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 GANAB 23193 broad.mit.edu 37 11 62398507 62398512 + In_Frame_Del DEL AGACTA AGACTA - TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 AGACTA - AGACTA AGACTA Valid Somatic Phase_I WXS RNA Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr11:62398507_62398512delAGACTA ENST00000356638.3 - 10 1156_1161 c.1140_1145delTAGTCT c.(1138-1146)gctagtctc>gcc p.SL381del GANAB_ENST00000534779.1_In_Frame_Del_p.SL289del|GANAB_ENST00000534422.1_5'Flank|GANAB_ENST00000346178.4_In_Frame_Del_p.SL403del|GANAB_ENST00000540933.1_In_Frame_Del_p.SL284del NM_198334.1 NP_938148.1 Q14697 GANAB_HUMAN glucosidase, alpha; neutral AB 35 Miglitol(DB00491) TGTACCTGTGAGACTAGCATATTGCC 0.495000 Melanoma(23;1005 1074 15747 18937) 0 SO:0001651 inframe_deletion ENST00000356638.3 1 1 hg19 CCDS8026.1 TCGA-2J-AAB4-01A-12D-A40W-08 GANAB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000395689.1 1 0 0 74 668 0 174 1 1 5 321 0 174 2 0 0 0 0 1 1.000000 93 679 0 170 2 -19.981250 1 1 0 0 1 1 2 3 2.015408 0 0.300000 1.950000 0.301048 0.660000 5.200000e-01 0.820000 0.660000 0.670947 0.660000 0 5.900000e-01 7.400000e-01 SMAD4 4089 broad.mit.edu 37 18 48584504 48584504 + Frame_Shift_Del DEL C C - TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 C - C C Valid Somatic Phase_I WXS targeted Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr18:48584504delC ENST00000342988.3 + 6 1215 c.677delC c.(676-678)gccfs p.A226fs SMAD4_ENST00000452201.2_3'UTR|SMAD4_ENST00000588745.1_Intron|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.A226fs NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) GGTCAGCCTGCCAGTATACTG 0.438000 38 Whole gene deletion(36)|Unknown(2) SO:0001589 frameshift_variant ENST00000342988.3 1 1 hg19 CCDS11950.1 TCGA-2J-AAB4-01A-12D-A40W-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 0 30 198 0 52 0 9.583934e-01 0 37 0 52 2 1 1 37 232 0 358 2 1 1.000000 32 189 0 51 2 -14.496740 1 1 0 0 1 0 1 1 1.716786 1 0.300000 1.950000 0.176471 0.730000 5.100000e-01 0.950000 0.730000 0.739496 0.730000 0 6.100000e-01 8.600000e-01 TMF1 7110 broad.mit.edu 37 3 69082709 69082710 + Frame_Shift_Del DEL AG AG - TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr3:69082709_69082710delAG ENST00000398559.2 - 10 2606_2607 c.2390_2391delCT c.(2389-2391)tctfs p.S797fs TMF1_ENST00000543976.1_Frame_Shift_Del_p.S800fs|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000597366.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA P82094 TMF1_HUMAN TATA element modulatory factor 1 22 Lung NSC(201;0.0193)|Prostate(884;0.174) CAAGCCTATCAGAAAGATTCTT 0.366000 0 SO:0001589 frameshift_variant ENST00000398559.2 1 1 hg19 CCDS43105.1 TCGA-2J-AAB4-01A-12D-A40W-08 TMF1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352106.1 1 0 0 34 365 0 111 0 9.524761e-01 0 56 0 111 2 0 0 0 0 1 1.000000 38 365 0 110 2 -2.716734 1 1 0 0 1 0 1 1 2.008791 0 0.300000 1.950000 0.297894 0.560000 4.000000e-01 0.760000 0.570000 0.576713 0.560000 0 4.700000e-01 6.700000e-01 SEC61B 10952 broad.mit.edu 37 9 101992661 101992668 + Frame_Shift_Del DEL TTCTGTAT TTCTGTAT - rs1804433 TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 TTCTGTAT - TTCTGTAT TTCTGTAT Valid Somatic Phase_I WXS RNA Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr9:101992661_101992668delTTCTGTAT ENST00000223641.4 + 4 309_316 c.246_253delTTCTGTAT c.(244-255)gcttctgtatttfs p.SVF83fs SEC61B_ENST00000498603.1_Frame_Shift_Del_p.SVF29fs NM_006808.2 NP_006799.1 P60468 SC61B_HUMAN Sec61 beta subunit 2 Acute lymphoblastic leukemia(62;0.0559) TGTTCATCGCTTCTGTATTTATGTTGCA 0.380000 0 SO:0001589 frameshift_variant ENST00000223641.4 1 1 hg19 CCDS6741.1 TCGA-2J-AAB4-01A-12D-A40W-08 SEC61B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053391.1 1 0 0 42 786 0 186 1 1 7 699 0 186 2 0 0 0 0 1 0.918239 81 813 4 190 34 -6.000279 1 1 0 0 1 0 0 0 2.001353 0 0.300000 1.950000 0.295775 0.330000 2.400000e-01 0.440000 0.330000 0.342323 0.330000 0 2.800000e-01 3.900000e-01 RASGEF1A 221002 broad.mit.edu 37 10 43697262 43697262 + Silent SNP A A G TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr10:43697262A>G ENST00000395809.1 - 4 2959 c.453T>C c.(451-453)tgT>tgC p.C151C RASGEF1A_ENST00000374459.1_Silent_p.C159C|RASGEF1A_ENST00000395810.1_Silent_p.C151C|RASGEF1A_ENST00000472864.1_5'UTR Q8N9B8 RGF1A_HUMAN RasGEF domain family, member 1A 11 TCACCTCATCACACTGGGTGA 0.617000 0 SO:0001819 synonymous_variant ENST00000395809.1 0 1 hg19 CCDS7202.2 . . . . . . . . . . A 2.707 -0.269595 0.05716 . . ENSG00000198915 ENST00000374455 . . . 5.5 -2.64 0.06114 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 13.2198 0.59881 0.6996:0.0:0.3004:0.0 . . . . R 53 . . X - 1 0 RASGEF1A 43017268 0.139000 0.22563 0.434000 0.26772 0.171000 0.22731 -0.404000 0.07205 -0.801000 0.04427 -1.215000 0.01618 TGA TCGA-2J-AAB4-01A-12D-A40W-08 RASGEF1A-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000313989.1 1 0 1 12 89 0 21 1 5.296683e-01 3 11 0 21 2 0 0 0 0 0 2 1 0.999223 11 88 0 21 2 -19.471930 1 1 0 0 1 0 1 1 2.007126 0 0.300000 1.950000 0.297894 0.790000 4.400000e-01 1.000000 1.000000 0.793284 0.790000 0 6.000000e-01 1 CXCL12 6387 broad.mit.edu 37 10 44876321 44876321 + Silent SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr10:44876321G>A ENST00000374429.2 - 2 155 c.69C>T c.(67-69)ccC>ccT p.P23P CXCL12_ENST00000496375.1_5'UTR|CXCL12_ENST00000395795.4_Silent_p.P23P|CXCL12_ENST00000343575.6_Silent_p.P23P|AL137026.1_ENST00000593376.1_Intron|CXCL12_ENST00000374426.2_Silent_p.P23P|CXCL12_ENST00000395794.2_Silent_p.P23P|CXCL12_ENST00000395793.3_Silent_p.P23P NM_000609.5|NM_001277990.1 NP_000600.1|NP_001264919.1 P48061 SDF1_HUMAN chemokine (C-X-C motif) ligand 12 p.P23P(3) 6 Tinzaparin(DB06822) TCAGGCTGACGGGCTTCCCTA 0.507000 3 Substitution - coding silent(3) SO:0001819 synonymous_variant ENST00000374429.2 1 1 hg19 CCDS44373.1 TCGA-2J-AAB4-01A-12D-A40W-08 CXCL12-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047738.2 1 0 1 92 568 0 163 0 7.376464e-01 0 18 0 163 2 0 0 0 0 0 2 1 1.000000 91 558 0 160 2 -2.744775 1 1 121412 7 42 1 0 1 1 2.007126 0 0.300000 1.950000 0.297894 0.920000 7.500000e-01 1.000000 1.000000 0.918657 0.920000 1 8.300000e-01 1 MARCH5 54708 broad.mit.edu 37 10 94109589 94109589 + Missense_Mutation SNP A A G TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr10:94109589A>G ENST00000358935.2 + 5 1047 c.715A>G c.(715-717)Atc>Gtc p.I239V NM_017824.4 NP_060294.1 Q9NX47 MARH5_HUMAN membrane-associated ring finger (C3HC4) 5 9 ACAAAGGACAATCTTGGTAAG 0.348000 0 SO:0001583 missense ENST00000358935.2 1 1 hg19 CCDS7420.1 . . . . . . . . . . A 16.49 3.139263 0.56936 . . ENSG00000198060 ENST00000358935 T 0.46819 0.86 5.91 5.91 0.95273 . 0.000000 0.85682 D 0.000000 T 0.36853 0.0982 N 0.25380 0.74 0.80722 D 1 B 0.21606 0.058 B 0.15484 0.013 T 0.10917 -1.0609 10 0.27785 T 0.31 -6.4219 16.3512 0.83208 1.0:0.0:0.0:0.0 . 239 Q9NX47 MARH5_HUMAN V 239 ENSP00000351813:I239V ENSP00000351813:I239V I + 1 0 MARCH5 94099569 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.102000 0.94226 2.266000 0.75297 0.533000 0.62120 ATC TCGA-2J-AAB4-01A-12D-A40W-08 MARCH5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049388.1 0 0 1 48 322 0 136 1 9.999970e-01 35 93 0 136 2 0 0 0 0 0 2 1 1.000000 48 319 0 136 2 -20.000000 1 1 121412 2 35 1 1 2 3 2.031374 0 0.300000 1.950000 0.304175 0.870000 6.500000e-01 1.000000 1.000000 0.871807 0.870000 1 7.500000e-01 1 ADAMTS15 170689 broad.mit.edu 37 11 130343247 130343247 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr11:130343247G>A ENST00000299164.2 + 8 2384 c.2384G>A c.(2383-2385)cGc>cAc p.R795H NM_139055.2 NP_620686.1 Q8TE58 ATS15_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 15 36 all_hematologic(175;0.0429) Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837) CCCCGGGTCCGCTACTCCTTC 0.657000 0 SO:0001583 missense ENST00000299164.2 1 1 hg19 CCDS8488.1 . . . . . . . . . . G 28.9 4.964311 0.92791 . . ENSG00000166106 ENST00000299164 T 0.52526 0.66 5.91 4.99 0.66335 ADAM-TS Spacer 1 (1); . . . . T 0.58177 0.2104 L 0.38692 1.165 0.80722 D 1 D 0.89917 1.0 D 0.70016 0.967 T 0.55366 -0.8152 9 0.30854 T 0.27 . 16.5512 0.84473 0.0:0.0:0.8684:0.1316 . 795 Q8TE58 ATS15_HUMAN H 795 ENSP00000299164:R795H ENSP00000299164:R795H R + 2 0 ADAMTS15 129848457 1.000000 0.71417 0.997000 0.53966 0.995000 0.86356 6.428000 0.73383 1.498000 0.48600 0.655000 0.94253 CGC TCGA-2J-AAB4-01A-12D-A40W-08 ADAMTS15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385638.1 0 0 1 218 693 1 146 1 5.773642e-02 2 0 1 146 2 0 0 0 0 0 2 1 1.000000 215 673 1 144 21 -20.000000 1 1 121380 2 36 1 1 2 3 2.315870 1 0.300000 1.950000 0.384886 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2J-AAB4-01A-12D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 18 165 0 67 1 5.240795e-01 9 8 0 67 2 1 9.999992e-01 28 215 0 343 2 1 0.999986 18 164 0 67 2 -8.782162 1 1 0 0 1 0 2 2 1.894994 1 0.300000 1.950000 0.300000 0.720000 4.200000e-01 1.000000 0.650000 0.752612 0.720000 0 5.500000e-01 1 LMBR1L 55716 broad.mit.edu 37 12 49491751 49491751 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr12:49491751G>A ENST00000267102.8 - 16 1720 c.1378C>T c.(1378-1380)Cgg>Tgg p.R460W LMBR1L_ENST00000395141.4_Missense_Mutation_p.R455W|LMBR1L_ENST00000547382.1_Missense_Mutation_p.R440W NM_018113.2 NP_060583.2 Q6UX01 LMBRL_HUMAN limb development membrane protein 1-like 15 AGCTCTGCCCGCACAGCTGCA 0.562000 OREG0021783 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000267102.8 0 1 hg19 CCDS8780.2 . . . . . . . . . . G 22.0 4.231485 0.79688 2.27E-4 0.0 ENSG00000139636 ENST00000267102;ENST00000547382;ENST00000395141 T;T;T 0.58506 0.41;0.33;0.37 5.84 2.54 0.30619 . 0.054147 0.64402 D 0.000001 T 0.66287 0.2774 L 0.43923 1.385 0.41689 D 0.989332 D;D;D 0.89917 0.996;0.993;1.0 P;P;D 0.67231 0.649;0.548;0.95 T 0.69439 -0.5145 10 0.87932 D 0 . 13.789 0.63128 0.0:0.0:0.5232:0.4768 . 440;460;455 Q6UX01-3;Q6UX01;Q6UX01-4 .;LMBRL_HUMAN;. W 460;440;455 ENSP00000267102:R460W;ENSP00000447329:R440W;ENSP00000378573:R455W ENSP00000267102:R460W R - 1 2 LMBR1L 47778018 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 6.523000 0.73787 0.620000 0.30215 0.563000 0.77884 CGG TCGA-2J-AAB4-01A-12D-A40W-08 LMBR1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318696.1 0 0 0 6 521 1 93 0 3.575592e-03 0 90 1 93 6 0 0 0 0 0 2 0 0.005661 6 509 1 92 19 -1.997445 0 1 121412 3 40 1 0.300000 1.950000 0 0 FBXO34 55030 broad.mit.edu 37 14 55818287 55818287 + Silent SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr14:55818287G>A ENST00000313833.4 + 2 1424 c.1179G>A c.(1177-1179)tcG>tcA p.S393S FBXO34_ENST00000440021.1_Silent_p.S393S NM_017943.3 NP_060413.2 Q9NWN3 FBX34_HUMAN F-box protein 34 22 AGCCGGGTTCGCAAACTGCCG 0.507000 0 SO:0001819 synonymous_variant ENST00000313833.4 0 1 hg19 CCDS32086.1 TCGA-2J-AAB4-01A-12D-A40W-08 FBXO34-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411322.1 0 0 0 7 515 0 129 0 2.978547e-01 0 71 0 129 2 0 0 0 0 0 2 1 0.979640 6 509 0 125 2 -2.032865 0 1 121412 1 33 1 1 2 3 2.023443 0 0.300000 1.950000 0.302094 0.090000 3.000000e-02 0.190000 0.090000 0.110434 0.090000 0 6.000000e-02 1.400000e-01 VPS13C 54832 broad.mit.edu 37 15 62255003 62255003 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr15:62255003G>A ENST00000261517.5 - 33 3453 c.3380C>T c.(3379-3381)gCc>gTc p.A1127V VPS13C_ENST00000395896.4_Missense_Mutation_p.A1127V|VPS13C_ENST00000395898.3_Missense_Mutation_p.A1084V|VPS13C_ENST00000249837.3_Missense_Mutation_p.A1084V NM_020821.2 NP_065872.1 vacuolar protein sorting 13 homolog C (S. cerevisiae) 117 TTCTAGTCGGGCAAAAAGTGA 0.328000 0 SO:0001583 missense ENST00000261517.5 0 1 hg19 CCDS32257.1 . . . . . . . . . . G 12.69 2.012850 0.35511 . . ENSG00000129003 ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898 T;T;T 0.45276 0.9;0.9;0.9 5.93 5.01 0.66863 . 0.386164 0.25909 N 0.027516 T 0.38214 0.1032 M 0.62266 1.93 0.53005 D 0.999967 B;B;B;B 0.29232 0.238;0.238;0.238;0.153 B;B;B;B 0.30855 0.121;0.121;0.121;0.076 T 0.12293 -1.0553 10 0.23891 T 0.37 . 9.4557 0.38753 0.0712:0.0:0.7853:0.1436 . 1084;1127;1084;1127 Q709C8-4;Q709C8-2;Q709C8-3;Q709C8 .;.;.;VP13C_HUMAN V 1084;1127;1127;1127 ENSP00000249837:A1084V;ENSP00000261517:A1127V;ENSP00000379233:A1127V ENSP00000249837:A1084V A - 2 0 VPS13C 60042295 1.000000 0.71417 1.000000 0.80357 0.139000 0.21198 6.845000 0.75394 2.805000 0.96524 0.655000 0.94253 GCC TCGA-2J-AAB4-01A-12D-A40W-08 VPS13C-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000415997.1 0 0 0 5 249 0 65 0 1.990316e-02 0 9 0 65 2 0 0 0 0 0 2 1 0.935521 6 244 0 65 2 -2.522317 1 1 0 0 1 0 1 1 2.013936 0 0.300000 1.950000 0.298948 0.140000 5.000000e-02 0.290000 0.130000 0.154581 0.140000 0 8.000000e-02 2.100000e-01 DNAH3 55567 broad.mit.edu 37 16 21080894 21080894 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr16:21080894G>A ENST00000261383.3 - 23 3222 c.3223C>T c.(3223-3225)Cgc>Tgc p.R1075C DNAH3_ENST00000415178.1_Missense_Mutation_p.R1075C NM_017539.1 NP_060009.1 Q8TD57 DYH3_HUMAN dynein, axonemal, heavy chain 3 p.R1075C(2) 202 TCTTGTATGCGAATTAGCTTT 0.458000 2 Substitution - Missense(2) SO:0001583 missense ENST00000261383.3 1 1 hg19 CCDS10594.1 . . . . . . . . . . G 11.04 1.521152 0.27211 . . ENSG00000158486 ENST00000261383;ENST00000415178 T;T 0.62232 0.04;0.04 5.4 4.38 0.52667 Dynein heavy chain, domain-2 (1); 0.726956 0.12981 N 0.423277 T 0.67571 0.2907 M 0.61703 1.905 0.09310 N 0.999999 D 0.71674 0.998 P 0.56916 0.809 T 0.59920 -0.7363 10 0.49607 T 0.09 . 5.2981 0.15764 0.0831:0.1449:0.6224:0.1496 . 1075 Q8TD57 DYH3_HUMAN C 1075 ENSP00000261383:R1075C;ENSP00000394245:R1075C ENSP00000261383:R1075C R - 1 0 DNAH3 20988395 0.019000 0.18553 0.931000 0.37212 0.665000 0.39181 1.662000 0.37418 2.696000 0.92011 0.655000 0.94253 CGC TCGA-2J-AAB4-01A-12D-A40W-08 DNAH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207361.1 1 0 1 46 313 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 1.000000 46 311 0 114 2 -19.241680 1 1 121410 3 35 1 1 2 3 2.023048 0 0.300000 1.950000 0.302094 0.850000 6.400000e-01 1.000000 1.000000 0.858019 0.850000 1 7.400000e-01 9.900000e-01 CASKIN1 57524 broad.mit.edu 37 16 2228635 2228635 + Silent SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr16:2228635C>T ENST00000343516.6 - 20 4304 c.4212G>A c.(4210-4212)gcG>gcA p.A1404A NM_020764.3 NP_065815.1 Q8WXD9 CSKI1_HUMAN CASK interacting protein 1 28 TGCTCTTTTCCGCCGCCGAGT 0.716000 0 SO:0001819 synonymous_variant ENST00000343516.6 1 1 hg19 CCDS42103.1 TCGA-2J-AAB4-01A-12D-A40W-08 CASKIN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000435055.1 1 0 0 14 106 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 0.999792 14 104 0 38 2 -3.323279 1 1 119936 9 37 1 1 2 3 2.023048 0 0.300000 1.950000 0.302094 0.790000 4.600000e-01 1.000000 1.000000 0.789378 0.790000 0 6.100000e-01 1 MEFV 4210 broad.mit.edu 37 16 3293521 3293521 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr16:3293521C>T ENST00000219596.1 - 10 2005 c.1966G>A c.(1966-1968)Gag>Aag p.E656K MEFV_ENST00000339854.4_Missense_Mutation_p.E476K|MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000536379.1_Missense_Mutation_p.E445K NM_000243.2 NP_000234.1 O15553 MEFV_HUMAN Mediterranean fever 50 ACCTCCACCTCCCAGTAACGG 0.542000 0 SO:0001583 missense ENST00000219596.1 1 1 hg19 CCDS10498.1 . . . . . . . . . . C 19.25 3.791684 0.70452 . . ENSG00000103313 ENST00000545159;ENST00000219596;ENST00000339854;ENST00000536379 T;T;T 0.77620 -1.11;-1.11;-1.11 5.03 4.02 0.46733 Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1); 0.139173 0.33110 N 0.005270 D 0.92750 0.7695 H 0.99312 4.51 0.37407 D 0.913101 D 0.89917 1.0 D 0.85130 0.997 D 0.96110 0.9076 10 0.87932 D 0 . 13.8796 0.63674 0.0:0.846:0.154:0.0 . 656 O15553 MEFV_HUMAN K 656;656;476;445 ENSP00000219596:E656K;ENSP00000339639:E476K;ENSP00000445079:E445K ENSP00000219596:E656K E - 1 0 MEFV 3233522 1.000000 0.71417 1.000000 0.80357 0.788000 0.44548 3.985000 0.56930 2.496000 0.84212 0.650000 0.86243 GAG TCGA-2J-AAB4-01A-12D-A40W-08 MEFV-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251464.1 1 0 1 95 471 0 134 0 0 0 0 134 2 0 0 0 0 0 2 1 1.000000 94 452 0 132 2 -3.331202 1 1 0 0 1 1 2 3 2.023048 0 0.300000 1.950000 0.302094 0.990000 9.200000e-01 1.000000 1.000000 0.994754 0.990000 1 9.900000e-01 1 DLG4 1742 broad.mit.edu 37 17 7100076 7100076 + Splice_Site SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr17:7100076C>T ENST00000399506.2 - 9 1274 c.1083G>A c.(1081-1083)tcG>tcA p.S361S DLG4_ENST00000399510.2_Splice_Site_p.S404S|DLG4_ENST00000302955.6_Splice_Site_p.S358S P78352 DLG4_HUMAN discs, large homolog 4 (Drosophila) 18 Guanidine(DB00536) CTTCCCTCACCGACAGGATCT 0.667000 0 SO:0001630 splice_region_variant ENST00000399506.2 0 1 hg19 TCGA-2J-AAB4-01A-12D-A40W-08 DLG4-002 KNOWN non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000259419.2 0 0 0 6 37 0 13 0 9.190821e-01 0 31 0 13 2 0 0 0 0 0 2 1 0.963670 5 36 0 13 2 -12.956960 1 1 0 0 1 0 1 1 1.759855 1 0.300000 1.950000 0.185099 0.720000 3.300000e-01 1.000000 1.000000 0.716573 0.720000 0 5.000000e-01 9.300000e-01 TP53 7157 broad.mit.edu 37 17 7578554 7578554 + Splice_Site SNP A A T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 A T A A Valid Somatic Phase_I WXS targeted Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr17:7578554A>T ENST00000269305.4 - 5 565 c.376T>A c.(376-378)Tac>Aac p.Y126N TP53_ENST00000445888.2_Splice_Site_p.Y126N|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site_p.Y126N|TP53_ENST00000420246.2_Splice_Site_p.Y126N|TP53_ENST00000359597.4_Splice_Site_p.Y126N|TP53_ENST00000413465.2_Splice_Site_p.Y126N 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.Y126D(9)|p.0?(8)|p.Y126N(6)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.Y33D(2)|p.V73fs*9(1)|p.?(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)|p.Y126fs*18(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCAGGGGAGTACTGTAGGAAG 0.557000 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 40 Substitution - Missense(17)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(4)|Insertion - In frame(1)|Unknown(1) GRCh37 CI004819 TP53 I SO:0001630 splice_region_variant Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 0 hg19 CCDS11118.1 . . . . . . . . . . A 25.5 4.639687 0.87760 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591 D;D;D;D;D;D;D;D;D 0.99869 -7.33;-7.33;-7.33;-7.33;-7.33;-7.33;-7.33;-7.33;-7.33 5.48 5.48 0.80851 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99869 0.9938 M 0.90483 3.12 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;0.998;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.999;0.999;1.0;0.961;1.0;1.0;1.0 D 0.96375 0.9277 10 0.87932 D 0 -28.2517 13.8301 0.63375 1.0:0.0:0.0:0.0 . 87;126;126;33;126;126;126 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. N 126;126;126;126;126;126;115;33;33;126;126 ENSP00000410739:Y126N;ENSP00000352610:Y126N;ENSP00000269305:Y126N;ENSP00000398846:Y126N;ENSP00000391127:Y126N;ENSP00000391478:Y126N;ENSP00000423862:Y33N;ENSP00000424104:Y126N;ENSP00000426252:Y126N ENSP00000269305:Y126N Y - 1 0 TP53 7519279 1.000000 0.71417 1.000000 0.80357 0.927000 0.56198 9.240000 0.95396 2.206000 0.71126 0.533000 0.62120 TAC TCGA-2J-AAB4-01A-12D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 20 81 0 31 1 9.977699e-01 9 35 0 31 2 1 1 215 1138 0 1826 2 1 0.999998 20 80 0 31 2 -20.000000 1 1 0 0 1 0 1 1 1.759855 1 0.300000 1.950000 0.185099 0.930000 6.600000e-01 1.000000 1.000000 0.911469 0.930000 1 8.000000e-01 1 RBBP8 5932 broad.mit.edu 37 18 20602110 20602110 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr18:20602110G>A ENST00000399722.2 + 18 2824 c.2473G>A c.(2473-2475)Gca>Aca p.A825T RBBP8_ENST00000360790.5_Missense_Mutation_p.A830T|RBBP8_ENST00000581687.1_Missense_Mutation_p.A3T|RBBP8_ENST00000399725.2_Silent_p.Q792Q|RBBP8_ENST00000327155.5_Missense_Mutation_p.A825T|Y_RNA_ENST00000411091.1_RNA NM_203291.1 NP_976036.1 Q99708 COM1_HUMAN retinoblastoma binding protein 8 24 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) AGATATGCCAGCAGAAGAAAG 0.353000 Homologous recombination 0 SO:0001583 missense ENST00000399722.2 0 1 hg19 CCDS11875.1 . . . . . . . . . . G 14.30 2.495044 0.44352 . . ENSG00000101773 ENST00000327155;ENST00000399722;ENST00000360790 T;T;T 0.32272 1.47;1.47;1.46 5.93 3.14 0.36123 . 0.054739 0.64402 D 0.000001 T 0.25606 0.0623 L 0.29908 0.895 0.32479 N 0.541741 P;P 0.47191 0.891;0.656 P;B 0.46419 0.516;0.297 T 0.22695 -1.0209 10 0.25751 T 0.34 -9.1687 10.6324 0.45545 0.0674:0.2497:0.6829:0.0 . 830;825 E7ETY1;Q99708 .;COM1_HUMAN T 825;825;830 ENSP00000323050:A825T;ENSP00000382628:A825T;ENSP00000354024:A830T ENSP00000323050:A825T A + 1 0 RBBP8 18856108 1.000000 0.71417 0.997000 0.53966 0.993000 0.82548 7.513000 0.81739 0.384000 0.24942 0.585000 0.79938 GCA TCGA-2J-AAB4-01A-12D-A40W-08 RBBP8-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446387.1 0 0 0 6 773 0 181 0 1.998452e-01 0 91 0 181 2 0 0 0 0 0 2 1 0.963331 6 761 0 181 2 -2.510822 1 1 0 0 1 2 2 4 2.345917 1 0.300000 1.950000 0.400685 0.070000 1.000000e-02 1.000000 0.060000 0.291718 0.070000 0 4.000000e-02 1 SYT4 6860 broad.mit.edu 37 18 40853958 40853958 + Missense_Mutation SNP T T A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr18:40853958T>A ENST00000255224.3 - 2 804 c.436A>T c.(436-438)Act>Tct p.T146S SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Missense_Mutation_p.T128S NM_020783.3 NP_065834.1 Q9H2B2 SYT4_HUMAN synaptotagmin IV 44 TCTTCTGAAGTAAGGGAAGTG 0.448000 NSCLC(85;81 1419 2855 22820 35912) 0 SO:0001583 missense ENST00000255224.3 1 1 hg19 CCDS11922.1 . . . . . . . . . . T 0 -2.718377 0.00093 . . ENSG00000132872 ENST00000255224 T 0.07800 3.16 5.87 0.661 0.17874 . 0.510618 0.23724 N 0.045196 T 0.02230 0.0069 N 0.02539 -0.55 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.04013 0.001;0.001 T 0.45977 -0.9224 10 0.02654 T 1 . 6.2987 0.21101 0.5002:0.1473:0.0:0.3526 . 128;146 B4DEU3;Q9H2B2 .;SYT4_HUMAN S 146 ENSP00000255224:T146S ENSP00000255224:T146S T - 1 0 SYT4 39107956 0.020000 0.18652 0.091000 0.20842 0.126000 0.20510 0.155000 0.16362 -0.290000 0.09025 -1.427000 0.01099 ACT TCGA-2J-AAB4-01A-12D-A40W-08 SYT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255851.2 1 0 1 36 163 0 60 0 7.797522e-01 0 15 0 60 2 0 0 0 0 0 2 1 1.000000 36 162 0 60 2 -20.000000 1 1 0 0 1 0 1 1 1.716786 1 0.300000 1.950000 0.176471 0.900000 6.900000e-01 1.000000 0.990000 0.893530 0.900000 1 8.000000e-01 9.700000e-01 ZNF506 440515 broad.mit.edu 37 19 19905821 19905821 + Missense_Mutation SNP T T C TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr19:19905821T>C ENST00000540806.2 - 4 963 c.875A>G c.(874-876)aAa>aGa p.K292R CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000589657.1_RNA|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000450683.2_Missense_Mutation_p.K260R|ZNF506_ENST00000587461.1_Intron|ZNF506_ENST00000443905.2_Missense_Mutation_p.K292R Q5JVG8 ZN506_HUMAN zinc finger protein 506 14 AATAAAGGCTTTGCCACATTT 0.383000 0 SO:0001583 missense ENST00000540806.2 1 1 hg19 CCDS42531.1 . . . . . . . . . . - 12.46 1.944705 0.34283 . . ENSG00000081665 ENST00000443905;ENST00000540806;ENST00000450683 T;T;T 0.35789 1.75;1.75;1.29 0.974 0.974 0.19715 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.28366 0.0701 L 0.33339 1.005 0.30874 N 0.732139 B;B 0.20368 0.044;0.005 B;B 0.32465 0.146;0.009 T 0.37174 -0.9717 9 0.62326 D 0.03 . 5.7771 0.18285 0.0:0.0:0.0:1.0 . 292;260 Q5JVG8;Q5JVG8-2 ZN506_HUMAN;. R 292;292;260 ENSP00000393835:K292R;ENSP00000440625:K292R;ENSP00000408892:K260R ENSP00000393835:K292R K - 2 0 ZNF506 19766821 0.999000 0.42202 0.339000 0.25562 0.301000 0.27625 5.174000 0.65015 0.358000 0.24211 0.347000 0.21830 AAA TCGA-2J-AAB4-01A-12D-A40W-08 ZNF506-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000460794.1 1 0 1 44 281 0 98 1 7.496107e-01 3 16 0 98 2 0 0 0 0 0 2 1 0.999996 44 275 1 98 13 -20.000000 1 1 0 0 1 1 2 3 2.064520 0 0.300000 1.950000 0.310345 0.920000 6.800000e-01 1.000000 1.000000 0.909832 0.920000 1 7.900000e-01 1 ZNF345 25850 broad.mit.edu 37 19 37368703 37368703 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr19:37368703G>A ENST00000529555.1 + 2 1759 c.971G>A c.(970-972)aGa>aAa p.R324K ZNF345_ENST00000589046.1_Missense_Mutation_p.R324K|ZNF345_ENST00000420450.1_Missense_Mutation_p.R324K|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron Q14585 ZN345_HUMAN zinc finger protein 345 24 Esophageal squamous(110;0.183) COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) AAAGCCTTTAGAAGTGGTTCA 0.413000 0 SO:0001583 missense ENST00000529555.1 1 1 hg19 CCDS12497.1 . . . . . . . . . . G 11.11 1.543390 0.27563 . . ENSG00000251247 ENST00000420450;ENST00000529555;ENST00000344705 T;T 0.07327 3.2;3.2 3.8 2.71 0.32032 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.03695 0.0105 N 0.03304 -0.355 0.09310 N 0.999994 B 0.13594 0.008 B 0.18561 0.022 T 0.39482 -0.9612 9 0.45353 T 0.12 . 5.1601 0.15056 0.117:0.2162:0.6668:0.0 . 324 Q14585 ZN345_HUMAN K 324;324;88 ENSP00000431216:R324K;ENSP00000431202:R324K ENSP00000442320:R88K R + 2 0 ZNF345 42060543 0.000000 0.05858 0.999000 0.59377 0.978000 0.69477 -1.214000 0.02988 0.857000 0.35407 0.462000 0.41574 AGA TCGA-2J-AAB4-01A-12D-A40W-08 ZNF345-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388258.1 1 0 1 60 342 0 86 0 1.116853e-01 0 4 0 86 2 0 0 0 0 0 2 1 1.000000 60 339 0 86 2 -20.000000 1 1 0 0 1 1 2 3 2.258037 1 0.300000 1.950000 0.386503 0.990000 8.800000e-01 1.000000 1.000000 0.991548 0.990000 1 9.900000e-01 1 PSG1 5669 broad.mit.edu 37 19 43383710 43383710 + Silent SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr19:43383710G>A ENST00000436291.2 - 1 140 c.24C>T c.(22-24)ccC>ccT p.P8P PSG1_ENST00000403380.3_Silent_p.P8P|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000595356.1_Silent_p.P8P|PSG1_ENST00000244296.2_Silent_p.P8P|PSG1_ENST00000312439.6_Silent_p.P8P|PSG1_ENST00000595124.1_Silent_p.P8P NM_001184825.1|NM_001184826.1 NP_001171754.1|NP_001171755.1 P11464 PSG1_HUMAN pregnancy specific beta-1-glycoprotein 1 30 Prostate(69;0.00682) GCTGTGTGCAGGGAGGGGCTG 0.572000 0 SO:0001819 synonymous_variant ENST00000436291.2 1 1 hg19 CCDS54275.1 TCGA-2J-AAB4-01A-12D-A40W-08 PSG1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000321426.1 1 0 1 89 417 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 87 404 0 108 2 -2.921238 1 1 121344 3 37 1 0 2 2 1.866741 1 0.300000 1.950000 0.300000 0.990000 9.500000e-01 1.000000 1.000000 0.997662 0.990000 1 9.900000e-01 1 NTNG1 22854 broad.mit.edu 37 1 107867468 107867468 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr1:107867468G>A ENST00000370068.1 + 3 1657 c.811G>A c.(811-813)Gtt>Att p.V271I NTNG1_ENST00000370070.2_Missense_Mutation_p.V271I|NTNG1_ENST00000542803.1_Missense_Mutation_p.V271I|NTNG1_ENST00000370073.2_Missense_Mutation_p.V271I|NTNG1_ENST00000370066.1_Missense_Mutation_p.V271I|NTNG1_ENST00000370074.4_Missense_Mutation_p.V271I|NTNG1_ENST00000370065.1_Missense_Mutation_p.V271I|NTNG1_ENST00000370072.3_Missense_Mutation_p.V271I|NTNG1_ENST00000370067.1_Missense_Mutation_p.V271I|NTNG1_ENST00000477948.1_3'UTR|NTNG1_ENST00000370061.3_Missense_Mutation_p.V271I|NTNG1_ENST00000370071.2_Missense_Mutation_p.V271I Q9Y2I2 NTNG1_HUMAN netrin G1 p.V271I(2) 37 all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243) AAGACCAGCCGTTGGGGAAAT 0.458000 2 Substitution - Missense(2) SO:0001583 missense ENST00000370068.1 1 1 hg19 CCDS44180.1 . . . . . . . . . . G 11.41 1.630818 0.28978 . . ENSG00000162631 ENST00000370076;ENST00000370073;ENST00000370071;ENST00000542803;ENST00000370061;ENST00000370072;ENST00000370070;ENST00000535584;ENST00000370064;ENST00000370062;ENST00000370074;ENST00000370068;ENST00000294649;ENST00000370067;ENST00000370066;ENST00000370065 T;T;T;T;T;T;T;T;T;T;T 0.75154 -0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91 5.94 3.92 0.45320 Laminin, N-terminal (3); 0.336633 0.24492 N 0.038046 T 0.29850 0.0746 N 0.04508 -0.205 0.33178 D 0.549223 B;B;B;B;B 0.25772 0.001;0.134;0.007;0.021;0.076 B;B;B;B;B 0.28709 0.007;0.093;0.019;0.024;0.046 T 0.05435 -1.0885 10 0.40728 T 0.16 . 4.7071 0.12855 0.6449:0.0:0.3551:0.0 . 271;271;271;271;271 B4DKF0;Q9Y2I2;Q9Y2I2-4;Q9Y2I2-2;Q9Y2I2-1 .;NTNG1_HUMAN;.;.;. I 271;271;271;271;271;271;271;271;32;32;271;271;271;271;271;271 ENSP00000359090:V271I;ENSP00000359088:V271I;ENSP00000440561:V271I;ENSP00000359078:V271I;ENSP00000359089:V271I;ENSP00000359087:V271I;ENSP00000359091:V271I;ENSP00000359085:V271I;ENSP00000359084:V271I;ENSP00000359083:V271I;ENSP00000359082:V271I ENSP00000294649:V271I V + 1 0 NTNG1 107668991 1.000000 0.71417 0.787000 0.31911 0.994000 0.84299 7.637000 0.83313 0.752000 0.32923 0.655000 0.94253 GTT TCGA-2J-AAB4-01A-12D-A40W-08 NTNG1-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000030340.1 1 0 1 42 340 0 57 0 0 0 0 57 2 0 0 0 0 0 2 1 1.000000 41 336 0 56 2 -3.221884 1 1 0 0 1 1 2 3 2.043436 0 0.300000 1.950000 0.306244 0.740000 5.400000e-01 1.000000 0.730000 0.759956 0.740000 0 6.300000e-01 8.800000e-01 CD1B 910 broad.mit.edu 37 1 158300606 158300606 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr1:158300606G>A ENST00000368168.3 - 2 415 c.308C>T c.(307-309)gCc>gTc p.A103V NM_001764.2 NP_001755.1 P29016 CD1B_HUMAN CD1b molecule 30 all_hematologic(112;0.0378) GAAATCACCGGCAAAGTCTTG 0.433000 0 SO:0001583 missense ENST00000368168.3 0 1 hg19 CCDS1176.1 . . . . . . . . . . G 7.665 0.685781 0.14973 . . ENSG00000158485 ENST00000368168 T 0.06371 3.31 4.28 -3.93 0.04143 MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1); 1.257440 0.05775 N 0.607617 T 0.00845 0.0028 N 0.11023 0.085 0.09310 N 1 B;B 0.32396 0.369;0.008 B;B 0.24541 0.054;0.012 T 0.44907 -0.9297 10 0.13108 T 0.6 -2.4627 10.7361 0.46126 0.7119:0.0:0.2881:0.0 . 103;103 B4E0D2;P29016 .;CD1B_HUMAN V 103 ENSP00000357150:A103V ENSP00000357150:A103V A - 2 0 CD1B 156567230 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -0.975000 0.03790 -0.705000 0.05035 0.655000 0.94253 GCC TCGA-2J-AAB4-01A-12D-A40W-08 CD1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046350.2 0 0 0 7 1201 1 303 0 4.913636e-05 0 2 1 303 2 0 0 0 0 0 2 0 0.061823 7 1185 1 302 15 -2.219813 0 1 0 0 1 1 2 3 2.016659 0 0.300000 1.950000 0.301048 0.030000 0 0.080000 0.040000 0.044061 0.030000 0 2.000000e-02 6.000000e-02 ITLN1 55600 broad.mit.edu 37 1 160850421 160850421 + Silent SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr1:160850421G>A ENST00000326245.3 - 6 757 c.642C>T c.(640-642)ggC>ggT p.G214G ITLN1_ENST00000487531.1_5'UTR NM_017625.2 NP_060095.2 Q8WWA0 ITLN1_HUMAN intelectin 1 (galactofuranose binding) 21 all_cancers(52;2.99e-17)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00737) TCTGGGCGTCGCCAAAATCAT 0.443000 0 SO:0001819 synonymous_variant ENST00000326245.3 0 1 hg19 CCDS1211.1 TCGA-2J-AAB4-01A-12D-A40W-08 ITLN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071462.1 0 0 0 7 793 0 201 0 6.581063e-04 0 4 0 201 2 0 0 0 0 0 2 0 0.060036 7 780 1 201 15 -1.626615 0 1 121412 3 42 1 1 2 3 2.016659 0 0.300000 1.950000 0.301048 0.050000 2.000000e-02 0.120000 0.060000 0.066443 0.050000 0 3.000000e-02 9.000000e-02 DNAJC6 9829 broad.mit.edu 37 1 65845149 65845149 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr1:65845149G>A ENST00000395325.3 + 5 594 c.437G>A c.(436-438)cGg>cAg p.R146Q DNAJC6_ENST00000371069.4_Missense_Mutation_p.R203Q|DNAJC6_ENST00000263441.7_Missense_Mutation_p.R133Q NM_014787.3 NP_055602.1 O75061 AUXI_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 6 39 GCTGTGTGTCGGAATATGTAT 0.458000 0 SO:0001583 missense ENST00000395325.3 1 1 hg19 CCDS30739.1 . . . . . . . . . . G 20.5 4.005156 0.74932 . . ENSG00000116675 ENST00000263441;ENST00000395325;ENST00000371069 D;D;D 0.98649 -5.05;-5.05;-5.05 5.41 3.42 0.39159 Phosphatase tensin type (1); 0.055637 0.64402 D 0.000001 D 0.90937 0.7151 N 0.17474 0.49 0.31432 N 0.672981 P;P;D 0.54397 0.932;0.811;0.966 B;B;B 0.40444 0.124;0.058;0.329 D 0.89605 0.3837 10 0.44086 T 0.13 . 4.517 0.11939 0.3974:0.0:0.6026:0.0 . 203;146;133 O75061-2;O75061;D3DQ66 .;AUXI_HUMAN;. Q 133;146;203 ENSP00000263441:R133Q;ENSP00000378735:R146Q;ENSP00000360108:R203Q ENSP00000263441:R133Q R + 2 0 DNAJC6 65617737 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.122000 0.77169 1.520000 0.48965 0.561000 0.74099 CGG TCGA-2J-AAB4-01A-12D-A40W-08 DNAJC6-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000025134.1 1 0 1 87 490 0 124 0 2.286730e-01 0 6 0 124 2 0 0 0 0 0 2 1 1.000000 87 480 0 123 2 -2.416268 0 1 121412 4 39 1 1 2 3 2.043436 0 0.300000 1.950000 0.306244 0.990000 8.200000e-01 1.000000 1.000000 0.970232 0.990000 1 9.100000e-01 1 TGM3 7053 broad.mit.edu 37 20 2290352 2290352 + Silent SNP G G T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr20:2290352G>T ENST00000381458.5 + 2 120 c.57G>T c.(55-57)gcG>gcT p.A19A NM_003245.3 NP_003236.3 Q08188 TGM3_HUMAN transglutaminase 3 39 L-Glutamine(DB00130) ACCGACAAGCGCATCACACAG 0.517000 0 SO:0001819 synonymous_variant ENST00000381458.5 1 1 hg19 CCDS33435.1 TCGA-2J-AAB4-01A-12D-A40W-08 TGM3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077579.2 1 0 1 74 477 0 123 0 0 0 0 123 2 0 0 0 0 0 2 1 1.000000 72 472 0 123 2 -3.221898 1 1 0 0 1 0 1 1 2.008187 0 0.300000 1.950000 0.297894 0.880000 7.100000e-01 1.000000 1.000000 0.889781 0.880000 1 7.900000e-01 9.900000e-01 RPRD1B 58490 broad.mit.edu 37 20 36687836 36687836 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr20:36687836C>T ENST00000373433.4 + 5 971 c.569C>T c.(568-570)gCc>gTc p.A190V NM_021215.3 NP_067038.1 Q9NQG5 RPR1B_HUMAN regulation of nuclear pre-mRNA domain containing 1B 12 CTGGAAAATGCCGCATCAGGG 0.413000 0 SO:0001583 missense ENST00000373433.4 0 1 hg19 CCDS13301.1 . . . . . . . . . . C 36 5.667224 0.96745 . . ENSG00000101413 ENST00000373433;ENST00000449186 . . . 5.4 5.4 0.78164 . 0.046127 0.85682 D 0.000000 T 0.71005 0.3289 M 0.68593 2.085 0.80722 D 1 P 0.51653 0.947 P 0.50537 0.643 T 0.74438 -0.3665 9 0.72032 D 0.01 -10.9352 18.3479 0.90328 0.0:1.0:0.0:0.0 . 190 Q9NQG5 RPR1B_HUMAN V 190;72 . ENSP00000362532:A190V A + 2 0 RPRD1B 36121250 1.000000 0.71417 0.997000 0.53966 0.992000 0.81027 7.651000 0.83577 2.814000 0.96858 0.563000 0.77884 GCC TCGA-2J-AAB4-01A-12D-A40W-08 RPRD1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079142.2 0 0 0 5 336 0 69 0 1.192916e-01 0 33 0 69 2 0 0 0 0 0 2 1 0.935032 5 330 0 69 2 -2.228903 0 1 0 0 1 0 1 1 2.008187 0 0.300000 1.950000 0.297894 0.100000 3.000000e-02 0.210000 0.100000 0.115468 0.100000 0 6.000000e-02 1.600000e-01 ABCG1 9619 broad.mit.edu 37 21 43706012 43706012 + Missense_Mutation SNP A A G TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr21:43706012A>G ENST00000361802.2 + 8 1026 c.881A>G c.(880-882)cAa>cGa p.Q294R ABCG1_ENST00000398449.3_Missense_Mutation_p.Q294R|ABCG1_ENST00000398457.2_Missense_Mutation_p.Q296R|ABCG1_ENST00000340588.4_Missense_Mutation_p.Q402R|ABCG1_ENST00000343687.3_Missense_Mutation_p.Q305R|ABCG1_ENST00000462050.1_3'UTR|ABCG1_ENST00000347800.2_Missense_Mutation_p.Q291R|ABCG1_ENST00000398437.1_Missense_Mutation_p.Q440R NM_004915.3 NP_004906.3 P45844 ABCG1_HUMAN ATP-binding cassette, sub-family G (WHITE), member 1 29 Adenosine triphosphate(DB00171) AGTCAAGGACAATGTGTGTAC 0.493000 0 SO:0001583 missense ENST00000361802.2 1 1 hg19 CCDS13682.1 . . . . . . . . . . A 17.08 3.296969 0.60086 . . ENSG00000160179 ENST00000398457;ENST00000347800;ENST00000398449;ENST00000361802;ENST00000343687;ENST00000398437;ENST00000340588 T;T;T;T;T;T;T 0.45668 0.89;0.89;0.89;0.89;0.89;0.89;0.89 4.04 4.04 0.47022 ABC transporter-like (1); 0.000000 0.85682 D 0.000000 T 0.29389 0.0732 N 0.00841 -1.15 0.80722 D 1 B;B;D;B;B;D 0.67145 0.11;0.02;0.996;0.057;0.049;0.981 B;B;P;B;B;D 0.67900 0.074;0.032;0.889;0.032;0.061;0.954 T 0.44787 -0.9305 9 . . . -14.5189 13.2943 0.60288 1.0:0.0:0.0:0.0 . 305;305;294;294;291;296 B4DPT7;P45844-2;P45844;P45844-4;P45844-5;P45844-3 .;.;ABCG1_HUMAN;.;.;. R 296;291;294;294;305;440;402 ENSP00000381475:Q296R;ENSP00000291524:Q291R;ENSP00000381467:Q294R;ENSP00000354995:Q294R;ENSP00000339744:Q305R;ENSP00000381464:Q440R;ENSP00000343820:Q402R . Q + 2 0 ABCG1 42579081 1.000000 0.71417 0.993000 0.49108 0.997000 0.91878 8.449000 0.90337 1.581000 0.49865 0.482000 0.46254 CAA TCGA-2J-AAB4-01A-12D-A40W-08 ABCG1-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000195318.2 1 0 1 115 796 0 256 1 9.999769e-01 38 66 0 256 2 0 0 0 0 0 2 1 1.000000 112 786 0 253 2 -20.000000 1 1 0 0 1 0 1 1 2.008717 0 0.300000 1.950000 0.297894 0.830000 6.900000e-01 0.980000 0.830000 0.841728 0.830000 0 7.600000e-01 9.100000e-01 DNER 92737 broad.mit.edu 37 2 230312173 230312173 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr2:230312173C>T ENST00000341772.4 - 8 1479 c.1345G>A c.(1345-1347)Ggg>Agg p.G449R NM_139072.3 NP_620711.3 Q8NFT8 DNER_HUMAN delta/notch-like EGF repeat containing 63 all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175) AAGTGTACCCCGTCCACATAG 0.572000 0 SO:0001583 missense ENST00000341772.4 1 1 hg19 CCDS33390.1 . . . . . . . . . . C 5.804 0.332713 0.11013 . . ENSG00000187957 ENST00000341772 D 0.87412 -2.25 4.94 4.01 0.46588 EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1); 0.209202 0.49916 D 0.000132 T 0.78660 0.4318 L 0.42529 1.33 0.46499 D 0.999072 B 0.25719 0.132 B 0.18871 0.023 T 0.70952 -0.4732 10 0.15066 T 0.55 . 9.0768 0.36527 0.0:0.6526:0.2599:0.0876 . 449 Q8NFT8 DNER_HUMAN R 449 ENSP00000345229:G449R ENSP00000345229:G449R G - 1 0 DNER 230020417 0.942000 0.31987 0.080000 0.20451 0.198000 0.23893 2.742000 0.47434 2.442000 0.82660 0.655000 0.94253 GGG TCGA-2J-AAB4-01A-12D-A40W-08 DNER-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331902.1 1 0 1 19 128 0 25 0 0 0 1 0 25 2 0 0 0 0 0 2 1 0.999990 18 122 0 25 2 -2.723487 1 1 121412 2 38 1 0 0 0 2.001658 0 0.300000 1.950000 0.295775 0.850000 5.400000e-01 1.000000 1.000000 0.846710 0.850000 1 6.800000e-01 1 USP34 9736 broad.mit.edu 37 2 61448662 61448662 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr2:61448662G>A ENST00000398571.2 - 66 7950 c.7874C>T c.(7873-7875)tCt>tTt p.S2625F USP34_ENST00000472689.1_5'UTR NM_014709.3 NP_055524.3 Q70CQ2 UBP34_HUMAN ubiquitin specific peptidase 34 138 Epithelial(17;0.229) CAGAATATAAGATGCAAAGGG 0.383000 0 SO:0001583 missense ENST00000398571.2 1 1 hg19 CCDS42686.1 . . . . . . . . . . G 25.3 4.619780 0.87460 . . ENSG00000115464 ENST00000263989;ENST00000398569;ENST00000398571 T 0.36699 1.24 6.07 6.07 0.98685 Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.43366 0.1244 L 0.36672 1.1 0.80722 D 1 D 0.56968 0.978 P 0.54664 0.758 T 0.04811 -1.0925 10 0.09590 T 0.72 . 20.6593 0.99626 0.0:0.0:1.0:0.0 . 2625 Q70CQ2 UBP34_HUMAN F 2473;2473;2625 ENSP00000381577:S2625F ENSP00000263989:S2473F S - 2 0 USP34 61302166 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.701000 0.98710 2.885000 0.99019 0.655000 0.94253 TCT TCGA-2J-AAB4-01A-12D-A40W-08 USP34-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000325650.4 1 0 1 25 150 0 42 1 8.705726e-01 5 19 0 42 2 0 0 0 0 0 2 1 1.000000 25 149 0 39 2 -3.332045 1 1 0 0 1 0 0 0 2.001658 0 0.300000 1.950000 0.295775 0.940000 6.400000e-01 1.000000 1.000000 0.908524 0.940000 1 7.800000e-01 1 FBLN2 2199 broad.mit.edu 37 3 13679189 13679189 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr3:13679189G>A ENST00000295760.7 + 17 3394 c.3325G>A c.(3325-3327)Gcg>Acg p.A1109T FBLN2_ENST00000492059.1_Missense_Mutation_p.A1156T|FBLN2_ENST00000404922.3_Missense_Mutation_p.A1156T|FBLN2_ENST00000535798.1_Missense_Mutation_p.A1135T NM_001998.2 NP_001989.2 P98095 FBLN2_HUMAN fibulin 2 p.A1156T(2)|p.A575T(2) 24 UCEC - Uterine corpus endometrioid carcinoma (1;0.00416) CATTGGCCCCGCGCCAGCCTT 0.622000 4 Substitution - Missense(4) SO:0001583 missense ENST00000295760.7 0 1 hg19 CCDS46762.1 . . . . . . . . . . G 12.47 1.946543 0.34377 . . ENSG00000163520 ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059 T;T;T;T 0.79554 -1.28;-1.24;-1.19;-1.24 4.6 2.63 0.31362 . 0.194173 0.46442 D 0.000286 T 0.44871 0.1314 N 0.01729 -0.75 0.35567 D 0.805155 B;P;P 0.48998 0.313;0.918;0.72 B;B;B 0.34138 0.058;0.176;0.131 T 0.54221 -0.8326 10 0.14656 T 0.56 . 5.867 0.18781 0.1026:0.0:0.5213:0.376 . 1109;1156;1135 P98095;P98095-2;F5H1F3 FBLN2_HUMAN;.;. T 1135;1156;1109;1156 ENSP00000445705:A1135T;ENSP00000384169:A1156T;ENSP00000295760:A1109T;ENSP00000420042:A1156T ENSP00000295760:A1109T A + 1 0 FBLN2 13654190 0.993000 0.37304 0.747000 0.31113 0.616000 0.37450 3.099000 0.50267 1.157000 0.42530 0.462000 0.41574 GCG TCGA-2J-AAB4-01A-12D-A40W-08 FBLN2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000340083.3 0 0 0 6 145 0 34 0 9.763739e-01 0 169 0 34 2 1 9.998847e-01 8 555 0 651 2 1 0.962180 6 140 0 34 2 -8.786218 1 1 0 0 1 0 1 1 2.008791 0 0.300000 1.950000 0.297894 0.280000 1.100000e-01 0.530000 0.260000 0.299381 0.280000 0 1.800000e-01 4.000000e-01 ACAP2 23527 broad.mit.edu 37 3 195027287 195027287 + Nonsense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr3:195027287G>A ENST00000326793.6 - 13 1299 c.1069C>T c.(1069-1071)Cag>Tag p.Q357* NM_012287.5 NP_036419.3 Q15057 ACAP2_HUMAN ArfGAP with coiled-coil, ankyrin repeat and PH domains 2 27 ATACTGGTCTGAACAGCCTTA 0.383000 0 SO:0001587 stop_gained ENST00000326793.6 0 1 hg19 CCDS33924.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 37|37 6.017412|6.017412 0.97205|0.97205 .|. .|. ENSG00000114331|ENSG00000114331 ENST00000326793|ENST00000439758 .|. .|. .|. 5.55|5.55 5.55|5.55 0.83447|0.83447 .|. 0.051792|. 0.85682|. D|. 0.000000|. .|T .|0.74869 .|0.3773 .|. .|. .|. 0.80722|0.80722 A|A 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.73167 .|-0.4068 .|3 0.72032|. D|. 0.01|. .|. 18.484|18.484 0.90821|0.90821 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|. .|. .|. X|L 357|231 .|. ENSP00000324287:Q357X|. Q|S -|- 1|2 0|0 ACAP2|ACAP2 196508576|196508576 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.997000|0.997000 0.91878|0.91878 9.869000|9.869000 0.99810|0.99810 2.593000|2.593000 0.87608|0.87608 0.511000|0.511000 0.50034|0.50034 CAG|TCA TCGA-2J-AAB4-01A-12D-A40W-08 ACAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342126.2 1 0 1 95 650 0 196 0 7.679020e-01 0 21 0 196 2 0 0 0 0 0 2 1 1.000000 95 639 0 195 2 -20.000000 1 1 0 0 1 0 1 1 2.008791 0 0.300000 1.950000 0.297894 0.840000 6.900000e-01 1.000000 0.850000 0.850098 0.840000 0 7.600000e-01 9.300000e-01 WDR48 57599 broad.mit.edu 37 3 39136218 39136218 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr3:39136218G>A ENST00000302313.5 + 19 2046 c.2018G>A c.(2017-2019)cGt>cAt p.R673H WDR48_ENST00000418020.1_Missense_Mutation_p.R117H|WDR48_ENST00000396258.3_Missense_Mutation_p.R591H|WDR48_ENST00000544962.1_Missense_Mutation_p.R398H|WDR48_ENST00000466405.1_3'UTR NM_020839.2 NP_065890.1 Q8TAF3 WDR48_HUMAN WD repeat domain 48 15 CTCCATTACCGTCAGAAGTCC 0.473000 0 SO:0001583 missense ENST00000302313.5 1 1 hg19 CCDS33738.1 . . . . . . . . . . G 35 5.507838 0.96386 . . ENSG00000114742 ENST00000302313;ENST00000544962;ENST00000396258;ENST00000418020 T;D;T 0.92699 0.47;-3.09;0.2 5.86 5.86 0.93980 . 0.000000 0.85682 D 0.000000 D 0.96355 0.8811 M 0.79926 2.475 0.80722 D 1 D;D;D;D 0.89917 0.999;1.0;1.0;1.0 D;D;D;D 0.74674 0.984;0.961;0.961;0.975 D 0.96242 0.9176 10 0.87932 D 0 -14.2076 20.1865 0.98220 0.0:0.0:1.0:0.0 . 398;591;664;673 Q8TAF3-5;Q8TAF3-4;Q8TAF3-3;Q8TAF3 .;.;.;WDR48_HUMAN H 673;398;591;117 ENSP00000307491:R673H;ENSP00000445187:R398H;ENSP00000379557:R591H ENSP00000307491:R673H R + 2 0 WDR48 39111222 1.000000 0.71417 0.997000 0.53966 0.997000 0.91878 9.799000 0.99117 2.775000 0.95449 0.655000 0.94253 CGT TCGA-2J-AAB4-01A-12D-A40W-08 WDR48-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342529.1 1 0 1 73 371 0 92 1 9.919798e-01 6 34 0 92 2 0 0 0 0 0 2 1 1.000000 72 370 0 89 2 -20.000000 1 1 121412 4 37 1 0 1 1 2.008791 0 0.300000 1.950000 0.297894 0.990000 8.700000e-01 1.000000 1.000000 0.987584 0.990000 1 9.700000e-01 1 ADAMTS9 56999 broad.mit.edu 37 3 64526867 64526867 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr3:64526867G>A ENST00000498707.1 - 36 5767 c.5425C>T c.(5425-5427)Cgg>Tgg p.R1809W ADAMTS9_ENST00000295903.4_Missense_Mutation_p.R1781W NM_182920.1 NP_891550.1 Q9P2N4 ATS9_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 9 100 Lung NSC(201;0.00682) TCATCGCGCCGGCTCCCGTTA 0.473000 0 SO:0001583 missense ENST00000498707.1 1 1 hg19 CCDS2903.1 . . . . . . . . . . G 16.56 3.156860 0.57259 . . ENSG00000163638 ENST00000295903;ENST00000498707 T;T 0.19394 2.15;2.15 5.73 3.76 0.43208 Peptidase M12B, GON-ADAMTSs (2); 0.000000 0.85682 D 0.000000 T 0.49779 0.1577 M 0.86864 2.845 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.57015 -0.7883 10 0.87932 D 0 . 13.0992 0.59210 0.0:0.0:0.6673:0.3327 . 1781;1809 B7ZVX9;Q9P2N4 .;ATS9_HUMAN W 1781;1809 ENSP00000295903:R1781W;ENSP00000418735:R1809W ENSP00000295903:R1781W R - 1 2 ADAMTS9 64501907 1.000000 0.71417 0.998000 0.56505 0.359000 0.29487 2.444000 0.44890 2.706000 0.92434 0.655000 0.94253 CGG TCGA-2J-AAB4-01A-12D-A40W-08 ADAMTS9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351891.1 1 0 1 84 384 0 116 1 9.586280e-01 5 21 0 116 2 0 0 0 0 0 2 1 1.000000 83 375 0 116 2 -20.000000 1 1 121412 1 32 1 0 1 1 2.008791 0 0.300000 1.950000 0.297894 0.990000 9.600000e-01 1.000000 1.000000 0.998181 0.990000 1 9.900000e-01 1 PPP4R2 151987 broad.mit.edu 37 3 73047308 73047308 + Splice_Site SNP A A G rs150423598 TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr3:73047308A>G ENST00000356692.5 + 2 368 c.115A>G c.(115-117)Atg>Gtg p.M39V PPP4R2_ENST00000295862.9_5'UTR|PPP4R2_ENST00000495566.1_Splice_Site_p.M39V|PPP4R2_ENST00000394284.3_Splice_Site_p.I39V Q9NY27 PP4R2_HUMAN protein phosphatase 4, regulatory subunit 2 12 Prostate(10;0.0187)|Lung SC(41;0.236) TGGAGAAACAATGTGAGTTGA 0.348000 0 SO:0001630 splice_region_variant ENST00000356692.5 0 0 hg19 CCDS2917.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 9.536|9.536 1.112046|1.112046 0.20795|0.20795 0.0|0.0 1.16E-4|1.16E-4 ENSG00000163605|ENSG00000163605 ENST00000394284|ENST00000356692;ENST00000488810;ENST00000495566;ENST00000476505 T|T;T;T;T 0.40756|0.39406 1.02|1.08;1.08;1.08;1.08 5.46|5.46 5.46|5.46 0.80206|0.80206 .|. .|0.122413 .|0.64402 .|D .|0.000001 T|T 0.25606|0.25606 0.0623|0.0623 N|N 0.20328|0.20328 0.56|0.56 0.80722|0.80722 D|D 1|1 B|B 0.02656|0.02656 0.0|0.0 B|B 0.01281|0.04013 0.0|0.001 T|T 0.11179|0.11179 -1.0598|-1.0598 8|9 .|. .|. .|. .|. 9.1019|9.1019 0.36673|0.36673 0.9171:0.0:0.0829:0.0|0.9171:0.0:0.0829:0.0 .|. 39|39 Q9NY27-2|Q9NY27 .|PP4R2_HUMAN V|V 39|39;39;39;1 ENSP00000377825:I39V|ENSP00000349124:M39V;ENSP00000418750:M39V;ENSP00000418675:M39V;ENSP00000420098:M1V .|. I|M +|+ 1|1 0|0 PPP4R2|PPP4R2 73129998|73129998 0.996000|0.996000 0.38824|0.38824 1.000000|1.000000 0.80357|0.80357 0.994000|0.994000 0.84299|0.84299 3.326000|3.326000 0.52037|0.52037 2.077000|2.077000 0.62373|0.62373 0.533000|0.533000 0.62120|0.62120 ATT|ATG TCGA-2J-AAB4-01A-12D-A40W-08 PPP4R2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352321.1 1 0 1 70 478 0 155 0 9.609307e-01 1 37 0 155 2 0 0 0 0 0 2 1 1.000000 70 472 0 155 2 -20.000000 1 1 121410 1 36 1 0 1 1 2.008791 0 0.300000 1.950000 0.297894 0.840000 6.700000e-01 1.000000 1.000000 0.851242 0.840000 0 7.500000e-01 9.500000e-01 EVC 2121 broad.mit.edu 37 4 5800472 5800472 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr4:5800472C>T ENST00000264956.6 + 15 2441 c.2257C>T c.(2257-2259)Cgg>Tgg p.R753W EVC_ENST00000515113.1_3'UTR|EVC_ENST00000382674.2_Missense_Mutation_p.R753W NM_153717.2 NP_714928.1 P57679 EVC_HUMAN Ellis van Creveld syndrome 28 Myeloproliferative disorder(84;0.117) GGTGCATGCACGGAATGCAGC 0.637000 0 SO:0001583 missense ENST00000264956.6 0 1 hg19 CCDS3383.1 . . . . . . . . . . C 12.61 1.988209 0.35036 . . ENSG00000072840 ENST00000264956;ENST00000382674 T;T 0.59906 0.23;0.23 5.08 4.21 0.49690 . 0.273076 0.32640 N 0.005837 T 0.72334 0.3447 M 0.66939 2.045 0.38150 D 0.938729 D 0.89917 1.0 D 0.87578 0.998 T 0.76602 -0.2899 10 0.62326 D 0.03 . 12.2208 0.54433 0.178:0.822:0.0:0.0 . 753 P57679 EVC_HUMAN W 753 ENSP00000264956:R753W;ENSP00000372120:R753W ENSP00000264956:R753W R + 1 2 EVC 5851373 0.143000 0.22626 0.024000 0.17045 0.027000 0.11550 0.701000 0.25616 1.068000 0.40764 0.561000 0.74099 CGG TCGA-2J-AAB4-01A-12D-A40W-08 EVC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206859.1 1 0 0 8 74 0 11 0 9.700929e-02 0 5 0 11 2 0 0 0 0 0 2 1 0.990089 8 73 0 11 2 -13.816400 1 1 121222 2 26 1 0 0 0 1.999802 0 0.300000 1.950000 0.295775 0.660000 3.200000e-01 1.000000 1.000000 0.678718 0.660000 0 4.700000e-01 8.900000e-01 PCDHA11 56138 broad.mit.edu 37 5 140250312 140250312 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr5:140250312C>T ENST00000398640.2 + 1 1624 c.1624C>T c.(1624-1626)Ccg>Tcg p.P542S PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron NM_018902.3 NP_061725.1 Q9Y5I1 PCDAB_HUMAN protocadherin alpha 11 2 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGCGGGCGTGCCGCCTCTGAG 0.692000 0 SO:0001583 missense ENST00000398640.2 0 1 hg19 CCDS47284.1 . . . . . . . . . . C 19.23 3.788483 0.70337 . . ENSG00000249158 ENST00000398640 T 0.56776 0.44 5.15 5.15 0.70609 Cadherin (4);Cadherin-like (1); . . . . T 0.78698 0.4324 M 0.92026 3.265 0.35643 D 0.811176 D;D 0.89917 1.0;1.0 D;D 0.71414 0.969;0.973 D 0.87476 0.2417 9 0.87932 D 0 . 18.2779 0.90089 0.0:1.0:0.0:0.0 . 542;542 Q9Y5I1-2;Q9Y5I1 .;PCDAB_HUMAN S 542 ENSP00000381636:P542S ENSP00000381636:P542S P + 1 0 PCDHA11 140230496 0.999000 0.42202 0.994000 0.49952 0.949000 0.60115 5.585000 0.67497 2.398000 0.81561 0.556000 0.70494 CCG TCGA-2J-AAB4-01A-12D-A40W-08 PCDHA11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372885.2 0 0 0 7 661 0 159 0 0 0 0 159 2 0 0 0 0 0 2 1 0.977381 8 631 0 156 2 -2.017701 0 1 0 0 1 1 2 3 2.015780 0 0.300000 1.950000 0.301048 0.070000 2.000000e-02 0.140000 0.070000 0.079458 0.070000 0 4.000000e-02 1.100000e-01 SYNE1 23345 broad.mit.edu 37 6 152539461 152539461 + Missense_Mutation SNP T T C TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr6:152539461T>C ENST00000367255.5 - 121 22723 c.22122A>G c.(22120-22122)atA>atG p.I7374M SYNE1_ENST00000341594.5_Missense_Mutation_p.I6986M|SYNE1_ENST00000265368.4_Missense_Mutation_p.I7374M|SYNE1_ENST00000448038.1_Missense_Mutation_p.I7303M|SYNE1_ENST00000356820.4_Missense_Mutation_p.I1898M|SYNE1_ENST00000423061.1_Missense_Mutation_p.I7303M NM_182961.3 NP_892006.3 Q8NF91 SYNE1_HUMAN spectrin repeat containing, nuclear envelope 1 524 Ovarian(120;0.0955) BRCA - Breast invasive adenocarcinoma(37;0.243) GCCCTTGTAGTATTTCTTCAG 0.433000 HNSCC(10;0.0054) 0 SO:0001583 missense ENST00000367255.5 1 1 hg19 CCDS5236.2 . . . . . . . . . . T 12.11 1.839662 0.32513 . . ENSG00000131018 ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251 T;T;T;T;T;T;T;T 0.52754 0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65 5.68 -11.4 0.00090 . 0.421595 0.22458 N 0.059793 T 0.14917 0.0360 L 0.34521 1.04 0.09310 N 1 P;P;P;P 0.48764 0.915;0.915;0.896;0.915 P;P;P;P 0.52514 0.701;0.701;0.575;0.701 T 0.26538 -1.0100 10 0.46703 T 0.11 . 1.5785 0.02629 0.2272:0.2006:0.369:0.2032 . 7374;7374;7303;7303 Q8NF91;E7EQI5;Q8NF91-4;E9PEL9 SYNE1_HUMAN;.;.;. M 7374;20;7303;7374;7303;6986;1898;296 ENSP00000356224:I7374M;ENSP00000356226:I20M;ENSP00000396024:I7303M;ENSP00000265368:I7374M;ENSP00000390975:I7303M;ENSP00000341887:I6986M;ENSP00000349276:I1898M;ENSP00000356220:I296M ENSP00000265368:I7374M I - 3 3 SYNE1 152581154 0.000000 0.05858 0.000000 0.03702 0.251000 0.25915 -1.289000 0.02780 -2.729000 0.00385 -0.321000 0.08615 ATA TCGA-2J-AAB4-01A-12D-A40W-08 SYNE1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000334755.2 1 0 1 206 1185 0 330 0 7.399696e-01 0 17 0 330 2 0 0 0 0 0 2 1 1.000000 202 1166 0 328 2 -20.000000 1 1 0 0 1 0 0 0 2.000252 0 0.300000 1.950000 0.295775 0.970000 8.500000e-01 1.000000 1.000000 0.965202 0.970000 1 9.100000e-01 1 GABBR1 2550 broad.mit.edu 37 6 29574715 29574715 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr6:29574715C>T ENST00000377034.4 - 18 2511 c.2176G>A c.(2176-2178)Gcc>Acc p.A726T GABBR1_ENST00000355973.3_Missense_Mutation_p.A609T|GABBR1_ENST00000377016.4_Missense_Mutation_p.A664T|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000377012.4_Missense_Mutation_p.A609T NM_001470.2 NP_001461.1 Q9UBS5 GABR1_HUMAN gamma-aminobutyric acid (GABA) B receptor, 1 p.A726T(1) 47 Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080) TGCCAGATGGCGAGAGTGAGG 0.577000 1 Substitution - Missense(1) SO:0001583 missense ENST00000377034.4 1 1 hg19 CCDS4663.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 8.202|8.202 0.798448|0.798448 0.16397|0.16397 .|. .|. ENSG00000204681|ENSG00000204681 ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034|ENST00000485026 D;D;D;D|. 0.87491|. -2.26;-2.26;-2.26;-2.26|. 4.27|4.27 4.27|4.27 0.50696|0.50696 GPCR, family 3, C-terminal (2);|. 0.374080|. 0.26109|. N|. 0.026294|. T|T 0.14227|0.14227 0.0344|0.0344 N|N 0.01624|0.01624 -0.795|-0.795 0.47308|0.47308 D|D 0.999387|0.999387 P;P;P|. 0.48503|. 0.911;0.91;0.91|. B;B;B|. 0.38056|. 0.224;0.264;0.195|. T|T 0.16100|0.16100 -1.0414|-1.0414 10|5 0.14656|. T|. 0.56|. -14.1093|-14.1093 14.5609|14.5609 0.68136|0.68136 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 664;726;609|. Q9UBS5-3;Q9UBS5;Q5SUJ9|. .;GABR1_HUMAN;.|. T|H 609;664;609;726|106 ENSP00000348248:A609T;ENSP00000366215:A664T;ENSP00000366211:A609T;ENSP00000366233:A726T|. ENSP00000348248:A609T|. A|R -|- 1|2 0|0 GABBR1|GABBR1 29682694|29682694 0.852000|0.852000 0.29690|0.29690 0.930000|0.930000 0.37139|0.37139 0.882000|0.882000 0.50991|0.50991 1.632000|1.632000 0.37102|0.37102 2.075000|2.075000 0.62263|0.62263 0.563000|0.563000 0.77884|0.77884 GCC|CGC TCGA-2J-AAB4-01A-12D-A40W-08 GABBR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076141.3 1 0 1 35 207 0 48 1 9.867191e-01 5 38 0 48 2 0 0 0 0 0 2 1 1.000000 34 204 0 48 2 -3.228534 1 1 121408 1 32 1 0 1 1 1.716742 1 0.300000 1.950000 0.179367 0.800000 5.800000e-01 0.990000 0.810000 0.805092 0.800000 0 6.800000e-01 9.200000e-01 ABCC10 89845 broad.mit.edu 37 6 43413586 43413586 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr6:43413586C>T ENST00000372530.4 + 15 3495 c.3280C>T c.(3280-3282)Cgc>Tgc p.R1094C ABCC10_ENST00000244533.3_Missense_Mutation_p.R1066C NM_001198934.1 NP_001185863.1 Q5T3U5 MRP7_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 10 56 all_lung(25;0.00536) Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804) Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541) GGAGCTGCGGCGCCTGGGCAG 0.652000 0 SO:0001583 missense ENST00000372530.4 1 1 hg19 CCDS56430.1 . . . . . . . . . . C 22.5 4.299799 0.81136 . . ENSG00000124574 ENST00000372530;ENST00000244533 D;D 0.94376 -3.41;-3.41 4.81 3.92 0.45320 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.000000 0.85682 D 0.000000 D 0.97321 0.9124 H 0.97131 3.945 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.98014 1.0367 10 0.87932 D 0 -11.614 12.2499 0.54591 0.3088:0.6912:0.0:0.0 . 1066;1094 Q5T3U5-2;Q5T3U5 .;MRP7_HUMAN C 1094;1066 ENSP00000361608:R1094C;ENSP00000244533:R1066C ENSP00000244533:R1066C R + 1 0 ABCC10 43521564 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.755000 0.68750 1.200000 0.43188 0.655000 0.94253 CGC TCGA-2J-AAB4-01A-12D-A40W-08 ABCC10-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040603.2 1 0 1 39 221 0 42 1 9.322959e-01 7 21 0 42 2 0 0 0 0 0 2 1 1.000000 38 214 0 42 2 -3.231492 1 1 121400 5 37 1 0 0 0 2.000252 0 0.300000 1.950000 0.295775 0.980000 7.200000e-01 1.000000 1.000000 0.943224 0.980000 1 8.500000e-01 1 KLHL31 401265 broad.mit.edu 37 6 53519025 53519025 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr6:53519025G>A ENST00000407079.1 - 1 1045 c.1046C>T c.(1045-1047)aCg>aTg p.T349M KLHL31_ENST00000370905.3_Missense_Mutation_p.T349M Q9H511 KLH31_HUMAN kelch-like family member 31 20 Lung NSC(77;0.0158) TGGCATTTCCGTAAGCTTGCT 0.483000 0 SO:0001583 missense ENST00000407079.1 0 1 hg19 CCDS34478.1 . . . . . . . . . . G 17.70 3.453374 0.63290 . . ENSG00000124743 ENST00000370905;ENST00000407079 T;T 0.68025 -0.3;-0.3 5.25 5.25 0.73442 Galactose oxidase, beta-propeller (1); 0.095468 0.64402 D 0.000001 T 0.75852 0.3906 M 0.82716 2.605 0.58432 D 0.999994 D 0.76494 0.999 P 0.57283 0.817 T 0.80621 -0.1301 10 0.87932 D 0 . 15.4902 0.75600 0.0:0.1482:0.8518:0.0 . 349 Q9H511 KLH31_HUMAN M 349 ENSP00000359942:T349M;ENSP00000384644:T349M ENSP00000359942:T349M T - 2 0 KLHL31 53626984 1.000000 0.71417 0.994000 0.49952 0.980000 0.70556 7.818000 0.86416 2.467000 0.83353 0.561000 0.74099 ACG TCGA-2J-AAB4-01A-12D-A40W-08 KLHL31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040965.1 0 0 0 5 358 0 102 0 3.143948e-04 0 2 0 102 2 0 0 0 0 0 2 1 0.936587 5 355 0 102 2 -2.509486 1 1 0 0 1 0 0 0 2.000252 0 0.300000 1.950000 0.295775 0.090000 3.000000e-02 0.200000 0.090000 0.108222 0.090000 0 5.000000e-02 1.500000e-01 DNAH11 8701 broad.mit.edu 37 7 21727066 21727066 + Silent SNP C C A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr7:21727066C>A ENST00000409508.3 + 34 5876 c.5845C>A c.(5845-5847)Cga>Aga p.R1949R DNAH11_ENST00000328843.6_Silent_p.R1956R NM_001277115.1 NP_001264044.1 Q96DT5 DYH11_HUMAN dynein, axonemal, heavy chain 11 230 TGAGTTCAACCGAATCTCTGT 0.443000 Kartagener syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000409508.3 1 1 hg19 TCGA-2J-AAB4-01A-12D-A40W-08 DNAH11-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000326582.6 0 0 1 21 114 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999998 20 112 0 32 2 -3.016489 1 1 121396 2 35 1 0 0 0 2.006018 0 0.300000 1.950000 0.295775 0.990000 6.700000e-01 1.000000 1.000000 0.940766 0.990000 1 8.300000e-01 1 HECW1 23072 broad.mit.edu 37 7 43580819 43580819 + Silent SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr7:43580819C>T ENST00000395891.2 + 25 4682 c.4077C>T c.(4075-4077)gaC>gaT p.D1359D HECW1_ENST00000453890.1_Silent_p.D1325D NM_015052.3 NP_055867.3 Q76N89 HECW1_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 125 ACCTTCTTGACGCTTTCTTCA 0.522000 0 SO:0001819 synonymous_variant ENST00000395891.2 1 1 hg19 CCDS5469.2 . . . . . . . . . . C 7.599 0.672376 0.14776 . . ENSG00000002746 ENST00000429529 . . . 5.83 -11.7 0.00046 . . . . . T 0.64260 0.2582 . . . 0.80722 D 1 . . . . . . T 0.77778 -0.2460 4 . . . . 19.7666 0.96346 0.0:0.5708:0.0:0.4292 . . . . M 83 . . T + 2 0 HECW1 43547344 0.161000 0.22892 0.071000 0.20095 0.828000 0.46876 -0.564000 0.05936 -2.493000 0.00515 -0.965000 0.02619 ACG TCGA-2J-AAB4-01A-12D-A40W-08 HECW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250893.2 1 0 0 48 425 0 100 0 1.083591e-02 0 2 0 100 2 0 0 0 0 0 2 1 1.000000 48 424 0 98 2 -16.041640 1 1 120934 1 27 1 0 0 0 2.006018 0 0.300000 1.950000 0.295775 0.670000 5.000000e-01 0.860000 0.670000 0.680132 0.670000 0 5.800000e-01 7.700000e-01 SUMF2 25870 broad.mit.edu 37 7 56142409 56142409 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr7:56142409C>T ENST00000413756.1 + 5 538 c.515C>T c.(514-516)gCc>gTc p.A172V SUMF2_ENST00000434526.2_Missense_Mutation_p.A191V|SUMF2_ENST00000437307.2_Intron|SUMF2_ENST00000395435.2_Intron|SUMF2_ENST00000395436.2_Missense_Mutation_p.A176V|SUMF2_ENST00000342190.6_Missense_Mutation_p.A191V|SUMF2_ENST00000275607.9_Missense_Mutation_p.A84V Q8NBJ7 SUMF2_HUMAN sulfatase modifying factor 2 14 Breast(14;0.214) Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099) TGGGAGTTTGCCGCCCGAGGG 0.567000 OREG0018081 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000413756.1 0 1 hg19 . . . . . . . . . . C 36 5.686691 0.96784 . . ENSG00000129103 ENST00000395436;ENST00000434526;ENST00000275607;ENST00000413952;ENST00000342190;ENST00000413756;ENST00000451338 D;D;D;D;D;D;D 0.98968 -5.28;-5.28;-5.28;-5.28;-5.28;-5.28;-5.28 5.53 5.53 0.82687 C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2); 0.000000 0.85682 D 0.000000 D 0.99309 0.9758 M 0.90198 3.095 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;0.951 D 0.99226 1.0880 10 0.87932 D 0 -11.665 18.8414 0.92186 0.0:1.0:0.0:0.0 . 176;172;191 A8MXB9;Q8NBJ7;F8WA42 .;SUMF2_HUMAN;. V 176;191;84;194;191;172;189 ENSP00000378824:A176V;ENSP00000400922:A191V;ENSP00000275607:A84V;ENSP00000414434:A194V;ENSP00000341938:A191V;ENSP00000406445:A172V;ENSP00000410796:A189V ENSP00000275607:A84V A + 2 0 SUMF2 56109903 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.607000 0.82883 2.777000 0.95525 0.591000 0.81541 GCC TCGA-2J-AAB4-01A-12D-A40W-08 SUMF2-013 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000341457.2 0 0 0 6 435 0 105 0 9.294211e-01 0 345 0 105 2 0 0 0 0 0 2 1 0.963187 6 428 0 103 2 -1.915724 0 1 0 0 1 0 0 0 2.006018 0 0.300000 1.950000 0.295775 0.090000 3.000000e-02 0.190000 0.090000 0.104150 0.090000 0 6.000000e-02 1.400000e-01 ZP3 7784 broad.mit.edu 37 7 76062797 76062797 + Silent SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr7:76062797C>T ENST00000394857.3 + 4 604 c.546C>T c.(544-546)aaC>aaT p.N182N ZP3_ENST00000416245.1_Silent_p.N6N|ZP3_ENST00000336517.4_Silent_p.N131N NM_001110354.1 NP_001103824.1 P21754 ZP3_HUMAN zona pellucida glycoprotein 3 (sperm receptor) 7 AGAACTGGAACGCTGAGAAGA 0.597000 0 SO:0001819 synonymous_variant ENST00000394857.3 1 1 hg19 CCDS47618.1 . . . . . . . . . . C 3.906 -0.021105 0.07634 . . ENSG00000188372 ENST00000394860 . . . 5.4 -2.82 0.05787 . . . . . T 0.18593 0.0446 . . . 0.09310 N 1 . . . . . . T 0.27088 -1.0084 4 . . . -12.4296 1.8203 0.03109 0.1105:0.2938:0.2176:0.3782 . . . . M 4 . . T + 2 0 ZP3 75900733 0.000000 0.05858 0.006000 0.13384 0.117000 0.20001 -3.225000 0.00550 -0.242000 0.09667 -0.258000 0.10820 ACG TCGA-2J-AAB4-01A-12D-A40W-08 ZP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253004.1 1 0 1 52 251 0 58 1 7.558091e-01 2 13 0 58 2 0 0 0 0 0 2 1 1.000000 51 246 0 58 2 -20.000000 1 1 121410 5 37 1 0 0 0 2.006018 0 0.300000 1.950000 0.295775 0.990000 8.700000e-01 1.000000 1.000000 0.989322 0.990000 1 9.900000e-01 1 ZNF483 158399 broad.mit.edu 37 9 114304261 114304261 + Missense_Mutation SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr9:114304261G>A ENST00000309235.5 + 6 1204 c.1046G>A c.(1045-1047)cGc>cAc p.R349H ZNF483_ENST00000358151.4_Intron NM_133464.2 NP_597721.2 Q8TF39 ZN483_HUMAN zinc finger protein 483 p.R349H(1) 31 GTTCTGAACCGCAAGGAGAAA 0.423000 1 Substitution - Missense(1) SO:0001583 missense ENST00000309235.5 0 1 hg19 CCDS35106.1 . . . . . . . . . . G 10.19 1.281994 0.23392 . . ENSG00000173258 ENST00000309235 T 0.04917 3.53 4.55 2.71 0.32032 . 0.470780 0.18592 N 0.136701 T 0.01489 0.0048 N 0.00138 -2.015 0.25163 N 0.990339 B 0.18968 0.032 B 0.10450 0.005 T 0.43798 -0.9369 10 0.30854 T 0.27 -6.2832 9.1112 0.36730 0.1807:0.0:0.8193:0.0 . 349 Q8TF39 ZN483_HUMAN H 349 ENSP00000311679:R349H ENSP00000311679:R349H R + 2 0 ZNF483 113344082 0.000000 0.05858 0.765000 0.31456 0.035000 0.12851 0.761000 0.26489 0.858000 0.35431 -0.150000 0.13652 CGC TCGA-2J-AAB4-01A-12D-A40W-08 ZNF483-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053641.1 0 0 0 9 693 0 167 0 0 0 1 0 167 2 0 0 0 0 0 2 1 0.993865 9 683 0 167 2 -2.058381 0 1 121412 4 41 1 0 0 0 2.001353 0 0.300000 1.950000 0.295775 0.080000 3.000000e-02 0.160000 0.080000 0.093809 0.080000 0 5.000000e-02 1.200000e-01 DENND1A 57706 broad.mit.edu 37 9 126144428 126144428 + Silent SNP G G C TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr9:126144428G>C ENST00000373624.2 - 22 2514 c.2313C>G c.(2311-2313)ggC>ggG p.G771G DENND1A_ENST00000542603.1_Silent_p.G556G|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Silent_p.G782G NM_020946.1 NP_065997.1 Q8TEH3 DEN1A_HUMAN DENN/MADD domain containing 1A 43 CAGCCCCGGGGCCAGGGCTGA 0.716000 0 SO:0001819 synonymous_variant ENST00000373624.2 0 1 hg19 CCDS35133.1 TCGA-2J-AAB4-01A-12D-A40W-08 DENND1A-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053997.1 1 0 0 11 51 0 12 1 3.859287e-01 2 5 0 12 2 0 0 0 0 0 2 1 0.998611 11 49 0 12 2 -19.934610 1 1 0 0 1 1 2 3 2.021689 0 0.300000 1.950000 0.302094 0.990000 6.500000e-01 1.000000 1.000000 0.958306 0.990000 1 8.900000e-01 1 KCNV2 169522 broad.mit.edu 37 9 2718192 2718192 + Silent SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr9:2718192C>T ENST00000382082.3 + 1 691 c.453C>T c.(451-453)ttC>ttT p.F151F NM_133497.3 NP_598004.1 Q8TDN2 KCNV2_HUMAN potassium channel, subfamily V, member 2 35 AATACTTCTTCGACCGCGACC 0.652000 0 SO:0001819 synonymous_variant ENST00000382082.3 0 1 hg19 CCDS6447.1 TCGA-2J-AAB4-01A-12D-A40W-08 KCNV2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051528.1 1 0 1 8 69 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 0.990670 8 69 0 13 2 -14.404920 1 1 121358 3 29 1 0 0 0 2.001353 0 0.300000 1.950000 0.295775 0.700000 3.400000e-01 1.000000 1.000000 0.714261 0.700000 0 5.000000e-01 9.500000e-01 DOCK8 81704 broad.mit.edu 37 9 372257 372257 + Missense_Mutation SNP C C T TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr9:372257C>T ENST00000453981.1 + 18 2192 c.2080C>T c.(2080-2082)Cca>Tca p.P694S DOCK8_ENST00000432829.2_Missense_Mutation_p.P626S|DOCK8_ENST00000382331.1_5'UTR|DOCK8_ENST00000382329.1_Missense_Mutation_p.P161S|DOCK8_ENST00000469391.1_Missense_Mutation_p.P626S Q8NF50 DOCK8_HUMAN dedicator of cytokinesis 8 65 all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128) GGAAAAATTGCCACCCAACTA 0.448000 0 SO:0001583 missense ENST00000453981.1 0 1 hg19 CCDS6440.2 . . . . . . . . . . C 28.8 4.948470 0.92593 . . ENSG00000107099 ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329 T;T;T;T 0.14766 2.48;2.48;2.48;2.48 5.63 5.63 0.86233 . 0.000000 0.85682 D 0.000000 T 0.42653 0.1212 M 0.78223 2.4 0.80722 D 1 D;D;D 0.89917 1.0;0.999;1.0 D;D;D 0.97110 1.0;0.996;1.0 T 0.24261 -1.0165 10 0.72032 D 0.01 . 20.0442 0.97604 0.0:1.0:0.0:0.0 . 626;161;694 E9PH09;A2A369;Q8NF50 .;.;DOCK8_HUMAN S 694;694;626;626;161 ENSP00000408464:P694S;ENSP00000394888:P626S;ENSP00000419438:P626S;ENSP00000371766:P161S ENSP00000287364:P694S P + 1 0 DOCK8 362257 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.329000 0.79170 2.814000 0.96858 0.655000 0.94253 CCA TCGA-2J-AAB4-01A-12D-A40W-08 DOCK8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171792.5 0 0 0 5 430 1 84 0 2.115534e-03 0 5 1 84 2 0 0 0 0 0 2 0 0.004233 5 423 1 83 18 -2.040655 0 1 0 0 1 0 0 0 2.001353 0 0.300000 1.950000 0.295775 0.080000 2.000000e-02 0.170000 0.080000 0.090490 0.080000 0 4.000000e-02 1.300000e-01 RLN2 6019 broad.mit.edu 37 9 5304440 5304440 + Silent SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chr9:5304440G>A ENST00000381627.3 - 1 529 c.141C>T c.(139-141)tgC>tgT p.C47C RLN2_ENST00000308420.3_Silent_p.C47C NM_134441.2 NP_604390.1 P04090 REL2_HUMAN relaxin 2 11 all_hematologic(13;0.137) Acute lymphoblastic leukemia(23;0.158) TGCTCATGCCGCAAATGGCAA 0.552000 0 SO:0001819 synonymous_variant ENST00000381627.3 0 1 hg19 CCDS6460.1 TCGA-2J-AAB4-01A-12D-A40W-08 RLN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051619.1 0 0 0 6 222 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 0.964115 6 219 0 65 2 -3.071627 1 1 121400 1 34 1 0 0 0 2.001353 0 0.300000 1.950000 0.295775 0.180000 7.000000e-02 0.350000 0.170000 0.199585 0.180000 0 1.200000e-01 2.700000e-01 GK 2710 broad.mit.edu 37 X 30718984 30718984 + Silent SNP G G A TCGA-2J-AAB4-01A-12D-A40W-08 TCGA-2J-AAB4-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c536d586-b6ba-4e8d-9ada-9ec4e90a0197 dd10ada8-8304-481c-bf31-f471efa940a3 g.chrX:30718984G>A ENST00000378943.3 + 10 974 c.795G>A c.(793-795)gtG>gtA p.V265V GK_ENST00000378945.3_Silent_p.V265V|GK-AS1_ENST00000464659.1_RNA|GK_ENST00000378946.3_Silent_p.V271V|GK_ENST00000427190.1_Silent_p.V66V|RP11-242C19.2_ENST00000497961.1_RNA NM_001128127.2 NP_001121599.1 P32189 GLPK_HUMAN glycerol kinase 4 CTGCATTGGTGGGACAAATGT 0.353000 0 SO:0001819 synonymous_variant ENST00000378943.3 1 1 hg19 CCDS48090.1 TCGA-2J-AAB4-01A-12D-A40W-08 GK-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056170.1 1 0 1 58 126 0 67 0 8.690327e-01 1 9 0 67 2 0 0 0 0 0 2 1 1.000000 58 126 0 66 2 -6.638431 1 1 0 0 1 0 1 1 0.300000 1.950000 0.300000 0.930000 7.800000e-01 1.000000 0.990000 0.930090 0.930000 1 8.600000e-01 9.900000e-01