T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 - T - - Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr14:105180688_105180689insT ENST00000392634.4 + 21 3301_3302 c.3189_3190insT c.(3190-3192)ttgfs p.L1064fs INF2_ENST00000330634.7_Frame_Shift_Ins_p.L1064fs NM_022489.3 NP_071934.3 Q27J81 INF2_HUMAN inverted formin, FH2 and WH2 domain containing 8 all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172) all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116) CCCTGGAGCAGTTGGAGGAGGG 0.663000 0 SO:0001589 frameshift_variant ENST00000392634.4 0 1 hg19 CCDS9989.2 TCGA-IB-AAUN-01A-12D-A38G-08 INF2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000074371.4 1 0 0 10 45 0 33 0 1 0 245 0 33 2 0 0 0 0 1 0.996711 9 42 0 34 2 0 0 0 0 0 0 -19.620090 1 1 0 0 1 0 1 1 1.546377 1 0.560000 1.800000 0.388889 0.460000 2.500000e-01 0.730000 0.460000 0.482168 0.460000 0 0.340000 0.610000 MBD1 4152 broad.mit.edu 37 18 47797907 47797914 + Splice_Site DEL GGACCTAG GGACCTAG - TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 GGACCTAG - GGACCTAG GGACCTAG Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr18:47797907_47797914delGGACCTAG ENST00000591416.1 - 16 2210_2213 c.1779_1782delCTAGGTCC c.(1777-1782)agctag>ag p.S*593fs MBD1_ENST00000349085.2_Splice_Site_p.S*491fs|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000353909.3_Splice_Site_p.S*544fs|MBD1_ENST00000269471.5_Intron|MBD1_ENST00000398488.1_Splice_Site_p.S*491fs|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000398493.1_Splice_Site_p.S*537fs|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000347968.3_Splice_Site_p.S*537fs|MBD1_ENST00000585595.1_Splice_Site_p.S*618fs|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000457839.2_Splice_Site_p.S*618fs|MBD1_ENST00000591535.1_Splice_Site_p.S*524fs|MBD1_ENST00000382948.5_Splice_Site_p.S*593fs|MBD1_ENST00000436910.1_Splice_Site_p.S*524fs|MBD1_ENST00000269468.5_Splice_Site_p.S*593fs|MBD1_ENST00000424334.2_Splice_Site_p.S*644fs|MBD1_ENST00000398495.2_Splice_Site_p.S*554fs Q9UIS9 MBD1_HUMAN methyl-CpG binding domain protein 1 36 TAAGGTCTTTGGACCTAGGGAAAAGGGA 0.442000 0 SO:0001630 splice_region_variant ENST00000591416.1 1 1 hg19 CCDS11943.1 TCGA-IB-AAUN-01A-12D-A38G-08 MBD1-004 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000255926.3 0 0 0 115 459 0 355 0 9.997315e-01 0 50 0 355 2 0 0 0 0 1 1.000000 208 519 28 374 69 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.553807 1 0.560000 1.800000 0.388889 0.510000 4.200000e-01 0.600000 0.510000 0.516442 0.510000 0 0.460000 0.560000 SMAD4 4089 broad.mit.edu 37 18 48586256 48586262 + Frame_Shift_Del DEL GCATTCC GCATTCC - TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 GCATTCC - GCATTCC GCATTCC Valid Somatic Phase_I WXS targeted Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr18:48586256_48586262delGCATTCC ENST00000342988.3 + 8 1463_1469 c.925_931delGCATTCC c.(925-933)gcattccagfs p.AFQ309fs SMAD4_ENST00000588745.1_Intron|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.AFQ309fs NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(3)|p.Q311*(2)|p.F310L(1) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) CAATGAGCTTGCATTCCAGCCTCCCAT 0.329000 42 Whole gene deletion(36)|Unknown(3)|Substitution - Nonsense(2)|Substitution - Missense(1) GRCh37 CI064731 SMAD4 I SO:0001589 frameshift_variant ENST00000342988.3 1 1 hg19 CCDS11950.1 TCGA-IB-AAUN-01A-12D-A38G-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 0 56 247 0 177 0 9.971798e-01 1 41 0 177 2 1 1 95 607 0 692 2 1 1.000000 66 242 1 177 8 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.553807 1 0.560000 1.800000 0.388889 0.470000 3.600000e-01 0.590000 0.470000 0.478078 0.470000 0 0.410000 0.530000 SHOC2 8036 broad.mit.edu 37 10 112724158 112724158 + Silent SNP A A G TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr10:112724158A>G ENST00000369452.4 + 2 387 c.42A>G c.(40-42)aaA>aaG p.K14K SHOC2_ENST00000265277.5_Silent_p.K14K|SHOC2_ENST00000489390.1_Intron NM_007373.3 NP_031399.2 Q9UQ13 SHOC2_HUMAN soc-2 suppressor of clear homolog (C. elegans) 17 CTAAAGAAAAAGATCCCAAAG 0.383000 0 SO:0001819 synonymous_variant ENST00000369452.4 0 1 hg19 CCDS7568.1 TCGA-IB-AAUN-01A-12D-A38G-08 SHOC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050355.1 0 0 0 4 170 0 106 0 2.699243e-01 0 36 0 106 2 0 0 0 0 0 2 1 0.884373 4 165 0 106 2 0 0 0 0 106 2 -3.183656 1 1 0 0 1 1 2 3 2.169384 0 0.560000 1.800000 0.566075 0.090000 2.000000e-02 1.000000 0.080000 0.136499 0.090000 0 0.050000 0.160000 TDRD1 56165 broad.mit.edu 37 10 115970681 115970681 + Missense_Mutation SNP G G T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr10:115970681G>T ENST00000369280.1 + 13 2075 c.1615G>T c.(1615-1617)Gat>Tat p.D539Y TDRD1_ENST00000369281.2_Missense_Mutation_p.D539Y|TDRD1_ENST00000369282.1_Missense_Mutation_p.D539Y|TDRD1_ENST00000251864.2_Missense_Mutation_p.D539Y|TDRD1_ENST00000422662.1_Missense_Mutation_p.D200Y Q9BXT4 TDRD1_HUMAN tudor domain containing 1 48 Colorectal(252;0.172)|Breast(234;0.188) TCCACGCTCTGATTTTTATCC 0.348000 0 SO:0001583 missense ENST00000369280.1 1 1 hg19 . . . . . . . . . . G 13.84 2.356797 0.41801 . . ENSG00000095627 ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280 T;T;T;T;T 0.09723 2.95;2.95;2.95;2.95;2.95 5.9 4.05 0.47172 Maternal tudor protein (1); 0.205916 0.39985 N 0.001202 T 0.27098 0.0664 M 0.75884 2.315 0.09310 N 1 D;D;D;D;D 0.89917 0.999;0.999;1.0;0.999;1.0 D;D;D;D;D 0.81914 0.978;0.973;0.995;0.955;0.991 T 0.07366 -1.0776 10 0.66056 D 0.02 -14.3001 5.4576 0.16600 0.2129:0.0:0.6388:0.1482 . 200;539;539;539;539 Q9BXT4-4;Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2 .;TDRD1_HUMAN;.;.;. Y 539;539;539;200;539 ENSP00000358288:D539Y;ENSP00000251864:D539Y;ENSP00000358287:D539Y;ENSP00000402794:D200Y;ENSP00000358286:D539Y ENSP00000251864:D539Y D + 1 0 TDRD1 115960671 0.914000 0.31030 0.540000 0.28089 0.698000 0.40448 1.437000 0.34991 1.498000 0.48600 0.563000 0.77884 GAT TCGA-IB-AAUN-01A-12D-A38G-08 TDRD1-001 KNOWN basic protein_coding protein_coding OTTHUMT00000050457.2 0 0 1 77 199 0 123 0 0 0 0 123 2 0 0 0 0 0 2 1 1.000000 75 196 0 122 2 0 0 0 0 123 2 -6.472448 1 0 0 0 1 1 2 3 2.169384 0 0.560000 1.800000 0.566075 0.990000 8.200000e-01 1.000000 1.000000 0.968727 0.990000 1 0.910000 1.000000 GFRA1 2674 broad.mit.edu 37 10 118030528 118030528 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr10:118030528C>T ENST00000355422.6 - 3 690 c.140G>A c.(139-141)cGc>cAc p.R47H GFRA1_ENST00000369236.1_Missense_Mutation_p.R47H|GFRA1_ENST00000439649.3_Missense_Mutation_p.R47H|GFRA1_ENST00000490345.1_5'Flank NM_005264.4 NP_005255.1 P56159 GFRA1_HUMAN GDNF family receptor alpha 1 26 Lung NSC(174;0.21) CCTTAGCGTGCGGTACTTGGT 0.637000 Ovarian(128;329 1725 45498 46808 50759) 0 SO:0001583 missense ENST00000355422.6 0 1 hg19 CCDS44481.1 . . . . . . . . . . C 35 5.527077 0.96431 . . ENSG00000151892 ENST00000439649;ENST00000369236;ENST00000355422;ENST00000369234 T;T;T;T 0.65178 -0.14;-0.14;-0.14;-0.14 3.95 3.95 0.45737 GDNF/GAS1 (2); 0.000000 0.85682 D 0.000000 T 0.76190 0.3953 L 0.61036 1.89 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 T 0.78682 -0.2109 10 0.52906 T 0.07 -20.05 16.2431 0.82426 0.0:1.0:0.0:0.0 . 47;47 P56159;P56159-2 GFRA1_HUMAN;. H 47 ENSP00000393725:R47H;ENSP00000358239:R47H;ENSP00000347591:R47H;ENSP00000358237:R47H ENSP00000347591:R47H R - 2 0 GFRA1 118020518 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.617000 0.83032 2.044000 0.60594 0.549000 0.68633 CGC TCGA-IB-AAUN-01A-12D-A38G-08 GFRA1-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050512.2 0 0 0 7 277 0 134 0 8.179766e-03 0 5 0 134 2 0 0 0 0 0 2 1 0.980472 7 275 0 134 2 0 0 0 0 134 2 -3.567326 1 1 0 0 1 1 2 3 2.169384 0 0.560000 1.800000 0.566075 0.090000 3.000000e-02 1.000000 0.090000 0.135162 0.090000 0 0.060000 0.140000 HKDC1 80201 broad.mit.edu 37 10 71005968 71005968 + Missense_Mutation SNP C C T rs148723879 TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr10:71005968C>T ENST00000354624.5 + 8 1142 c.1009C>T c.(1009-1011)Cgg>Tgg p.R337W HKDC1_ENST00000395086.2_Missense_Mutation_p.R337W NM_025130.3 NP_079406 Q2TB90 HKDC1_HUMAN hexokinase domain containing 1 34 GATCGAAACACGGCACGTGGC 0.572000 0 SO:0001583 missense ENST00000354624.5 1 1 hg19 CCDS7288.1 . . . . . . . . . . C 15.66 2.900111 0.52227 0.0 2.33E-4 ENSG00000156510 ENST00000354624;ENST00000395087;ENST00000395086 D;D 0.96554 -4.05;-4.05 4.68 2.69 0.31865 Hexokinase, C-terminal (1); 0.498975 0.22141 N 0.064050 D 0.93716 0.7992 M 0.63843 1.955 0.09310 N 1 D 0.69078 0.997 B 0.41917 0.37 D 0.88588 0.3141 10 0.87932 D 0 -9.0294 8.3136 0.32086 0.3743:0.5092:0.1165:0.0 . 337 Q2TB90 HKDC1_HUMAN W 337 ENSP00000346643:R337W;ENSP00000378521:R337W ENSP00000346643:R337W R + 1 2 HKDC1 70675974 0.065000 0.20965 0.684000 0.30055 0.622000 0.37654 2.558000 0.45879 1.172000 0.42781 0.561000 0.74099 CGG TCGA-IB-AAUN-01A-12D-A38G-08 HKDC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048389.1 1 0 1 73 196 0 130 1 1 23 64 0 130 2 0 0 0 0 0 2 1 1.000000 72 192 0 126 2 0 0 0 0 130 2 -20.000000 1 1 121412 11 41 1 1 2 3 2.169384 0 0.560000 1.800000 0.566075 0.980000 7.900000e-01 1.000000 1.000000 0.955245 0.980000 1 0.880000 1.000000 SLIT1 6585 broad.mit.edu 37 10 98762035 98762035 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr10:98762035C>T ENST00000266058.4 - 36 4491 c.4246G>A c.(4246-4248)Ggg>Agg p.G1416R ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Intron NM_003061.2 NP_003052.2 O75093 SLIT1_HUMAN slit homolog 1 (Drosophila) 78 Colorectal(252;0.162) GCCAGGGCCCCGGCCTGGTTG 0.662000 0 SO:0001583 missense ENST00000266058.4 1 1 hg19 CCDS7453.1 . . . . . . . . . . C 4.285 0.052094 0.08291 . . ENSG00000187122 ENST00000266058 T 0.80480 -1.38 4.42 2.57 0.30868 . 0.164002 0.53938 N 0.000048 T 0.58323 0.2114 N 0.04203 -0.255 0.45354 D 0.998344 B 0.06786 0.001 B 0.04013 0.001 T 0.45804 -0.9236 10 0.29301 T 0.29 . 10.0301 0.42096 0.0:0.771:0.0:0.229 . 1416 O75093 SLIT1_HUMAN R 1416 ENSP00000266058:G1416R ENSP00000266058:G1416R G - 1 0 SLIT1 98752025 0.007000 0.16637 0.178000 0.23040 0.155000 0.21991 0.849000 0.27723 0.499000 0.27970 -0.221000 0.12465 GGG TCGA-IB-AAUN-01A-12D-A38G-08 SLIT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049636.1 1 0 1 16 45 0 28 0 7.589286e-02 0 2 0 28 2 0 0 0 0 0 2 1 0.999969 16 44 0 28 2 0 0 0 0 28 2 -20.000000 1 1 121164 1 23 1 1 2 3 2.169384 0 0.560000 1.800000 0.566075 0.960000 6.000000e-01 1.000000 1.000000 0.905226 0.960000 1 0.760000 1.000000 HINFP 25988 broad.mit.edu 37 11 119004822 119004822 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr11:119004822C>T ENST00000350777.2 + 10 1231 c.1168C>T c.(1168-1170)Cgg>Tgg p.R390W HINFP_ENST00000527410.1_Silent_p.C410C NM_001243259.1|NM_015517.4|NM_198971.2 NP_001230188.1|NP_056332.2|NP_945322.1 Q9BQA5 HINFP_HUMAN histone H4 transcription factor p.R390W(1) 23 TGGCTATATGCGGCTGCAGCT 0.567000 OREG0021397 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 1 Substitution - Missense(1) SO:0001583 missense ENST00000350777.2 0 1 hg19 CCDS8414.1 . . . . . . . . . . C 20.3 3.964717 0.74131 . . ENSG00000172273 ENST00000350777 T 0.10573 2.86 5.31 2.36 0.29203 . 0.000000 0.85682 D 0.000000 T 0.29458 0.0734 M 0.64170 1.965 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.02646 -1.1129 10 0.87932 D 0 -27.7523 14.9379 0.70970 0.5073:0.4927:0.0:0.0 . 390 Q9BQA5 HINFP_HUMAN W 390 ENSP00000318085:R390W ENSP00000318085:R390W R + 1 2 HINFP 118510032 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 2.333000 0.43912 0.360000 0.24265 -0.152000 0.13540 CGG TCGA-IB-AAUN-01A-12D-A38G-08 HINFP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388201.2 0 0 0 5 326 0 188 0 6.408095e-02 0 22 0 188 2 0 0 0 0 0 2 1 0.935475 5 321 0 187 2 0 0 0 0 188 2 -2.500008 1 1 0 0 1 1 2 3 2.138887 0 0.560000 1.800000 0.561229 0.050000 1.000000e-02 0.130000 0.060000 0.064355 0.050000 0 0.030000 0.090000 OR10G7 390265 broad.mit.edu 37 11 123909404 123909404 + Missense_Mutation SNP A A G TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr11:123909404A>G ENST00000330487.5 - 1 313 c.305T>C c.(304-306)tTt>tCt p.F102S NM_001004463.1 NP_001004463.1 Q8NGN6 O10G7_HUMAN olfactory receptor, family 10, subfamily G, member 7 47 Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22) GAAGTGGAAAAAATAGAGCTG 0.532000 0 SO:0001583 missense ENST00000330487.5 1 1 hg19 CCDS31705.1 . . . . . . . . . . A 0.908 -0.719988 0.03182 . . ENSG00000182634 ENST00000330487 T 0.00502 6.95 3.39 -2.56 0.06268 GPCR, rhodopsin-like superfamily (1); 1.214850 0.05929 N 0.634898 T 0.00524 0.0017 M 0.64630 1.985 0.09310 N 1 B 0.02656 0.0 B 0.06405 0.002 T 0.39165 -0.9627 10 0.41790 T 0.15 . 5.7826 0.18314 0.3487:0.4967:0.1546:0.0 . 102 Q8NGN6 O10G7_HUMAN S 102 ENSP00000329689:F102S ENSP00000329689:F102S F - 2 0 OR10G7 123414614 0.000000 0.05858 0.311000 0.25182 0.042000 0.13812 0.173000 0.16724 -0.386000 0.07821 -0.666000 0.03841 TTT TCGA-IB-AAUN-01A-12D-A38G-08 OR10G7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387271.1 1 0 0 63 578 0 327 0 0 0 0 327 2 0 0 0 0 0 2 1 1.000000 57 508 0 374 2 0 0 0 0 327 2 -20.000000 1 1 0 0 1 1 2 3 2.138887 0 0.560000 1.800000 0.561229 0.340000 2.700000e-01 0.440000 0.350000 0.356037 0.340000 0 0.300000 0.400000 BCL7A 605 broad.mit.edu 37 12 122492809 122492809 + Missense_Mutation SNP G G A rs148056282 TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr12:122492809G>A ENST00000261822.4 + 5 744 c.538G>A c.(538-540)Gca>Aca p.A180T BCL7A_ENST00000538010.1_Missense_Mutation_p.A180T NM_001024808.1 NP_001019979.1 Q4VC05 BCL7A_HUMAN B-cell CLL/lymphoma 7A 18 all_neural(191;0.0837)|Medulloblastoma(191;0.163) GGGTCTGGCCGCAGAGACGTC 0.567000 T MYC BNHL OREG0022214 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) GBM(17;197 467 16477 23242 44349) Dom yes 12 12q24.1 605 B-cell CLL/lymphoma 7A L 0 SO:0001583 missense ENST00000261822.4 0 1 hg19 CCDS53841.1 . . . . . . . . . . G 0.318 -0.963497 0.02249 0.0 1.16E-4 ENSG00000110987 ENST00000538010;ENST00000261822 T;T 0.44083 0.93;1.01 6.07 0.0514 0.14297 . 0.533452 0.21468 N 0.074043 T 0.12774 0.0310 N 0.02539 -0.55 0.09310 N 1 B;B 0.11235 0.004;0.003 B;B 0.08055 0.003;0.002 T 0.28299 -1.0048 10 0.08837 T 0.75 . 5.2306 0.15420 0.4794:0.0:0.3844:0.1362 . 180;180 Q4VC05;Q4VC05-2 BCL7A_HUMAN;. T 180 ENSP00000445868:A180T;ENSP00000261822:A180T ENSP00000261822:A180T A + 1 0 BCL7A 120977192 0.318000 0.24598 0.000000 0.03702 0.001000 0.01503 0.660000 0.25009 -0.097000 0.12307 -0.137000 0.14449 GCA TCGA-IB-AAUN-01A-12D-A38G-08 BCL7A-002 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000401712.1 0 0 0 6 294 0 194 0 4.996645e-02 0 15 0 194 2 0 0 0 0 0 2 1 0.963916 6 290 0 193 2 0 0 0 0 194 2 -2.695311 1 1 121412 4 39 1 0 1 1 1.768437 1 0.560000 1.800000 0.413958 0.050000 1.000000e-02 0.110000 0.050000 0.061866 0.050000 0 0.030000 0.080000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 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-AAUN-01A-12D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 76 221 0 119 1 9.884392e-01 9 14 0 119 2 1 1 116 335 0 303 2 1 1.000000 75 217 0 117 2 1 1 2229 5800 0 119 2 -20.000000 1 1 121404 2 44 1 2 2 4 2.495063 1 0.560000 1.800000 0.626866 0.990000 8.800000e-01 1.000000 1.000000 0.989790 0.990000 1 0.980000 1.000000 CCNA1 8900 broad.mit.edu 37 13 37012789 37012789 + Silent SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr13:37012789C>T ENST00000255465.4 + 5 942 c.678C>T c.(676-678)caC>caT p.H226H CCNA1_ENST00000440264.1_Silent_p.H182H|CCNA1_ENST00000449823.1_Silent_p.H182H|CCNA1_ENST00000418263.1_Silent_p.H225H P78396 CCNA1_HUMAN cyclin A1 35 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) AGATAAGGCACAGACCCAAAG 0.418000 0 SO:0001819 synonymous_variant ENST00000255465.4 1 1 hg19 CCDS9357.1 TCGA-IB-AAUN-01A-12D-A38G-08 CCNA1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000044514.2 1 0 0 41 107 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 40 106 0 74 2 0 0 0 0 74 2 -20.000000 1 1 0 0 1 0 0 0 2.116285 0 0.560000 1.800000 0.560000 0.980000 7.400000e-01 1.000000 1.000000 0.945373 0.980000 1 0.850000 1.000000 KIAA0586 9786 broad.mit.edu 37 14 58915077 58915077 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr14:58915077C>T ENST00000556134.1 + 8 1056 c.782C>T c.(781-783)gCa>gTa p.A261V KIAA0586_ENST00000261244.5_Missense_Mutation_p.A276V|KIAA0586_ENST00000354386.6_Missense_Mutation_p.A329V|KIAA0586_ENST00000423743.3_Missense_Mutation_p.A232V|KIAA0586_ENST00000538571.2_3'UTR NM_001244190.1|NM_001244193.1 NP_001231119.1|NP_001231122.1 Q9BVV6 TALD3_HUMAN KIAA0586 34 ATTAGTGCTGCACTCAAGACT 0.328000 0 SO:0001583 missense ENST00000556134.1 1 1 hg19 CCDS58321.1 . . . . . . . . . . C 27.1 4.801789 0.90538 . . ENSG00000100578 ENST00000354386;ENST00000556134;ENST00000423743;ENST00000555833;ENST00000261244;ENST00000546216 T;T;T;T;T 0.61158 0.13;0.13;0.13;0.13;0.13 5.41 5.41 0.78517 . 0.000000 0.64402 D 0.000002 T 0.75102 0.3804 M 0.68952 2.095 0.45239 D 0.998243 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;0.998;1.0;1.0 D;D;D;D;D;D 0.87578 0.998;0.998;0.998;0.994;0.998;0.998 T 0.77038 -0.2736 10 0.87932 D 0 . 17.3225 0.87239 0.0:1.0:0.0:0.0 . 136;136;329;276;261;232 F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20 .;.;.;.;K0586_HUMAN;. V 329;261;232;191;276;136 ENSP00000346359:A329V;ENSP00000452351:A261V;ENSP00000399427:A232V;ENSP00000450855:A191V;ENSP00000261244:A276V ENSP00000261244:A276V A + 2 0 KIAA0586 57984830 1.000000 0.71417 0.998000 0.56505 0.980000 0.70556 4.520000 0.60524 2.696000 0.92011 0.585000 0.79938 GCA TCGA-IB-AAUN-01A-12D-A38G-08 KIAA0586-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000411887.1 1 0 1 70 105 0 115 0 0 0 1 0 115 2 0 0 0 0 0 2 1 1.000000 69 104 0 115 2 0 0 0 0 115 2 -20.000000 1 1 0 0 1 0 1 1 1.546377 1 0.560000 1.800000 0.388889 0.940000 8.000000e-01 1.000000 0.990000 0.936437 0.940000 1 0.870000 0.990000 MYO5C 55930 broad.mit.edu 37 15 52536564 52536564 + Silent SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr15:52536564C>T ENST00000261839.7 - 19 2540 c.2379G>A c.(2377-2379)caG>caA p.Q793Q MYO5C_ENST00000443683.2_3'UTR NM_018728.3 NP_061198.2 Q9NQX4 MYO5C_HUMAN myosin VC 66 TCACAGTTTGCTGACCCCGGA 0.527000 0 SO:0001819 synonymous_variant ENST00000261839.7 0 1 hg19 CCDS42036.1 TCGA-IB-AAUN-01A-12D-A38G-08 MYO5C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000419562.1 0 0 0 5 369 0 123 0 1.123582e-01 0 35 0 123 2 0 0 0 0 0 2 1 0.934810 5 363 0 122 2 0 0 0 0 123 2 -2.808618 1 1 0 0 1 1 2 3 2.134988 0 0.560000 1.800000 0.561229 0.040000 1.000000e-02 0.110000 0.050000 0.056967 0.040000 0 0.020000 0.080000 RAB27A 5873 broad.mit.edu 37 15 55497880 55497880 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr15:55497880G>A ENST00000396307.2 - 6 742 c.491C>T c.(490-492)gCt>gTt p.A164V RAB27A_ENST00000569493.1_Missense_Mutation_p.A164V|RAB27A_ENST00000336787.1_Missense_Mutation_p.A164V|RAB27A_ENST00000564609.1_Missense_Mutation_p.A164V NM_004580.4 NP_004571.2 P51159 RB27A_HUMAN RAB27A, member RAS oncogene family 9 CCCATTGGCAGCACTAGTTTC 0.443000 0 SO:0001583 missense ENST00000396307.2 0 1 hg19 CCDS10153.1 . . . . . . . . . . G 35 5.584941 0.96578 . . ENSG00000069974 ENST00000396307;ENST00000396304;ENST00000336787 D;D 0.88818 -2.43;-2.43 5.49 5.49 0.81192 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.95494 0.8536 M 0.88377 2.95 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.96017 0.9006 10 0.87932 D 0 -18.6991 18.3593 0.90370 0.0:0.0:1.0:0.0 . 164 P51159 RB27A_HUMAN V 164;156;164 ENSP00000379601:A164V;ENSP00000337761:A164V ENSP00000337761:A164V A - 2 0 RAB27A 53285172 1.000000 0.71417 0.998000 0.56505 0.992000 0.81027 9.751000 0.98889 2.585000 0.87301 0.655000 0.94253 GCT TCGA-IB-AAUN-01A-12D-A38G-08 RAB27A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254918.1 0 0 0 5 358 0 151 0 2.308849e-01 0 55 0 151 2 0 0 0 0 0 2 1 0.935186 5 352 0 149 2 0 0 0 0 151 2 -3.138838 1 1 0 0 1 1 2 3 2.134988 0 0.560000 1.800000 0.561229 0.050000 1.000000e-02 0.120000 0.050000 0.058695 0.050000 0 0.020000 0.080000 BANP 54971 broad.mit.edu 37 16 88061097 88061097 + Missense_Mutation SNP T T C TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr16:88061097T>C ENST00000393207.1 + 8 1101 c.880T>C c.(880-882)Ttc>Ctc p.F294L BANP_ENST00000393208.2_Missense_Mutation_p.F263L|BANP_ENST00000355163.5_Missense_Mutation_p.F269L|BANP_ENST00000479780.2_Missense_Mutation_p.F263L|BANP_ENST00000355022.4_Missense_Mutation_p.F263L|BANP_ENST00000538234.1_Missense_Mutation_p.F302L|BANP_ENST00000286122.7_Missense_Mutation_p.F294L NM_001173543.1 NP_001167014.1 Q8N9N5 BANP_HUMAN BTG3 associated nuclear protein 12 AGGTCACCTTTTCTATAAATT 0.617000 0 SO:0001583 missense ENST00000393207.1 1 1 hg19 CCDS54054.1 . . . . . . . . . . T 20.8 4.049507 0.75846 . . ENSG00000172530 ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207 T;T;T;T;T;T;T 0.24151 1.87;1.87;1.87;1.87;1.87;1.87;1.87 5.5 5.5 0.81552 BEN domain (2); 0.000000 0.85682 D 0.000000 T 0.34106 0.0886 N 0.14661 0.345 0.58432 D 0.999999 P;D;D;D;P;D 0.65815 0.951;0.973;0.963;0.995;0.954;0.993 P;P;D;D;D;D 0.77557 0.696;0.872;0.966;0.989;0.916;0.99 T 0.26538 -1.0100 10 0.51188 T 0.08 -0.7334 14.7894 0.69827 0.0:0.0:0.0:1.0 . 302;269;263;294;263;263 B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4 .;.;.;BANP_HUMAN;.;. L 294;269;259;263;263;263;263;302;294 ENSP00000286122:F294L;ENSP00000347290:F269L;ENSP00000432508:F263L;ENSP00000376903:F263L;ENSP00000347125:F263L;ENSP00000444352:F302L;ENSP00000376902:F294L ENSP00000286122:F294L F + 1 0 BANP 86618598 1.000000 0.71417 0.923000 0.36655 0.252000 0.25951 7.305000 0.78891 2.090000 0.63153 0.379000 0.24179 TTC TCGA-IB-AAUN-01A-12D-A38G-08 BANP-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000269166.1 1 0 1 94 222 0 141 1 9.833710e-01 3 15 0 141 2 0 0 0 0 0 2 1 1.000000 92 216 0 140 2 0 0 0 0 141 2 -20.000000 1 1 0 0 1 1 2 3 2.131575 0 0.560000 1.800000 0.561229 0.990000 8.800000e-01 1.000000 1.000000 0.987920 0.990000 1 0.970000 1.000000 MYH2 4620 broad.mit.edu 37 17 10436865 10436865 + Silent SNP G G A rs146411264 TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr17:10436865G>A ENST00000245503.5 - 20 2649 c.2265C>T c.(2263-2265)atC>atT p.I755I RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000397183.2_Silent_p.I755I|CTC-297N7.11_ENST00000587182.2_RNA NM_017534.5 NP_060004.3 Q9UKX2 MYH2_HUMAN myosin, heavy chain 2, skeletal muscle, adult 176 GGTCAATGTCGATGGATGCAA 0.403000 0 SO:0001819 synonymous_variant ENST00000245503.5 0 1 hg19 CCDS11156.1 TCGA-IB-AAUN-01A-12D-A38G-08 MYH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252726.3 0 0 0 7 468 1 286 0 0 0 1 286 2 0 0 0 0 0 2 0 0.488302 7 463 1 285 8 0 0 0 1 286 2 -2.425391 0 1 121412 5 43 1 0 1 1 1.564307 1 0.560000 1.800000 0.388889 0.030000 1.000000e-02 0.070000 0.040000 0.042978 0.030000 0 0.020000 0.060000 DBF4B 80174 broad.mit.edu 37 17 42828492 42828492 + Silent SNP G G A rs148114647 byFrequency TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr17:42828492G>A ENST00000315005.3 + 14 1857 c.1719G>A c.(1717-1719)ccG>ccA p.P573P DBF4B_ENST00000393547.2_Intron NM_145663.2 NP_663696.1 Q8NFT6 DBF4B_HUMAN DBF4 zinc finger B 7 Prostate(33;0.0322) CCTCACATCCGTGTACCCTTG 0.547000 0 SO:0001819 synonymous_variant ENST00000315005.3 1 1 hg19 CCDS11485.1 TCGA-IB-AAUN-01A-12D-A38G-08 DBF4B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000385930.1 1 0 1 100 434 0 239 0 3.579171e-02 1 1 0 239 2 0 0 0 0 0 2 1 1.000000 99 421 0 234 2 0 0 0 0 239 2 -3.439637 1 1 121412 14 47 1 1 2 3 2.182111 0 0.560000 1.800000 0.567270 0.680000 5.600000e-01 1.000000 0.680000 0.698179 0.680000 0 0.610000 0.760000 TP53 7157 broad.mit.edu 37 17 7574018 7574018 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr17:7574018G>A ENST00000269305.4 - 10 1198 c.1009C>T c.(1009-1011)Cgc>Tgc p.R337C TP53_ENST00000445888.2_Missense_Mutation_p.R337C|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000359597.4_Intron|TP53_ENST00000413465.2_Intron 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.R337C(18)|p.0?(8)|p.R337fs*8(2)|p.R337G(1)|p.?(1)|p.I332fs*5(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ATCTCGAAGCGCTCACGCCCA 0.522000 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 31 Substitution - Missense(19)|Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(1) GRCh37 CM981929 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 . . . . . . . . . . G 9.719 1.159246 0.21454 . . ENSG00000141510 ENST00000269305;ENST00000445888;ENST00000396473 D;D 0.95205 -3.64;-3.64 5.43 3.38 0.38709 p53, tetramerisation domain (3); 0.000000 0.85682 D 0.000000 D 0.94321 0.8175 M 0.82323 2.585 0.48341 D 0.999635 P 0.39940 0.696 B 0.40940 0.344 D 0.93083 0.6493 10 0.87932 D 0 -7.3279 12.447 0.55657 0.0:0.0:0.6947:0.3053 . 337 P04637 P53_HUMAN C 337;337;326 ENSP00000269305:R337C;ENSP00000391478:R337C ENSP00000269305:R337C R - 1 0 TP53 7514743 0.558000 0.26554 0.006000 0.13384 0.274000 0.26718 1.012000 0.29924 0.615000 0.30124 0.561000 0.74099 CGC TCGA-IB-AAUN-01A-12D-A38G-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 38 48 0 50 1 1 30 24 0 50 2 1 1 271 412 0 550 2 1 1.000000 37 45 0 50 2 0 0 0 0 50 2 -20.000000 1 1 121410 1 29 1 0 1 1 1.564307 1 0.560000 1.800000 0.388889 0.940000 7.800000e-01 1.000000 0.990000 0.932967 0.940000 1 0.870000 0.990000 TCF4 6925 broad.mit.edu 37 18 52899813 52899813 + Missense_Mutation SNP T T C TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr18:52899813T>C ENST00000356073.4 - 17 2187 c.1576A>G c.(1576-1578)Acg>Gcg p.T526A TCF4_ENST00000398339.1_Missense_Mutation_p.T628A|TCF4_ENST00000564999.1_Missense_Mutation_p.T526A|TCF4_ENST00000564403.2_Missense_Mutation_p.T532A|TCF4_ENST00000567880.1_Missense_Mutation_p.T466A|TCF4_ENST00000568740.1_Missense_Mutation_p.T501A|TCF4_ENST00000561831.3_Missense_Mutation_p.T366A|TCF4_ENST00000566286.1_Missense_Mutation_p.T523A|TCF4_ENST00000561992.1_Missense_Mutation_p.T396A|TCF4_ENST00000537578.1_Missense_Mutation_p.T502A|TCF4_ENST00000570287.2_Missense_Mutation_p.T366A|TCF4_ENST00000565018.2_Missense_Mutation_p.T526A|TCF4_ENST00000540999.1_Missense_Mutation_p.T502A|TCF4_ENST00000570177.2_Missense_Mutation_p.T396A|TCF4_ENST00000457482.3_Missense_Mutation_p.T366A|TCF4_ENST00000543082.1_Missense_Mutation_p.T484A|TCF4_ENST00000537856.3_Missense_Mutation_p.T396A|TCF4_ENST00000568673.1_Missense_Mutation_p.T502A|TCF4_ENST00000544241.2_Missense_Mutation_p.T455A|TCF4_ENST00000564228.1_Missense_Mutation_p.T455A|TCF4_ENST00000566279.1_Missense_Mutation_p.T466A|TCF4_ENST00000354452.3_Missense_Mutation_p.T526A NM_003199.2 NP_003190.1 P15884 ITF2_HUMAN transcription factor 4 41 GAAGATTTCGTGTCTTGCAGG 0.453000 0 SO:0001583 missense ENST00000356073.4 1 1 hg19 CCDS11960.1 . . . . . . . . . . T 2.304 -0.359529 0.05138 . . ENSG00000196628 ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339 T;T;T;T;T;T;T;T;T 0.16897 2.57;2.31;2.62;2.62;2.62;2.57;2.56;2.37;2.55 5.35 4.18 0.49190 . 0.176553 0.51477 D 0.000093 T 0.05777 0.0151 N 0.03050 -0.425 0.38345 D 0.944171 B;B;B;B;B;B;B;B;B 0.18310 0.0;0.016;0.001;0.027;0.0;0.0;0.001;0.0;0.01 B;B;B;B;B;B;B;B;B 0.23150 0.001;0.015;0.001;0.044;0.0;0.001;0.002;0.0;0.003 T 0.24977 -1.0145 10 0.09590 T 0.72 -5.2262 5.6177 0.17440 0.1509:0.0821:0.0:0.767 . 502;526;366;628;526;484;455;366;523 B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5 .;.;.;.;ITF2_HUMAN;.;.;.;. A 526;366;526;484;502;502;455;396;628 ENSP00000346440:T526A;ENSP00000409447:T366A;ENSP00000348374:T526A;ENSP00000439656:T484A;ENSP00000445202:T502A;ENSP00000440731:T502A;ENSP00000441562:T455A;ENSP00000439827:T396A;ENSP00000381382:T628A ENSP00000346440:T526A T - 1 0 TCF4 51050811 0.997000 0.39634 1.000000 0.80357 0.979000 0.70002 0.581000 0.23819 0.872000 0.35775 0.383000 0.25322 ACG TCGA-IB-AAUN-01A-12D-A38G-08 TCF4-002 KNOWN upstream_uORF|basic|CCDS protein_coding protein_coding OTTHUMT00000256014.1 1 0 1 115 148 0 151 1 1 2 49 0 151 2 0 0 0 0 0 2 1 1.000000 114 145 0 150 2 0 0 0 0 151 2 -20.000000 1 1 0 0 1 0 1 1 1.553807 1 0.560000 1.800000 0.388889 0.970000 8.900000e-01 1.000000 0.990000 0.970826 0.970000 1 0.930000 1.000000 LRRC30 339291 broad.mit.edu 37 18 7231664 7231664 + Silent SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr18:7231664G>A ENST00000383467.2 + 1 542 c.528G>A c.(526-528)gcG>gcA p.A176A NM_001105581.1 NP_001099051.1 A6NM36 LRC30_HUMAN leucine rich repeat containing 30 p.A176A(1) 31 ACTTCTTCGCGCACATCCCCA 0.552000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000383467.2 0 1 hg19 CCDS42409.1 TCGA-IB-AAUN-01A-12D-A38G-08 LRRC30-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000442140.1 0 0 0 5 416 1 195 0 0 0 1 195 2 0 0 0 0 0 2 0 0.139044 5 409 1 193 10 0 0 0 1 195 2 -2.239799 0 1 121082 2 31 1 1 2 3 2.180031 0 0.560000 1.800000 0.567270 0.040000 0 1.000000 0.040000 0.095817 0.040000 0 0.020000 0.080000 ACPT 93650 broad.mit.edu 37 19 51298323 51298323 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr19:51298323G>A ENST00000270593.1 + 11 1189 c.1189G>A c.(1189-1191)Gga>Aga p.G397R CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Missense_Mutation_p.G304R NM_033068.2 NP_149059.1 Q9BZG2 PPAT_HUMAN acid phosphatase, testicular 11 all_neural(266;0.057) CCTGCTGGCCGGAGCTGTAGC 0.677000 0 SO:0001583 missense ENST00000270593.1 0 1 hg19 CCDS12802.1 . . . . . . . . . . g 18.35 3.605092 0.66445 . . ENSG00000142513 ENST00000270593;ENST00000270594 T;T 0.13420 2.76;2.59 4.14 4.14 0.48551 . 0.282362 0.27117 N 0.020860 T 0.24198 0.0586 L 0.41824 1.3 0.33730 D 0.618158 D 0.89917 1.0 D 0.68483 0.958 T 0.16660 -1.0395 10 0.25106 T 0.35 -8.8258 12.3028 0.54884 0.0:0.0:1.0:0.0 . 397 Q9BZG2 PPAT_HUMAN R 397;304 ENSP00000270593:G397R;ENSP00000270594:G304R ENSP00000270593:G397R G + 1 0 ACPT 55990135 0.999000 0.42202 0.983000 0.44433 0.808000 0.45660 4.443000 0.59994 2.037000 0.60232 0.561000 0.74099 GGA TCGA-IB-AAUN-01A-12D-A38G-08 ACPT-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464434.1 0 0 0 10 32 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.997107 7 32 0 23 2 0 0 0 0 23 2 -19.904370 1 1 120938 1 30 1 1 2 3 2.162368 0 0.560000 1.800000 0.564873 0.870000 4.700000e-01 1.000000 1.000000 0.843443 0.870000 1 0.650000 1.000000 PEG3 5178 broad.mit.edu 37 19 57328906 57328906 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr19:57328906G>A ENST00000326441.9 - 10 1267 c.904C>T c.(904-906)Cgg>Tgg p.R302W PEG3_ENST00000598410.1_Missense_Mutation_p.R178W|PEG3_ENST00000423103.2_Missense_Mutation_p.R302W|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R176W|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron NM_006210.2 NP_006201.1 Q9GZU2 PEG3_HUMAN paternally expressed 3 170 Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243) CAAATCCCCCGCCGGTGGGTT 0.458000 0 SO:0001583 missense ENST00000326441.9 1 1 hg19 CCDS12948.1 . . . . . . . . . . G 17.79 3.475230 0.63737 . . ENSG00000198300 ENST00000326441;ENST00000423103;ENST00000292074 T;T 0.02737 4.18;4.18 4.27 3.22 0.36961 . 0.000000 0.43919 D 0.000511 T 0.06962 0.0177 L 0.27053 0.805 . . . D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.73708 0.972;0.972;0.981 T 0.36407 -0.9749 9 0.51188 T 0.08 -23.6433 11.7512 0.51849 0.0:0.0:0.8225:0.1775 . 178;302;237 A7E2B8;Q9GZU2;Q96Q96 .;PEG3_HUMAN;. W 302;302;272 ENSP00000326581:R302W;ENSP00000403051:R302W ENSP00000292074:R272W R - 1 2 ZIM2 62020718 0.147000 0.22687 0.499000 0.27577 0.991000 0.79684 3.450000 0.52957 1.367000 0.46095 0.561000 0.74099 CGG TCGA-IB-AAUN-01A-12D-A38G-08 PEG3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416099.2 1 0 1 122 346 1 193 0 0 0 1 193 2 0 0 0 0 0 2 1 1.000000 120 333 1 188 10 0 0 0 1 193 2 -5.989526 1 1 121376 2 36 1 1 2 3 2.158275 0 0.560000 1.800000 0.564873 0.940000 7.900000e-01 1.000000 1.000000 0.935868 0.940000 1 0.860000 1.000000 ATXN7L2 127002 broad.mit.edu 37 1 110032901 110032901 + Silent SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:110032901C>T ENST00000369870.3 + 9 1260 c.1245C>T c.(1243-1245)acC>acT p.T415T NM_153340.4 NP_699171.3 Q5T6C5 AT7L2_HUMAN ataxin 7-like 2 17 all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453) AGTTCTGCACCTTTGGGAGCC 0.597000 OREG0013635 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000369870.3 0 1 hg19 CCDS30794.1 TCGA-IB-AAUN-01A-12D-A38G-08 ATXN7L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000030331.1 0 0 0 6 282 0 186 0 6.635857e-04 0 2 0 186 2 0 0 0 0 0 2 1 0.963877 6 278 0 184 2 0 0 0 0 186 2 -2.434781 0 1 0 0 1 0 1 1 1.538419 1 0.560000 1.800000 0.388889 0.050000 1.000000e-02 0.110000 0.050000 0.061723 0.050000 0 0.030000 0.080000 AMPD2 271 broad.mit.edu 37 1 110172900 110172900 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:110172900G>A ENST00000256578.3 + 16 2551 c.2191G>A c.(2191-2193)Gcc>Acc p.A731T AMPD2_ENST00000393688.3_Missense_Mutation_p.A612T|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000528454.1_Missense_Mutation_p.A613T|AMPD2_ENST00000528667.1_Missense_Mutation_p.A731T|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000358729.4_Missense_Mutation_p.A656T|AMPD2_ENST00000342115.4_Missense_Mutation_p.A650T NM_004037.7 NP_004028.3 Q01433 AMPD2_HUMAN adenosine monophosphate deaminase 2 7 all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244) GATCGGCATCGCCATGTCTCC 0.652000 0 SO:0001583 missense ENST00000256578.3 0 1 hg19 CCDS805.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 34|34 5.324955|5.324955 0.95708|0.95708 .|. .|. ENSG00000116337|ENSG00000116337 ENST00000342115;ENST00000528667;ENST00000256578;ENST00000358729;ENST00000528454;ENST00000393688|ENST00000369840 D;D;D;D;D;D|. 0.83335|. -1.71;-1.71;-1.71;-1.71;-1.71;-1.71|. 4.66|4.66 4.66|4.66 0.58398|0.58398 Adenosine/AMP deaminase (1);|. 0.102270|. 0.64402|. D|. 0.000003|. T|T 0.67344|0.67344 0.2883|0.2883 M|M 0.69358|0.69358 2.11|2.11 0.80722|0.80722 D|D 1|1 D;D;D;D|. 0.89917|. 1.0;0.993;0.989;0.999|. D;P;P;P|. 0.85130|. 0.997;0.739;0.705;0.873|. T|T 0.66999|0.66999 -0.5781|-0.5781 10|5 0.54805|. T|. 0.06|. -24.088|-24.088 17.3347|17.3347 0.87277|0.87277 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 656;612;731;650|. Q01433-4;Q01433-3;Q01433;Q01433-2|. .;.;AMPD2_HUMAN;.|. T|H 650;731;731;656;613;612|701 ENSP00000345498:A650T;ENSP00000436541:A731T;ENSP00000256578:A731T;ENSP00000351573:A656T;ENSP00000437164:A613T;ENSP00000377292:A612T|. ENSP00000256578:A731T|. A|R +|+ 1|2 0|0 AMPD2|AMPD2 109974423|109974423 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.780000|0.780000 0.44128|0.44128 9.595000|9.595000 0.98260|0.98260 2.424000|2.424000 0.82194|0.82194 0.561000|0.561000 0.74099|0.74099 GCC|CGC TCGA-IB-AAUN-01A-12D-A38G-08 AMPD2-011 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000390615.1 0 0 0 6 390 1 303 0 1.784174e-01 0 43 1 303 2 0 0 0 0 0 2 1 0.962101 6 379 0 302 2 0 0 0 1 303 2 -2.420047 0 1 0 0 1 0 1 1 1.538419 1 0.560000 1.800000 0.388889 0.030000 1.000000e-02 0.080000 0.040000 0.045042 0.030000 0 0.020000 0.060000 MTOR 2475 broad.mit.edu 37 1 11217239 11217239 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:11217239C>T ENST00000361445.4 - 30 4515 c.4439G>A c.(4438-4440)cGc>cAc p.R1480H NM_004958.3 NP_004949.1 P42345 MTOR_HUMAN mechanistic target of rapamycin (serine/threonine kinase) 149 Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287) GCAGCGCATGCGGCCCAGCAT 0.532000 0 SO:0001583 missense ENST00000361445.4 0 1 hg19 CCDS127.1 . . . . . . . . . . C 18.23 3.577708 0.65878 . . ENSG00000198793 ENST00000361445;ENST00000539766 T 0.65549 -0.16 5.32 5.32 0.75619 PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.53867 0.1823 L 0.31926 0.97 0.80722 D 1 B 0.13145 0.007 B 0.01281 0.0 T 0.46190 -0.9209 10 0.30854 T 0.27 -1.1882 19.0009 0.92834 0.0:1.0:0.0:0.0 . 1480 P42345 MTOR_HUMAN H 1480 ENSP00000354558:R1480H ENSP00000354558:R1480H R - 2 0 MTOR 11139826 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.414000 0.80117 2.486000 0.83907 0.655000 0.94253 CGC TCGA-IB-AAUN-01A-12D-A38G-08 MTOR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005558.1 0 0 0 5 418 0 260 0 4.200110e-02 0 22 0 260 2 0 0 0 0 0 2 1 0.934298 5 409 0 259 2 0 0 0 0 260 2 -1.773933 0 1 121412 1 33 1 0 1 1 1.591539 1 0.560000 1.800000 0.391256 0.020000 0 0.070000 0.030000 0.036310 0.020000 0 0.010000 0.050000 PLA2G2C 391013 broad.mit.edu 37 1 20501534 20501534 + Missense_Mutation SNP C C A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:20501534C>A ENST00000429261.2 - 2 205 c.145G>T c.(145-147)Ggg>Tgg p.G49W PLA2G2C_ENST00000495760.2_5'UTR|PLA2G2C_ENST00000247992.5_Missense_Mutation_p.G52W Q5R387 PA2GC_HUMAN phospholipase A2, group IIC 7 Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427) CCTTTATCCCCAAGCCCACAG 0.502000 0 SO:0001583 missense ENST00000429261.2 0 1 hg19 . . . . . . . . . . C 18.49 3.635175 0.67130 . . ENSG00000187980 ENST00000429261;ENST00000247992 T;D 0.86030 1.34;-2.06 5.13 5.13 0.70059 . 0.000000 0.56097 D 0.000031 D 0.94621 0.8266 H 0.96142 3.775 0.50632 D 0.99988 . . . . . . D 0.95955 0.8957 8 0.87932 D 0 . 14.0795 0.64912 0.0:1.0:0.0:0.0 . . . . W 49;52 ENSP00000389335:G49W;ENSP00000247992:G52W ENSP00000247992:G52W G - 1 0 PLA2G2C 20374121 0.879000 0.30193 1.000000 0.80357 0.765000 0.43378 2.413000 0.44618 2.364000 0.80123 0.655000 0.94253 GGG TCGA-IB-AAUN-01A-12D-A38G-08 PLA2G2C-001 PUTATIVE not_organism_supported|basic|appris_candidate|exp_conf protein_coding protein_coding OTTHUMT00000007689.3 0 0 0 5 129 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 0.930963 5 123 0 115 2 0 0 0 0 115 2 -3.426894 1 1 0 0 1 0 1 1 1.605528 1 0.560000 1.800000 0.391256 0.100000 3.000000e-02 0.210000 0.100000 0.112572 0.100000 0 0.060000 0.150000 DTL 51514 broad.mit.edu 37 1 212209261 212209261 + Missense_Mutation SNP C C G TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:212209261C>G ENST00000366991.4 + 1 343 c.29C>G c.(28-30)cCc>cGc p.P10R DTL_ENST00000475419.1_3'UTR|DTL_ENST00000542077.1_Missense_Mutation_p.P10R|INTS7_ENST00000366993.3_5'Flank|INTS7_ENST00000440600.2_5'Flank|INTS7_ENST00000366994.3_5'Flank|INTS7_ENST00000366992.3_5'Flank|INTS7_ENST00000469606.1_5'Flank NM_016448.2 NP_057532.2 Q9NZJ0 DTL_HUMAN denticleless E3 ubiquitin protein ligase homolog (Drosophila) 23 CTCCGCCAGCCCCAGCTTGGC 0.572000 0 SO:0001583 missense ENST00000366991.4 1 1 hg19 CCDS1502.1 . . . . . . . . . . C 23.4 4.417373 0.83449 . . ENSG00000143476 ENST00000366991;ENST00000542077;ENST00000420235 T;T 0.71103 -0.5;-0.54 5.63 5.63 0.86233 . 0.118711 0.56097 D 0.000025 T 0.81884 0.4917 M 0.64997 1.995 0.40200 D 0.977506 D;P 0.89917 1.0;0.944 D;P 0.87578 0.998;0.587 T 0.82438 -0.0457 10 0.51188 T 0.08 -13.6374 15.2097 0.73209 0.0:1.0:0.0:0.0 . 10;10 F5GZ90;Q9NZJ0 .;DTL_HUMAN R 10 ENSP00000355958:P10R;ENSP00000443870:P10R ENSP00000355958:P10R P + 2 0 DTL 210275884 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.185000 0.50934 2.652000 0.90054 0.655000 0.94253 CCC TCGA-IB-AAUN-01A-12D-A38G-08 DTL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090182.1 1 0 1 38 100 0 78 1 6.180417e-01 3 4 0 78 2 0 0 0 0 0 2 1 1.000000 38 96 0 78 2 0 0 0 0 78 2 -20.000000 1 1 0 0 1 1 2 3 2.136668 0 0.560000 1.800000 0.561229 0.980000 7.300000e-01 1.000000 1.000000 0.942114 0.980000 1 0.850000 1.000000 DTL 51514 broad.mit.edu 37 1 212209262 212209262 + Silent SNP C C G TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:212209262C>G ENST00000366991.4 + 1 344 c.30C>G c.(28-30)ccC>ccG p.P10P DTL_ENST00000475419.1_3'UTR|DTL_ENST00000542077.1_Silent_p.P10P|INTS7_ENST00000366993.3_5'Flank|INTS7_ENST00000440600.2_5'Flank|INTS7_ENST00000366994.3_5'Flank|INTS7_ENST00000366992.3_5'Flank|INTS7_ENST00000469606.1_5'Flank NM_016448.2 NP_057532.2 Q9NZJ0 DTL_HUMAN denticleless E3 ubiquitin protein ligase homolog (Drosophila) 23 TCCGCCAGCCCCAGCTTGGCG 0.572000 0 SO:0001819 synonymous_variant ENST00000366991.4 1 1 hg19 CCDS1502.1 TCGA-IB-AAUN-01A-12D-A38G-08 DTL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090182.1 1 0 1 38 100 0 76 1 6.180417e-01 3 4 0 76 2 0 0 0 0 0 2 1 1.000000 38 96 0 76 2 0 0 0 0 76 2 -4.772945 1 1 0 0 1 1 2 3 2.136668 0 0.560000 1.800000 0.561229 0.980000 7.300000e-01 1.000000 1.000000 0.942114 0.980000 1 0.850000 1.000000 ESRRG 2104 broad.mit.edu 37 1 216680448 216680448 + Missense_Mutation SNP C C A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:216680448C>A ENST00000408911.3 - 7 1363 c.1210G>T c.(1210-1212)Gct>Tct p.A404S ESRRG_ENST00000463665.1_Missense_Mutation_p.A342S|ESRRG_ENST00000366938.2_Missense_Mutation_p.A381S|ESRRG_ENST00000361525.3_Missense_Mutation_p.A381S|ESRRG_ENST00000493603.1_Missense_Mutation_p.A381S|ESRRG_ENST00000487276.1_Missense_Mutation_p.A381S|ESRRG_ENST00000359162.2_Missense_Mutation_p.A381S|ESRRG_ENST00000391890.3_Missense_Mutation_p.A388S|ESRRG_ENST00000366937.1_Missense_Mutation_p.A416S|ESRRG_ENST00000361395.2_Missense_Mutation_p.A381S|ESRRG_ENST00000493748.1_Missense_Mutation_p.A381S|ESRRG_ENST00000360012.3_Missense_Mutation_p.A381S|ESRRG_ENST00000366940.2_Missense_Mutation_p.A381S NM_001438.3 NP_001429.2 P62508 ERR3_HUMAN estrogen-related receptor gamma 49 Diethylstilbestrol(DB00255) TGCTGGCCAGCTTCATAATCC 0.498000 0 SO:0001583 missense ENST00000408911.3 0 1 hg19 CCDS41468.1 . . . . . . . . . . C 12.14 1.847181 0.32606 . . ENSG00000196482 ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748 D;D;D;D;D;D;D;D;D;D;D;D;D 0.96427 -4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01 5.61 5.61 0.85477 Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2); 0.047654 0.85682 D 0.000000 D 0.91633 0.7356 N 0.12569 0.235 0.80722 D 1 B;B;B 0.10296 0.0;0.002;0.003 B;B;B 0.15052 0.008;0.012;0.012 D 0.86965 0.2094 10 0.19590 T 0.45 . 19.652 0.95819 0.0:1.0:0.0:0.0 . 342;416;404 E9PGB7;F8W8J3;P62508 .;.;ERR3_HUMAN S 381;381;416;404;381;381;381;381;381;388;342;381;381;381 ENSP00000355225:A381S;ENSP00000355907:A381S;ENSP00000355904:A416S;ENSP00000386171:A404S;ENSP00000352077:A381S;ENSP00000354584:A381S;ENSP00000355905:A381S;ENSP00000353108:A381S;ENSP00000419594:A381S;ENSP00000375761:A388S;ENSP00000418629:A342S;ENSP00000419155:A381S;ENSP00000417374:A381S ENSP00000346386:A381S A - 1 0 ESRRG 214747071 1.000000 0.71417 0.973000 0.42090 0.976000 0.68499 4.892000 0.63193 2.656000 0.90262 0.561000 0.74099 GCT TCGA-IB-AAUN-01A-12D-A38G-08 ESRRG-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000089882.2 0 0 0 8 442 1 244 0 4.376112e-04 0 2 1 244 2 0 0 0 0 0 2 0 0.479260 8 432 1 243 9 0 0 0 1 244 2 -3.176432 1 1 0 0 1 1 2 3 2.136668 0 0.560000 1.800000 0.561229 0.060000 2.000000e-02 0.130000 0.060000 0.071202 0.060000 0 0.040000 0.100000 CHML 1122 broad.mit.edu 37 1 241797637 241797637 + Missense_Mutation SNP T T C TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:241797637T>C ENST00000366553.1 - 1 1595 c.1432A>G c.(1432-1434)Ata>Gta p.I478V OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron NM_001821.3 NP_001812.2 P26374 RAE2_HUMAN choroideremia-like (Rab escort protein 2) 26 Ovarian(103;0.103)|all_lung(81;0.23) all_cancers(173;0.0231) OV - Ovarian serous cystadenocarcinoma(106;0.0125) GGAGGAACTATCAGAATGGAA 0.428000 0 SO:0001583 missense ENST00000366553.1 1 1 hg19 CCDS31073.1 . . . . . . . . . . T 6.570 0.473395 0.12461 . . ENSG00000203668 ENST00000366553 D 0.82167 -1.58 5.08 0.907 0.19321 . 0.297564 0.35013 N 0.003520 T 0.66954 0.2842 . . . 0.21147 N 0.999771 B 0.02656 0.0 B 0.09377 0.004 T 0.53236 -0.8467 9 0.42905 T 0.14 -1.3604 0.6338 0.00799 0.164:0.2371:0.1696:0.4293 . 478 P26374 RAE2_HUMAN V 478 ENSP00000355511:I478V ENSP00000355511:I478V I - 1 0 CHML 239864260 0.971000 0.33674 0.988000 0.46212 0.919000 0.55068 1.313000 0.33585 0.059000 0.16252 -0.313000 0.08912 ATA TCGA-IB-AAUN-01A-12D-A38G-08 CHML-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095712.1 1 0 0 31 388 0 210 0 2.312893e-01 0 12 0 210 2 0 0 0 0 0 2 1 1.000000 30 382 0 210 2 0 0 0 0 210 2 -20.000000 1 1 0 0 1 1 2 3 2.136668 0 0.560000 1.800000 0.561229 0.260000 1.800000e-01 0.370000 0.260000 0.271717 0.260000 0 0.220000 0.320000 OR2G2 81470 broad.mit.edu 37 1 247752184 247752184 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:247752184C>T ENST00000320065.1 + 1 523 c.523C>T c.(523-525)Cgc>Tgc p.R175C RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA NM_001001915.1 NP_001001915.1 Q8NGZ5 OR2G2_HUMAN olfactory receptor, family 2, subfamily G, member 2 p.R175C(1) 45 all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) OV - Ovarian serous cystadenocarcinoma(106;0.017) CTGTGGGCATCGCCAAGTGGA 0.557000 1 Substitution - Missense(1) SO:0001583 missense ENST00000320065.1 0 1 hg19 CCDS31092.1 . . . . . . . . . . C 14.53 2.563482 0.45694 . . ENSG00000177489 ENST00000320065 T 0.00137 8.68 4.29 2.22 0.28083 GPCR, rhodopsin-like superfamily (1); 0.910260 0.08981 U 0.865762 T 0.00384 0.0012 M 0.80616 2.505 0.09310 N 1 D 0.76494 0.999 D 0.65140 0.932 T 0.49872 -0.8893 10 0.54805 T 0.06 . 3.3058 0.07000 0.2201:0.5548:0.0:0.2251 . 175 Q8NGZ5 OR2G2_HUMAN C 175 ENSP00000326349:R175C ENSP00000326349:R175C R + 1 0 OR2G2 245818807 0.025000 0.19082 0.764000 0.31436 0.987000 0.75469 2.319000 0.43788 1.013000 0.39391 0.591000 0.81541 CGC TCGA-IB-AAUN-01A-12D-A38G-08 OR2G2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097623.1 0 0 0 5 396 0 231 0 0 0 0 231 2 0 0 0 0 0 2 1 0.934116 5 387 0 230 2 0 0 0 0 231 2 -2.512296 1 1 0 0 1 1 2 3 2.136668 0 0.560000 1.800000 0.561229 0.040000 0 0.110000 0.040000 0.053113 0.040000 0 0.020000 0.080000 ADPRHL2 54936 broad.mit.edu 37 1 36557583 36557583 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:36557583G>A ENST00000373178.4 + 4 619 c.589G>A c.(589-591)Gct>Act p.A197T NM_017825.2 NP_060295.1 Q9NX46 ARHL2_HUMAN ADP-ribosylhydrolase like 2 8 Myeloproliferative disorder(586;0.0393) GCAGGCCCTGGCTGTGCACCT 0.627000 0 SO:0001583 missense ENST00000373178.4 0 1 hg19 CCDS402.1 . . . . . . . . . . G 36 5.663119 0.96745 . . ENSG00000116863 ENST00000373178;ENST00000540867;ENST00000543954 T 0.35421 1.31 5.48 5.48 0.80851 . 0.000000 0.85682 D 0.000000 T 0.64929 0.2643 M 0.85710 2.77 0.80722 D 1 D 0.76494 0.999 D 0.72982 0.979 T 0.64067 -0.6494 10 0.30854 T 0.27 -11.8061 19.3486 0.94374 0.0:0.0:1.0:0.0 . 197 Q9NX46 ARHL2_HUMAN T 197;117;43 ENSP00000362273:A197T ENSP00000362273:A197T A + 1 0 ADPRHL2 36330170 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.845000 0.99498 2.546000 0.85860 0.655000 0.94253 GCT TCGA-IB-AAUN-01A-12D-A38G-08 ADPRHL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000020199.1 0 0 0 4 170 0 107 0 4.330435e-01 0 54 0 107 2 0 0 0 0 0 2 1 0.884336 4 165 0 106 2 0 0 0 0 107 2 -5.993319 1 1 0 0 1 0 1 1 1.571110 1 0.560000 1.800000 0.388889 0.060000 1.000000e-02 0.140000 0.060000 0.072386 0.060000 0 0.030000 0.100000 LRRC7 57554 broad.mit.edu 37 1 70488845 70488845 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr1:70488845C>T ENST00000035383.5 + 15 1498 c.1468C>T c.(1468-1470)Cgt>Tgt p.R490C LRRC7_ENST00000310961.5_Missense_Mutation_p.R495C|RP11-181B18.1_ENST00000425754.1_RNA|RP11-181B18.1_ENST00000414132.1_RNA|LRRC7_ENST00000415775.2_Intron NM_020794.2 NP_065845.1 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 162 AAGGGGCCAGCGTGGGATTAC 0.542000 0 SO:0001583 missense ENST00000035383.5 1 1 hg19 CCDS645.1 . . . . . . . . . . C 15.75 2.925926 0.52759 . . ENSG00000033122 ENST00000310961;ENST00000035383;ENST00000370957 T;T 0.38077 1.16;1.24 5.86 5.86 0.93980 . 0.257341 0.35495 N 0.003162 T 0.10981 0.0268 N 0.08118 0 0.80722 D 1 P 0.49358 0.923 B 0.35859 0.212 T 0.05273 -1.0895 10 0.72032 D 0.01 . 15.6849 0.77402 0.0:1.0:0.0:0.0 . 490 Q96NW7 LRRC7_HUMAN C 495;490;313 ENSP00000309245:R495C;ENSP00000035383:R490C ENSP00000035383:R490C R + 1 0 LRRC7 70261433 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.522000 0.53480 2.775000 0.95449 0.585000 0.79938 CGT TCGA-IB-AAUN-01A-12D-A38G-08 LRRC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131261.1 1 0 1 56 77 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 1.000000 56 74 0 95 2 0 0 0 0 96 2 -20.000000 1 1 0 0 1 0 1 1 1.571110 1 0.560000 1.800000 0.388889 0.940000 8.000000e-01 1.000000 0.990000 0.940533 0.940000 1 0.880000 0.990000 PMEPA1 56937 broad.mit.edu 37 20 56234669 56234669 + Missense_Mutation SNP T T C TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr20:56234669T>C ENST00000341744.3 - 2 513 c.194A>G c.(193-195)tAc>tGc p.Y65C PMEPA1_ENST00000395814.1_Missense_Mutation_p.Y15C|PMEPA1_ENST00000347215.4_Missense_Mutation_p.Y30C|PMEPA1_ENST00000265626.4_Missense_Mutation_p.Y15C|PMEPA1_ENST00000395816.3_Missense_Mutation_p.Y15C|PMEPA1_ENST00000472841.1_5'UTR NM_020182.4 NP_064567.2 Q969W9 PMEPA_HUMAN prostate transmembrane protein, androgen induced 1 16 AGACAGCTTGTAGTGGCTCAG 0.577000 0 SO:0001583 missense ENST00000341744.3 1 1 hg19 CCDS13463.1 . . . . . . . . . . T 16.66 3.185907 0.57909 . . ENSG00000124225 ENST00000341744;ENST00000347215;ENST00000395816;ENST00000265626;ENST00000395814;ENST00000414037;ENST00000395819 T;T;T;T;T;T;T 0.68903 -0.36;-0.24;-0.17;-0.17;-0.17;-0.14;-0.17 4.74 4.74 0.60224 . 0.131993 0.52532 D 0.000066 T 0.81413 0.4817 M 0.78049 2.395 0.54753 D 0.999985 D;D 0.89917 1.0;1.0 D;D 0.91635 0.998;0.999 D 0.84316 0.0513 10 0.87932 D 0 -27.9109 14.2249 0.65853 0.0:0.0:0.0:1.0 . 30;65 Q5JY37;Q969W9 .;PMEPA_HUMAN C 65;30;15;15;15;37;122 ENSP00000345826:Y65C;ENSP00000344014:Y30C;ENSP00000379161:Y15C;ENSP00000265626:Y15C;ENSP00000379159:Y15C;ENSP00000401506:Y37C;ENSP00000379164:Y122C ENSP00000265626:Y15C Y - 2 0 PMEPA1 55668075 1.000000 0.71417 1.000000 0.80357 0.072000 0.16883 7.867000 0.87062 1.774000 0.52232 0.459000 0.35465 TAC TCGA-IB-AAUN-01A-12D-A38G-08 PMEPA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079858.2 1 0 1 19 47 0 48 1 1 268 472 0 48 2 0 0 0 0 0 2 1 0.999997 18 47 0 48 2 0 0 0 0 48 2 -20.000000 1 1 0 0 1 0 0 0 2.108254 0 0.560000 1.800000 0.557522 0.990000 6.700000e-01 1.000000 1.000000 0.938576 0.990000 1 0.830000 1.000000 CSF2RB 1439 broad.mit.edu 37 22 37326748 37326748 + Silent SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr22:37326748G>A ENST00000403662.3 + 8 1110 c.888G>A c.(886-888)ggG>ggA p.G296G CSF2RB_ENST00000262825.5_Silent_p.G302G|CSF2RB_ENST00000536485.1_Silent_p.G243G|CSF2RB_ENST00000406230.1_Silent_p.G302G P32927 IL3RB_HUMAN colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) 42 Sargramostim(DB00020) TGAGGGAGGGGCTCGGCAGCC 0.657000 0 SO:0001819 synonymous_variant ENST00000403662.3 1 1 hg19 CCDS13936.1 TCGA-IB-AAUN-01A-12D-A38G-08 CSF2RB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318854.1 1 0 1 43 128 0 77 0 7.031130e-01 0 9 0 77 2 0 0 0 0 0 2 1 1.000000 42 122 0 76 2 0 0 0 0 77 2 -20.000000 1 1 0 0 1 1 2 3 2.175080 0 0.560000 1.800000 0.566075 0.910000 6.800000e-01 1.000000 1.000000 0.902919 0.910000 1 0.790000 1.000000 TTLL12 23170 broad.mit.edu 37 22 43575882 43575882 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr22:43575882G>A ENST00000216129.6 - 4 734 c.671C>T c.(670-672)aCg>aTg p.T224M NM_015140.3 NP_055955.1 Q14166 TTL12_HUMAN tubulin tyrosine ligase-like family, member 12 13 Ovarian(80;0.221)|Glioma(61;0.222) CCACAGCAGCGTGTAGGCCAC 0.657000 0 SO:0001583 missense ENST00000216129.6 0 1 hg19 CCDS14047.1 . . . . . . . . . . G 19.87 3.906526 0.72868 . . ENSG00000100304 ENST00000216129;ENST00000423379 T 0.54479 0.57 5.55 5.55 0.83447 . 0.057372 0.64402 D 0.000001 T 0.63426 0.2510 M 0.77820 2.39 0.58432 D 0.999999 D;D 0.53462 0.96;0.96 P;P 0.46237 0.508;0.508 T 0.70590 -0.4830 10 0.87932 D 0 -2.0841 19.5034 0.95105 0.0:0.0:1.0:0.0 . 224;224 B1AH89;Q14166 .;TTL12_HUMAN M 224 ENSP00000216129:T224M ENSP00000216129:T224M T - 2 0 TTLL12 41905826 1.000000 0.71417 1.000000 0.80357 0.206000 0.24218 9.272000 0.95707 2.593000 0.87608 0.655000 0.94253 ACG TCGA-IB-AAUN-01A-12D-A38G-08 TTLL12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319611.1 0 0 0 4 162 0 98 0 6.380330e-01 1 80 0 98 2 0 0 0 0 0 2 1 0.887017 4 159 0 96 2 0 0 0 0 98 2 -6.461489 1 1 121392 3 34 1 1 2 3 2.175080 0 0.560000 1.800000 0.566075 0.090000 2.000000e-02 1.000000 0.090000 0.141172 0.090000 0 0.050000 0.160000 TACR1 6869 broad.mit.edu 37 2 75425709 75425709 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr2:75425709C>T ENST00000305249.5 - 1 1117 c.352G>A c.(352-354)Gcc>Acc p.A118T TACR1_ENST00000409848.3_Missense_Mutation_p.A118T NM_001058.3 NP_001049.1 P25103 NK1R_HUMAN tachykinin receptor 1 24 Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894) TAGATACTGGCGAAGACAGCG 0.498000 Pancreas(64;62 1268 3653 14826 43765) 0 SO:0001583 missense ENST00000305249.5 0 1 hg19 CCDS1958.1 . . . . . . . . . . C 20.5 4.001310 0.74818 . . ENSG00000115353 ENST00000305249;ENST00000409848 T;T 0.76060 -0.99;-0.99 5.41 5.41 0.78517 GPCR, rhodopsin-like superfamily (1); 0.049231 0.85682 D 0.000000 T 0.66684 0.2814 L 0.51914 1.62 0.80722 D 1 P 0.47604 0.898 B 0.39660 0.306 T 0.67225 -0.5724 10 0.37606 T 0.19 . 11.5873 0.50925 0.1776:0.8224:0.0:0.0 . 118 P25103 NK1R_HUMAN T 118 ENSP00000303522:A118T;ENSP00000386448:A118T ENSP00000303522:A118T A - 1 0 TACR1 75279217 1.000000 0.71417 0.985000 0.45067 0.992000 0.81027 4.545000 0.60698 2.798000 0.96311 0.655000 0.94253 GCC TCGA-IB-AAUN-01A-12D-A38G-08 TACR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252239.3 0 0 0 8 355 0 193 0 6.700317e-04 0 2 0 193 2 0 0 0 0 0 2 1 0.988824 8 348 0 192 2 0 0 0 0 193 2 -2.630091 1 1 0 0 1 0 0 0 2.108370 0 0.560000 1.800000 0.557522 0.070000 3.000000e-02 0.150000 0.080000 0.087379 0.070000 0 0.050000 0.120000 FNDC3B 64778 broad.mit.edu 37 3 172096148 172096148 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr3:172096148G>A ENST00000336824.4 + 24 3196 c.3097G>A c.(3097-3099)Gca>Aca p.A1033T FNDC3B_ENST00000415807.2_Missense_Mutation_p.A1033T|FNDC3B_ENST00000416957.1_Missense_Mutation_p.A1033T NM_001135095.1 NP_001128567.1 Q53EP0 FND3B_HUMAN fibronectin type III domain containing 3B 69 all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) AATCCAGGCAGCAAGCGAGGC 0.483000 0 SO:0001583 missense ENST00000336824.4 0 1 hg19 CCDS3217.1 . . . . . . . . . . G 15.43 2.830279 0.50845 . . ENSG00000075420 ENST00000415807;ENST00000336824;ENST00000416957 T;T;T 0.57273 0.41;0.41;0.41 5.26 4.37 0.52481 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.215889 0.47852 N 0.000204 T 0.27629 0.0679 N 0.02916 -0.46 0.80722 D 1 B 0.02656 0.0 B 0.04013 0.001 T 0.05241 -1.0897 10 0.23302 T 0.38 -5.2768 12.8682 0.57951 0.0801:0.0:0.9199:0.0 . 1033 Q53EP0 FND3B_HUMAN T 1033 ENSP00000411242:A1033T;ENSP00000338523:A1033T;ENSP00000389094:A1033T ENSP00000338523:A1033T A + 1 0 FNDC3B 173578842 0.862000 0.29867 0.667000 0.29798 0.980000 0.70556 1.874000 0.39568 1.183000 0.42943 0.655000 0.94253 GCA TCGA-IB-AAUN-01A-12D-A38G-08 FNDC3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345618.2 0 0 0 4 223 0 100 0 5.539570e-01 0 92 0 100 2 0 0 0 0 0 2 1 0.883641 4 216 0 98 2 0 0 0 0 100 2 -3.057399 1 1 121412 1 28 1 0 0 0 2.118878 0 0.560000 1.800000 0.560000 0.060000 1.000000e-02 0.150000 0.060000 0.077647 0.060000 0 0.030000 0.110000 UGT8 7368 broad.mit.edu 37 4 115597336 115597336 + Silent SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr4:115597336G>A ENST00000310836.6 + 6 2040 c.1518G>A c.(1516-1518)ctG>ctA p.L506L UGT8_ENST00000394511.3_Silent_p.L506L NM_001128174.1 NP_001121646 Q16880 CGT_HUMAN UDP glycosyltransferase 8 31 Ovarian(17;0.156) TCAAAAGTCTGTGGTCTAGAA 0.353000 0 SO:0001819 synonymous_variant ENST00000310836.6 1 1 hg19 CCDS3705.1 TCGA-IB-AAUN-01A-12D-A38G-08 UGT8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256426.2 1 0 1 65 305 0 190 1 8.250520e-01 4 13 0 190 2 0 0 0 0 0 2 1 1.000000 63 298 0 189 2 0 0 0 0 190 2 -20.000000 1 1 0 0 1 1 2 3 2.131604 0 0.560000 1.800000 0.561229 0.620000 4.900000e-01 0.780000 0.630000 0.634075 0.620000 0 0.550000 0.700000 FAT4 79633 broad.mit.edu 37 4 126372375 126372375 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr4:126372375C>T ENST00000394329.3 + 9 10217 c.10204C>T c.(10204-10206)Ccc>Tcc p.P3402S FAT4_ENST00000335110.5_Missense_Mutation_p.P1700S NM_024582.4 NP_078858.4 Q6V0I7 FAT4_HUMAN FAT atypical cadherin 4 355 AAATGACCCACCCATTTTTAC 0.458000 0 SO:0001583 missense ENST00000394329.3 0 1 hg19 CCDS3732.3 . . . . . . . . . . C 18.63 3.665933 0.67700 . . ENSG00000196159 ENST00000394329;ENST00000335110 D;D 0.84800 -1.9;-1.9 5.14 5.14 0.70334 Cadherin (3);Cadherin-like (1); 0.000000 0.34362 U 0.004026 D 0.95500 0.8538 H 0.97440 4.005 0.80722 D 1 D;D;D 0.89917 1.0;0.999;1.0 D;D;D 0.87578 0.998;0.97;0.998 D 0.97250 0.9897 10 0.87932 D 0 . 18.629 0.91352 0.0:1.0:0.0:0.0 . 1700;3402;3402 Q6V0I7-2;Q6V0I7;Q6V0I7-3 .;FAT4_HUMAN;. S 3402;1700 ENSP00000377862:P3402S;ENSP00000335169:P1700S ENSP00000335169:P1700S P + 1 0 FAT4 126591825 1.000000 0.71417 0.944000 0.38274 0.741000 0.42261 7.662000 0.83803 2.392000 0.81423 0.561000 0.74099 CCC TCGA-IB-AAUN-01A-12D-A38G-08 FAT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256765.2 0 0 0 12 620 0 329 0 4.311475e-03 0 5 0 329 2 0 0 0 0 0 2 1 0.999015 12 608 0 328 2 0 0 0 0 329 2 -2.905452 1 1 0 0 1 1 2 3 2.131604 0 0.560000 1.800000 0.561229 0.060000 2.000000e-02 0.120000 0.070000 0.073339 0.060000 0 0.040000 0.090000 SLC12A7 10723 broad.mit.edu 37 5 1064314 1064314 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr5:1064314C>T ENST00000264930.5 - 19 2534 c.2491G>A c.(2491-2493)Gtc>Atc p.V831I MIR4635_ENST00000583759.1_RNA NM_006598.2 NP_006589.2 Q9Y666 S12A7_HUMAN solute carrier family 12 (potassium/chloride transporter), member 7 32 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09) Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165) Potassium Chloride(DB00761) AACGAGTCGACGTTCTTGGCC 0.677000 0 SO:0001583 missense ENST00000264930.5 1 1 hg19 CCDS34129.1 2|2 9.157509157509158E-4|9.157509157509158E-4 1|1 0.0020325203252032522|0.0020325203252032522 0|0 0.0|0.0 1|1 0.0017482517482517483|0.0017482517482517483 0|0 0.0|0.0 C|C 0.018|0.018 -1.479004|-1.479004 0.01035|0.01035 2.28E-4|2.28E-4 0.0|0.0 ENSG00000113504|ENSG00000113504 ENST00000513223|ENST00000264930 .|D .|0.86432 .|-2.12 4.26|4.26 -0.302|-0.302 0.12796|0.12796 .|. .|0.562347 .|0.17891 .|N .|0.158521 T|T 0.61324|0.61324 0.2338|0.2338 N|N 0.02286|0.02286 -0.61|-0.61 0.28050|0.28050 N|N 0.933393|0.933393 .|B .|0.06786 .|0.001 .|B .|0.04013 .|0.001 T|T 0.55885|0.55885 -0.8070|-0.8070 5|10 .|0.02654 .|T .|1 .|. 7.5601|7.5601 0.27847|0.27847 0.0:0.37:0.0:0.63|0.0:0.37:0.0:0.63 .|. .|831 .|Q9Y666 .|S12A7_HUMAN H|I 188|831 .|ENSP00000264930:V831I .|ENSP00000264930:V831I R|V -|- 2|1 0|0 SLC12A7|SLC12A7 1117314|1117314 0.943000|0.943000 0.32029|0.32029 0.959000|0.959000 0.39883|0.39883 0.022000|0.022000 0.10575|0.10575 0.148000|0.148000 0.16224|0.16224 0.072000|0.072000 0.16694|0.16694 -0.657000|-0.657000 0.03884|0.03884 CGT|GTC TCGA-IB-AAUN-01A-12D-A38G-08 SLC12A7-001 KNOWN non_canonical_TEC|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366446.2 1 0 0 43 113 0 102 1 1 47 49 0 102 2 0 0 0 0 0 2 1 1.000000 41 109 0 99 2 0 0 0 0 102 2 -20.000000 1 1 120850 4 35 1 1 2 3 2.129760 0 0.560000 1.800000 0.561229 0.980000 7.400000e-01 1.000000 1.000000 0.945383 0.980000 1 0.860000 1.000000 PCDHA1 56147 broad.mit.edu 37 5 140167552 140167552 + Silent SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr5:140167552C>T ENST00000504120.2 + 1 1677 c.1677C>T c.(1675-1677)aaC>aaT p.N559N PCDHA1_ENST00000378133.3_Silent_p.N559N|PCDHA1_ENST00000394633.3_Intron NM_018900.2 NP_061723.1 Q9Y5I3 PCDA1_HUMAN protocadherin alpha 1 70 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGGACGAGAACGACAACGCGC 0.672000 0 SO:0001819 synonymous_variant ENST00000504120.2 1 1 hg19 CCDS54913.1 TCGA-IB-AAUN-01A-12D-A38G-08 PCDHA1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000389127.1 1 0 1 147 405 0 285 0 0 0 0 285 2 0 0 0 0 0 2 1 1.000000 143 394 1 294 9 0 0 0 0 285 2 -20.000000 1 1 0 0 1 1 2 3 2.131117 0 0.560000 1.800000 0.561229 0.940000 8.200000e-01 1.000000 1.000000 0.944873 0.940000 1 0.880000 1.000000 FGF18 8817 broad.mit.edu 37 5 170876235 170876235 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr5:170876235G>A ENST00000274625.5 + 4 879 c.335G>A c.(334-336)cGc>cAc p.R112H NM_003862.2 NP_003853.1 O76093 FGF18_HUMAN fibroblast growth factor 18 9 Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) TGCATGAACCGCAAAGGCAAG 0.567000 0 SO:0001583 missense ENST00000274625.5 0 1 hg19 CCDS4378.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 g 21.3 4.124259 0.77436 . . ENSG00000156427 ENST00000274625 D 0.89343 -2.5 4.08 3.19 0.36642 . 0.556585 0.16736 U 0.201631 D 0.90769 0.7102 M 0.77820 2.39 0.25546 N 0.987134 D 0.55605 0.972 P 0.53809 0.735 T 0.83312 -0.0022 10 0.72032 D 0.01 -2.8976 6.6409 0.22909 0.0934:0.0:0.7276:0.1789 . 112 O76093 FGF18_HUMAN H 112 ENSP00000274625:R112H ENSP00000274625:R112H R + 2 0 FGF18 170808840 1.000000 0.71417 0.997000 0.53966 0.975000 0.68041 4.443000 0.59994 0.688000 0.31529 0.450000 0.29827 CGC TCGA-IB-AAUN-01A-12D-A38G-08 FGF18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252857.2 0 0 0 5 291 0 156 0 8.999583e-03 0 7 0 156 2 0 0 0 0 0 2 1 0.933476 5 284 0 154 2 0 0 0 0 156 2 -2.293342 0 1 121412 3 36 1 1 2 3 2.131117 0 0.560000 1.800000 0.561229 0.060000 1.000000e-02 0.140000 0.060000 0.071914 0.060000 0 0.030000 0.100000 ITGA2 3673 broad.mit.edu 37 5 52360796 52360796 + Nonsense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr5:52360796C>T ENST00000296585.5 + 14 1800 c.1657C>T c.(1657-1659)Cga>Tga p.R553* NM_002203.3 NP_002194.2 P17301 ITA2_HUMAN integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 47 Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181) TGAAAACACTCGATTTGGTTC 0.423000 0 SO:0001587 stop_gained ENST00000296585.5 0 1 hg19 CCDS3957.1 . . . . . . . . . . C 38 6.920610 0.97936 . . ENSG00000164171 ENST00000296585 . . . 5.67 2.83 0.33086 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 15.0088 0.71533 0.3736:0.6264:0.0:0.0 . . . . X 553 . ENSP00000296585:R553X R + 1 2 ITGA2 52396553 0.972000 0.33761 0.988000 0.46212 0.995000 0.86356 2.181000 0.42547 0.371000 0.24564 0.655000 0.94253 CGA TCGA-IB-AAUN-01A-12D-A38G-08 ITGA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253857.2 1 0 1 135 402 0 282 0 9.991600e-01 1 33 0 282 2 0 0 0 0 0 2 1 1.000000 135 394 0 275 2 0 0 0 0 282 2 -20.000000 1 1 0 0 1 1 2 3 2.129760 0 0.560000 1.800000 0.561229 0.890000 7.600000e-01 1.000000 1.000000 0.899938 0.890000 1 0.830000 0.970000 MAPK13 5603 broad.mit.edu 37 6 36106684 36106684 + Missense_Mutation SNP G G C TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr6:36106684G>C ENST00000211287.4 + 11 1132 c.870G>C c.(868-870)gaG>gaC p.E290D MAPK13_ENST00000373766.5_Missense_Mutation_p.A240P|MAPK13_ENST00000373759.1_3'UTR|MAPK13_ENST00000373761.6_Missense_Mutation_p.E280D|Z95152.1_ENST00000408816.1_RNA NM_002754.4 NP_002745.1 O15264 MK13_HUMAN mitogen-activated protein kinase 13 12 AGATGCTGGAGCTAGACGTGG 0.667000 0 SO:0001583 missense ENST00000211287.4 1 1 hg19 CCDS4818.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 13.12|13.12 2.143296|2.143296 0.37825|0.37825 .|. .|. ENSG00000156711|ENSG00000156711 ENST00000373766|ENST00000373761;ENST00000211287;ENST00000373770 T|T;T 0.66995|0.65364 -0.24|-0.15;-0.15 5.25|5.25 3.47|3.47 0.39725|0.39725 .|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); .|0.105229 .|0.41605 .|D .|0.000844 T|T 0.29684|0.29684 0.0741|0.0741 L|L 0.33245|0.33245 0.995|0.995 0.23632|0.23632 N|N 0.997245|0.997245 .|B .|0.09022 .|0.002 .|B .|0.09377 .|0.004 T|T 0.21827|0.21827 -1.0234|-1.0234 7|10 0.72032|0.42905 D|T 0.01|0.14 -45.63|-45.63 11.297|11.297 0.49284|0.49284 0.1481:0.0:0.8519:0.0|0.1481:0.0:0.8519:0.0 .|. .|290 .|O15264 .|MK13_HUMAN P|D 240|280;290;235 ENSP00000362871:A240P|ENSP00000362866:E280D;ENSP00000211287:E290D ENSP00000362871:A240P|ENSP00000211287:E290D A|E +|+ 1|3 0|2 MAPK13|MAPK13 36214662|36214662 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.831000|0.831000 0.47069|0.47069 1.350000|1.350000 0.34010|0.34010 0.605000|0.605000 0.29947|0.29947 0.484000|0.484000 0.47621|0.47621 GCT|GAG TCGA-IB-AAUN-01A-12D-A38G-08 MAPK13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040328.1 1 0 1 45 112 0 84 1 1 26 107 0 84 2 0 0 0 0 0 2 1 1.000000 45 110 0 83 2 0 0 0 0 84 2 -20.000000 1 1 0 0 1 0 1 1 2.114030 0 0.560000 1.800000 0.558765 0.990000 7.700000e-01 1.000000 1.000000 0.961069 0.990000 1 0.890000 1.000000 HOXA3 3200 broad.mit.edu 37 7 27148046 27148046 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr7:27148046C>T ENST00000396352.4 - 3 1019 c.820G>A c.(820-822)Ggt>Agt p.G274S HOXA3_ENST00000317201.2_Missense_Mutation_p.G274S|HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank NM_030661.4 NP_109377.1 O43365 HXA3_HUMAN homeobox A3 29 AGATAGCCACCGGCTCCGGGG 0.627000 Esophageal Squamous(136;1368 1743 5685 7935 50360) 0 SO:0001583 missense ENST00000396352.4 1 1 hg19 CCDS5404.1 . . . . . . . . . . C 13.78 2.340433 0.41498 . . ENSG00000105997 ENST00000396352;ENST00000317201;ENST00000396350 D;D 0.86297 -2.1;-2.1 5.41 5.41 0.78517 . 0.047410 0.85682 D 0.000000 D 0.91955 0.7452 L 0.54323 1.7 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.90337 0.4356 10 0.33940 T 0.23 . 19.215 0.93772 0.0:1.0:0.0:0.0 . 274 O43365 HXA3_HUMAN S 274;274;116 ENSP00000379640:G274S;ENSP00000324884:G274S ENSP00000324884:G274S G - 1 0 HOXA3 27114571 1.000000 0.71417 0.432000 0.26747 0.546000 0.35178 6.089000 0.71384 2.539000 0.85634 0.655000 0.94253 GGT TCGA-IB-AAUN-01A-12D-A38G-08 HOXA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358708.2 0 0 0 84 283 1 193 0 8.326117e-01 1 12 1 193 2 0 0 0 0 0 2 1 1.000000 82 270 1 190 9 0 0 0 1 193 2 -4.020497 1 1 0 0 1 0 0 0 2.116104 0 0.560000 1.800000 0.560000 0.810000 6.600000e-01 0.970000 0.820000 0.820510 0.810000 0 0.730000 0.900000 KCNQ3 3786 broad.mit.edu 37 8 133141815 133141815 + Silent SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr8:133141815C>T ENST00000388996.4 - 15 2733 c.2313G>A c.(2311-2313)tcG>tcA p.S771S KCNQ3_ENST00000521134.1_Silent_p.S651S|KCNQ3_ENST00000519445.1_Silent_p.S759S NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) AGATTCGGTCCGAGTAGGGGC 0.607000 0 SO:0001819 synonymous_variant ENST00000388996.4 0 1 hg19 CCDS34943.1 TCGA-IB-AAUN-01A-12D-A38G-08 KCNQ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268621.2 0 0 0 5 185 0 92 0 3.306781e-03 0 3 0 92 2 0 0 0 0 0 2 1 0.934835 5 181 0 92 2 0 0 0 0 92 2 -6.791372 1 1 121412 3 32 1 1 2 3 2.641472 1 0.560000 1.800000 0.650127 0.130000 4.000000e-02 1.000000 0.120000 0.195299 0.130000 0 0.080000 0.220000 SCARA5 286133 broad.mit.edu 37 8 27737142 27737142 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr8:27737142C>T ENST00000354914.3 - 8 1780 c.1295G>A c.(1294-1296)cGc>cAc p.R432H SCARA5_ENST00000380385.2_Missense_Mutation_p.R207H NM_173833.5 NP_776194.2 Q6ZMJ2 SCAR5_HUMAN scavenger receptor class A, member 5 18 Ovarian(32;0.0218) GCCGAGCATGCGGCACACCAC 0.642000 0 SO:0001583 missense ENST00000354914.3 0 1 hg19 CCDS6064.1 . . . . . . . . . . C 17.81 3.480662 0.63849 . . ENSG00000168079 ENST00000354914;ENST00000380385 T;T 0.42900 0.96;0.96 4.87 3.99 0.46301 Speract/scavenger receptor (4);Speract/scavenger receptor-related (2); 0.063343 0.64402 N 0.000010 T 0.48804 0.1520 M 0.88241 2.94 0.80722 D 1 B;B 0.25206 0.012;0.12 B;B 0.19946 0.008;0.027 T 0.54417 -0.8297 10 0.66056 D 0.02 . 11.0431 0.47842 0.0:0.907:0.0:0.093 . 207;432 Q6ZMJ2-4;Q6ZMJ2 .;SCAR5_HUMAN H 432;207 ENSP00000346990:R432H;ENSP00000369746:R207H ENSP00000346990:R432H R - 2 0 SCARA5 27793061 1.000000 0.71417 1.000000 0.80357 0.611000 0.37282 4.882000 0.63121 1.170000 0.42753 0.591000 0.81541 CGC TCGA-IB-AAUN-01A-12D-A38G-08 SCARA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255223.2 0 0 0 5 277 0 171 0 0 0 1 0 171 2 0 0 0 0 0 2 1 0.936322 4 273 0 169 2 0 0 0 0 171 2 -2.163064 0 1 0 0 1 0 1 1 1.575933 1 0.560000 1.800000 0.391256 0.040000 1.000000e-02 0.100000 0.050000 0.054242 0.040000 0 0.020000 0.070000 UNC5D 137970 broad.mit.edu 37 8 35608224 35608224 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr8:35608224C>T ENST00000404895.2 + 13 2388 c.2060C>T c.(2059-2061)gCc>gTc p.A687V UNC5D_ENST00000287272.2_Missense_Mutation_p.A618V|UNC5D_ENST00000449677.1_Missense_Mutation_p.A263V|UNC5D_ENST00000453357.2_Missense_Mutation_p.A682V|UNC5D_ENST00000416672.1_Missense_Mutation_p.A692V|UNC5D_ENST00000420357.1_Missense_Mutation_p.A620V NM_080872.2 NP_543148.2 Q6UXZ4 UNC5D_HUMAN unc-5 homolog D (C. elegans) p.A682V(1) 112 ACAGACTGTGCCGTGAAGCAA 0.502000 1 Substitution - Missense(1) SO:0001583 missense ENST00000404895.2 0 1 hg19 CCDS6093.2 . . . . . . . . . . C 35 5.426783 0.96131 . . ENSG00000156687 ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677 T;T;T;T;T;T 0.60299 0.23;0.64;0.63;0.23;0.2;2.1 5.9 5.9 0.94986 . 0.000000 0.85682 D 0.000000 T 0.72542 0.3473 M 0.83483 2.645 0.80722 D 1 D;P;P 0.56035 0.974;0.911;0.914 P;P;B 0.50490 0.638;0.642;0.439 T 0.76817 -0.2819 10 0.87932 D 0 -23.3889 20.2822 0.98520 0.0:1.0:0.0:0.0 . 263;682;687 E9PDS8;Q6UXZ4-2;Q6UXZ4 .;.;UNC5D_HUMAN V 687;620;618;692;682;263 ENSP00000385143:A687V;ENSP00000392739:A620V;ENSP00000287272:A618V;ENSP00000412652:A692V;ENSP00000394303:A682V;ENSP00000397211:A263V ENSP00000287272:A618V A + 2 0 UNC5D 35727766 1.000000 0.71417 0.987000 0.45799 0.959000 0.62525 5.359000 0.66074 2.806000 0.96561 0.655000 0.94253 GCC TCGA-IB-AAUN-01A-12D-A38G-08 UNC5D-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000347586.2 0 0 0 5 399 0 297 0 0 0 0 297 2 0 0 0 0 0 2 1 0.932385 5 386 0 296 2 0 0 0 0 297 2 -1.885794 0 1 0 0 1 0 1 1 1.575933 1 0.560000 1.800000 0.391256 0.030000 0 0.070000 0.030000 0.038005 0.030000 0 0.010000 0.050000 ODF2 4957 broad.mit.edu 37 9 131245096 131245096 + Splice_Site SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr9:131245096G>A ENST00000434106.3 + 10 1280 c.917G>A c.(916-918)cGc>cAc p.R306H ODF2_ENST00000351030.3_Splice_Site_p.R301H|ODF2_ENST00000546203.1_Splice_Site_p.R287H|ODF2_ENST00000444119.2_Splice_Site_p.R282H|ODF2_ENST00000393527.3_Splice_Site_p.R282H|ODF2_ENST00000604420.1_Splice_Site_p.R306H|ODF2_ENST00000448249.3_Splice_Site_p.R225H|ODF2_ENST00000535026.1_3'UTR|ODF2_ENST00000372791.3_Splice_Site_p.R287H|ODF2_ENST00000372807.5_Splice_Site_p.R301H|ODF2_ENST00000393533.2_Splice_Site_p.R306H|ODF2_ENST00000372814.3_Splice_Site_p.R350H NM_153433.1 NP_702911.1 Q5BJF6 ODFP2_HUMAN outer dense fiber of sperm tails 2 37 CTCTCCCAGCGCCTGCTGTTA 0.522000 0 SO:0001630 splice_region_variant ENST00000434106.3 0 1 hg19 CCDS56588.1 . . . . . . . . . . G 12.16 1.854984 0.32791 . . ENSG00000136811 ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791 T;T;T;T;T;T;T;T 0.44083 0.93;0.93;0.93;0.93;1.87;0.93;0.93;0.93 5.66 2.68 0.31781 . 0.552387 0.21440 N 0.074507 T 0.20333 0.0489 N 0.17474 0.49 0.80722 D 1 B;B;B;B;B;B;B;B;B;B 0.27316 0.025;0.006;0.115;0.003;0.175;0.066;0.01;0.025;0.024;0.017 B;B;B;B;B;B;B;B;B;B 0.12837 0.002;0.003;0.006;0.002;0.004;0.008;0.004;0.002;0.004;0.003 T 0.05920 -1.0856 10 0.34782 T 0.22 -7.0512 3.5239 0.07752 0.3275:0.0:0.5038:0.1688 . 287;301;225;240;306;350;301;287;306;282 Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;Q5BJF6-2;B4DX73;Q5BJF6-7;B1AND4;Q5BJF6-5;Q5BJF6;Q5BJF6-3 .;.;.;.;.;.;.;.;ODFP2_HUMAN;. H 306;350;301;306;282;225;287;287 ENSP00000377166:R306H;ENSP00000361901:R350H;ENSP00000342581:R301H;ENSP00000361882:R306H;ENSP00000307781:R282H;ENSP00000396687:R225H;ENSP00000437579:R287H;ENSP00000361877:R287H ENSP00000307781:R282H R + 2 0 ODF2 130284917 1.000000 0.71417 1.000000 0.80357 0.829000 0.46940 2.513000 0.45494 0.750000 0.32877 0.561000 0.74099 CGC TCGA-IB-AAUN-01A-12D-A38G-08 ODF2-011 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000054449.3 0 0 0 4 172 0 95 0 1.987764e-01 0 29 0 95 2 0 0 0 0 0 2 1 0.887246 4 169 0 94 2 0 0 0 0 95 2 -5.792634 1 0 121412 7 37 1 1 2 3 2.132803 0 0.560000 1.800000 0.561229 0.080000 2.000000e-02 0.200000 0.080000 0.100145 0.080000 0 0.050000 0.140000 KDM4C 23081 broad.mit.edu 37 9 6990510 6990510 + Missense_Mutation SNP C C T rs151291155 byFrequency TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr9:6990510C>T ENST00000381309.3 + 12 2337 c.1772C>T c.(1771-1773)gCg>gTg p.A591V KDM4C_ENST00000536108.1_Missense_Mutation_p.A410V|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.A591V|KDM4C_ENST00000535193.1_Missense_Mutation_p.A613V|KDM4C_ENST00000543771.1_Missense_Mutation_p.A591V|KDM4C_ENST00000428870.2_Missense_Mutation_p.A278V NM_015061.3 NP_055876.2 Q9H3R0 KDM4C_HUMAN lysine (K)-specific demethylase 4C 43 AAGCAGCAGGCGCCAAGTGAT 0.408000 0 SO:0001583 missense ENST00000381309.3 1 1 hg19 CCDS6471.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 13.18 2.159146 0.38119 2.27E-4 2.33E-4 ENSG00000107077 ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000536108;ENST00000428870 T;T;T;T;T;T 0.52526 0.66;0.66;0.66;0.66;0.66;0.66 4.8 2.93 0.34026 . 0.294931 0.36703 N 0.002452 T 0.31040 0.0784 L 0.35414 1.06 0.44366 D 0.997269 B;B;B;B 0.29627 0.043;0.252;0.026;0.077 B;B;B;B 0.21151 0.012;0.033;0.013;0.024 T 0.06127 -1.0844 10 0.30078 T 0.28 -39.5448 8.6521 0.34040 0.0:0.8202:0.0:0.1798 . 591;613;591;591 F5H347;F5H7P0;Q9H3R0;Q9H3R0-2 .;.;KDM4C_HUMAN;. V 613;591;591;591;410;278 ENSP00000442382:A613V;ENSP00000445427:A591V;ENSP00000370710:A591V;ENSP00000370707:A591V;ENSP00000440656:A410V;ENSP00000405739:A278V ENSP00000370707:A591V A + 2 0 KDM4C 6980510 0.990000 0.36364 0.839000 0.33178 0.756000 0.42949 2.883000 0.48554 0.600000 0.29862 0.557000 0.71058 GCG TCGA-IB-AAUN-01A-12D-A38G-08 KDM4C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051692.1 1 0 1 44 73 0 68 1 9.961661e-01 2 16 0 68 2 0 0 0 0 0 2 1 1.000000 43 71 0 66 2 0 0 0 0 68 2 -3.318795 1 1 121398 23 45 1 0 0 0 2.121522 0 0.560000 1.800000 0.560000 0.990000 9.900000e-01 1.000000 1.000000 0.999402 0.990000 1 0.990000 1.000000 HABP4 22927 broad.mit.edu 37 9 99227683 99227683 + Missense_Mutation SNP C C T TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chr9:99227683C>T ENST00000375249.4 + 3 652 c.577C>T c.(577-579)Cgc>Tgc p.R193C HABP4_ENST00000375251.3_Intron NM_014282.2 NP_055097.2 hyaluronan binding protein 4 13 Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214) AGGGGGTATGCGCGGCAGAGG 0.483000 0 SO:0001583 missense ENST00000375249.4 0 1 hg19 CCDS6719.1 . . . . . . . . . . C 15.45 2.837388 0.50951 . . ENSG00000130956 ENST00000375249 T 0.37752 1.18 4.86 2.77 0.32553 . 0.269438 0.30538 N 0.009418 T 0.42381 0.1200 L 0.43923 1.385 0.49213 D 0.999769 D 0.71674 0.998 P 0.53185 0.72 T 0.40515 -0.9559 10 0.72032 D 0.01 -7.7391 14.0166 0.64527 0.4686:0.5314:0.0:0.0 . 193 Q5JVS0 HABP4_HUMAN C 193 ENSP00000364398:R193C ENSP00000364398:R193C R + 1 0 HABP4 98267504 1.000000 0.71417 0.350000 0.25708 0.389000 0.30415 1.202000 0.32271 0.558000 0.29135 0.644000 0.83932 CGC TCGA-IB-AAUN-01A-12D-A38G-08 HABP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053269.1 0 0 0 6 443 1 193 0 3.750624e-02 1 43 1 193 3 0 0 0 0 0 2 0 0.215731 6 436 1 192 10 0 0 0 1 193 2 -1.649228 0 1 121412 3 38 1 1 2 3 2.124566 0 0.560000 1.800000 0.561229 0.040000 1.000000e-02 0.110000 0.050000 0.055506 0.040000 0 0.020000 0.080000 ATRX 546 broad.mit.edu 37 X 76938955 76938955 + Missense_Mutation SNP G G A TCGA-IB-AAUN-01A-12D-A38G-08 TCGA-IB-AAUN-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1c613c8d-8ef7-44da-8a5f-ed1ec5652f85 15447e58-6c71-422c-ae2a-31be9bc175d5 g.chrX:76938955G>A ENST00000373344.5 - 9 2007 c.1793C>T c.(1792-1794)tCc>tTc p.S598F ATRX_ENST00000395603.3_Missense_Mutation_p.S560F|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.3 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked p.?(1) 145 TTTAATTGGGGAATTAGAAAG 0.358000 Mis, F, N Pancreatic neuroendocrine tumors, paediatric GBM ATR-X (alpha thalassemia/mental retardation) syndrome Rec yes X Xq21.1 546 alpha thalassemia/mental retardation syndrome X-linked yes E 1 Unknown(1) SO:0001583 missense ENST00000373344.5 1 1 hg19 CCDS14434.1 . . . . . . . . . . g 12.65 2.001168 0.35320 . . ENSG00000085224 ENST00000373344;ENST00000395603 D;D 0.93019 -3.13;-3.15 5.22 5.22 0.72569 . 0.000000 0.52532 D 0.000066 D 0.95774 0.8625 L 0.53249 1.67 0.80722 D 1 D;D 0.71674 0.996;0.998 D;D 0.78314 0.939;0.991 D 0.96302 0.9222 10 0.72032 D 0.01 -2.9111 17.9679 0.89105 0.0:0.0:1.0:0.0 . 560;598 P46100-4;P46100 .;ATRX_HUMAN F 598;560 ENSP00000362441:S598F;ENSP00000378967:S560F ENSP00000362441:S598F S - 2 0 ATRX 76825611 1.000000 0.71417 0.987000 0.45799 0.962000 0.63368 4.326000 0.59241 2.177000 0.69029 0.509000 0.49947 TCC TCGA-IB-AAUN-01A-12D-A38G-08 ATRX-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058860.2 1 0 1 495 1387 1 896 0 9.813111e-01 0 20 1 896 2 0 0 0 0 0 2 1 1.000000 488 1363 2 888 13 0 0 0 1 896 2 -20.000000 1 1 0 0 1 0 1 1 0.560000 1.800000 0.560000 0.930000 8.600000e-01 1.000000 0.940000 0.938995 0.930000 1 0.890000 0.980000