#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
VPS13C	54832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	62256122	62256122	+	Missense_Mutation	SNP	A	A	C			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr15:62256122A>C	ENST00000261517.5	-	32	3316	c.3243T>G	c.(3241-3243)atT>atG	p.I1081M	VPS13C_ENST00000395898.3_Missense_Mutation_p.I1038M|VPS13C_ENST00000395896.4_Missense_Mutation_p.I1081M|VPS13C_ENST00000249837.3_Missense_Mutation_p.I1038M	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TGAAATCAATAATGTCACTAT	0.353																																																0													105.0	93.0	97.0					15																	62256122		2203	4300	6503	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3243T>G	15.37:g.62256122A>C	ENSP00000261517:p.Ile1081Met			Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	A	7.360	0.624589	0.14193	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.23348	1.91;1.91;1.91	5.66	-2.45	0.06481	.	0.656534	0.14066	N	0.343732	T	0.17066	0.0410	L	0.48642	1.525	0.09310	N	1	B;B;B;B	0.17268	0.012;0.007;0.017;0.021	B;B;B;B	0.17979	0.02;0.018;0.018;0.005	T	0.22068	-1.0227	10	0.28530	T	0.3	.	5.0159	0.14335	0.1816:0.4711:0.2552:0.0921	.	1038;1081;1038;1081	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	M	1038;1081;1081;1081	ENSP00000249837:I1038M;ENSP00000261517:I1081M;ENSP00000379233:I1081M	ENSP00000249837:I1038M	I	-	3	3	VPS13C	60043414	0.251000	0.23961	0.040000	0.18447	0.179000	0.23085	-0.264000	0.08658	-0.753000	0.04721	0.533000	0.62120	ATT		0.353	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		7	39	7	39
SMAD3	4088	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	67457635	67457635	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr15:67457635G>A	ENST00000327367.4	+	3	755	c.445G>A	c.(445-447)Gag>Aag	p.E149K	SMAD3_ENST00000439724.3_Missense_Mutation_p.E105K|SMAD3_ENST00000537194.2_5'Flank|SMAD3_ENST00000540846.2_Missense_Mutation_p.E44K	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	149	Linker.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GATCCCGGCCGAGTTCCCCCC	0.602																																																0													123.0	120.0	121.0					15																	67457635		2201	4299	6500	SO:0001583	missense	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.445G>A	15.37:g.67457635G>A	ENSP00000332973:p.Glu149Lys		A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.206858	0.79127	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724	D;D;D	0.97114	-3.71;-4.25;-3.68	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.95395	0.8505	M	0.68952	2.095	0.80722	D	1	P;B	0.39601	0.68;0.035	B;B	0.37480	0.251;0.018	D	0.95000	0.8142	10	0.11485	T	0.65	.	17.666	0.88203	0.0:0.0:1.0:0.0	.	105;149	B7Z4Z5;P84022	.;SMAD3_HUMAN	K	149;149;44;105	ENSP00000332973:E149K;ENSP00000437757:E44K;ENSP00000401133:E105K	ENSP00000332973:E149K	E	+	1	0	SMAD3	65244689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.686000	0.98664	2.171000	0.68590	0.561000	0.74099	GAG		0.602	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		56	81	56	81
CES3	23491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	67006756	67006756	+	Splice_Site	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr16:67006756G>A	ENST00000303334.4	+	13	1591		c.e13-1		CES3_ENST00000543856.1_Splice_Site|CES3_ENST00000394037.1_Splice_Site	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3							endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		CTCCCACCCAGGGACCCCAAT	0.602																																																0													86.0	92.0	90.0					16																	67006756		2200	4300	6500	SO:0001630	splice_region_variant	23491			AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1521-1G>A	16.37:g.67006756G>A			B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Splice_Site	SNP	ENST00000303334.4	37	CCDS10826.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374910	0.61735	.	.	ENSG00000172828	ENST00000303334;ENST00000394037;ENST00000543856	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.271	0.73702	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CES3	65564257	1.000000	0.71417	0.930000	0.37139	0.653000	0.38743	6.479000	0.73600	2.338000	0.79540	0.579000	0.79373	.		0.602	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	Intron	30	47	30	47
TP53	7157	hgsc.bcm.edu;broad.mit.edu	37	17	7577141	7577142	+	Missense_Mutation	DNP	CC	CC	TT	rs193920774		TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr17:7577141_7577142CC>TT	ENST00000269305.4	-	8	985_986	c.796_797GG>AA	c.(796-798)GGa>AAa	p.G266K	TP53_ENST00000359597.4_Missense_Mutation_p.G266K|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.G266K|TP53_ENST00000445888.2_Missense_Mutation_p.G266K|TP53_ENST00000455263.2_Missense_Mutation_p.G266K|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	266	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G266E(50)|p.G266R(46)|p.G266V(42)|p.G266*(14)|p.0?(8)|p.G266fs*79(5)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.N263fs*5(1)|p.G266T(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.G266fs*9(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCTGTTCCGTCCCAGTAGATTA	0.52		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"""	185	Substitution - Missense(141)|Substitution - Nonsense(14)|Deletion - In frame(9)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(3)|Insertion - Frameshift(1)	lung(36)|large_intestine(19)|oesophagus(15)|ovary(15)|breast(13)|upper_aerodigestive_tract(11)|urinary_tract(11)|haematopoietic_and_lymphoid_tissue(11)|central_nervous_system(8)|pancreas(8)|skin(7)|stomach(6)|liver(6)|endometrium(4)|bone(4)|biliary_tract(2)|vulva(1)|pleura(1)|peritoneum(1)|kidney(1)|thyroid(1)|cervix(1)|eye(1)|genital_tract(1)|salivary_gland(1)																																								SO:0001583	missense	7157	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;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.796_797delinsTT	17.37:g.7577141_7577142delinsTT	ENSP00000269305:p.Gly266Lys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.520	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		4	0	4	0
KRT34	3885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	39535942	39535942	+	Silent	SNP	G	G	A	rs144246640	byFrequency	TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr17:39535942G>A	ENST00000394001.1	-	4	786	c.756C>T	c.(754-756)aaC>aaT	p.N252N		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	252	Linker 12.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				CCACCTCCACGTTGAGGCGGT	0.557													g|||	2	0.000399361	0.0015	0.0	5008	,	,		22449	0.0		0.0	False		,,,				2504	0.0															0								A		2,4404	826.0+/-416.6	0,2,2201	84.0	67.0	73.0		756	-4.3	0.9	17	dbSNP_134	73	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous	KRT34	NM_021013.3		0,6,6497	AA,AG,GG		0.0465,0.0454,0.0461		252/437	39535942	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	3885			Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6452	protein-coding gene	gene with protein product	"""hard keratin type I 4"""	602763	"""keratin, hair, acidic, 4"""	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.756C>T	17.37:g.39535942G>A			Q8IUT8|Q8N4W2	Silent	SNP	ENST00000394001.1	37	CCDS11390.1																																																																																				0.557	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		13	18	13	18
REXO1	57455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	1828027	1828027	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr19:1828027C>T	ENST00000170168.4	-	2	855	c.761G>A	c.(760-762)cGg>cAg	p.R254Q	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	254						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGGCGGCCCGCTCATCCCG	0.652																																																0													18.0	24.0	22.0					19																	1828027		2195	4293	6488	SO:0001583	missense	57455			AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.761G>A	19.37:g.1828027C>T	ENSP00000170168:p.Arg254Gln		Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.162729	0.38217	.	.	ENSG00000079313	ENST00000170168;ENST00000413153	T	0.11604	2.76	3.83	2.75	0.32379	.	0.379404	0.24587	N	0.037252	T	0.20700	0.0498	M	0.65975	2.015	0.09310	N	1	D;D	0.69078	0.996;0.997	P;P	0.56088	0.69;0.791	T	0.01853	-1.1260	10	0.66056	D	0.02	-39.6384	8.4888	0.33086	0.0:0.8159:0.0:0.1841	.	208;254	F5H016;Q8N1G1	.;REXO1_HUMAN	Q	254;208	ENSP00000170168:R254Q	ENSP00000170168:R254Q	R	-	2	0	REXO1	1779027	0.000000	0.05858	0.525000	0.27900	0.020000	0.10135	0.377000	0.20552	1.980000	0.57719	0.561000	0.74099	CGG		0.652	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		10	14	10	14
RHPN2	85415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	33535237	33535237	+	Missense_Mutation	SNP	T	T	C			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr19:33535237T>C	ENST00000254260.3	-	2	138	c.103A>G	c.(103-105)Aaa>Gaa	p.K35E	RHPN2_ENST00000400226.4_5'UTR	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	35					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TTCTGCAATTTACTCCGGCCG	0.483																																																0													77.0	73.0	74.0					19																	33535237		2203	4300	6503	SO:0001583	missense	85415			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.103A>G	19.37:g.33535237T>C	ENSP00000254260:p.Lys35Glu		B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.176003	0.78564	.	.	ENSG00000131941	ENST00000254260	T	0.30714	1.52	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.40886	0.1135	M	0.68952	2.095	0.80722	D	1	P	0.37525	0.598	B	0.43194	0.411	T	0.40646	-0.9552	10	0.87932	D	0	-0.1404	14.5514	0.68070	0.0:0.0:0.0:1.0	.	35	Q8IUC4	RHPN2_HUMAN	E	35	ENSP00000254260:K35E	ENSP00000254260:K35E	K	-	1	0	RHPN2	38227077	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	4.499000	0.60380	2.141000	0.66446	0.459000	0.35465	AAA		0.483	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		16	29	16	29
CYP4A11	1579	hgsc.bcm.edu;broad.mit.edu	37	1	47395834	47395834	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr1:47395834G>A	ENST00000310638.4	-	12	1544	c.1513C>T	c.(1513-1515)Cgt>Tgt	p.R505C	CYP4A11_ENST00000371904.4_Missense_Mutation_p.R506C|CYP4A11_ENST00000462347.1_Missense_Mutation_p.R407C	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	505			NGIHLRLRRLPNPCEDKDQL -> MESTCVSGGSLTLVKTR TSFEGLHLPSCLPDPRFCPLPVCPYPVFCLPTFPSSHLPAV PQSACPSLSHLSPGLPTCLSTCLLPTCISCWEKS (in CYP4A11V).		arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CTCCTGAGACGCAGGTGGATT	0.587																																																0													91.0	77.0	82.0					1																	47395834		2203	4300	6503	SO:0001583	missense	1579			L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.1513C>T	1.37:g.47395834G>A	ENSP00000311095:p.Arg505Cys		Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	37	CCDS543.1	.	.	.	.	.	.	.	.	.	.	G	5.356	0.250906	0.10130	.	.	ENSG00000187048	ENST00000310638;ENST00000371904	T;T	0.70399	-0.48;-0.48	4.71	-1.24	0.09435	.	1.766020	0.02474	N	0.087836	T	0.70124	0.3188	M	0.82056	2.57	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.50162	-0.8860	10	0.54805	T	0.06	.	4.1033	0.10025	0.2876:0.0:0.3736:0.3388	.	505	Q02928	CP4AB_HUMAN	C	505;506	ENSP00000311095:R505C;ENSP00000360971:R506C	ENSP00000311095:R505C	R	-	1	0	CYP4A11	47168421	0.000000	0.05858	0.009000	0.14445	0.126000	0.20510	-1.751000	0.01821	-0.094000	0.12374	-0.150000	0.13652	CGT		0.587	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		18	27	18	27
DCLRE1B	64858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	114453833	114453833	+	Missense_Mutation	SNP	C	C	T	rs200186734		TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr1:114453833C>T	ENST00000369563.3	+	4	1065	c.619C>T	c.(619-621)Cgc>Tgc	p.R207C	DCLRE1B_ENST00000466480.1_3'UTR	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	207					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGTCCTCGGCGCCTGGAGTT	0.532								Other identified genes with known or suspected DNA repair function																																								0													91.0	89.0	90.0					1																	114453833		2203	4300	6503	SO:0001583	missense	64858			BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"""APOLLO"", ""PSO2 homolog (S. cerevisiae)"""	609683	"""DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"""				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.619C>T	1.37:g.114453833C>T	ENSP00000358576:p.Arg207Cys		Q9H9E5	Missense_Mutation	SNP	ENST00000369563.3	37	CCDS866.1	.	.	.	.	.	.	.	.	.	.	C	19.79	3.892843	0.72524	.	.	ENSG00000118655	ENST00000369563	T	0.74632	-0.86	5.47	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.78181	0.4243	M	0.72118	2.19	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.81161	-0.1059	10	0.87932	D	0	-15.3846	7.8508	0.29453	0.2774:0.6483:0.0:0.0743	.	207	Q9H816	DCR1B_HUMAN	C	207	ENSP00000358576:R207C	ENSP00000358576:R207C	R	+	1	0	DCLRE1B	114255356	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.475000	0.45162	1.319000	0.45190	0.561000	0.74099	CGC		0.532	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836		19	19	19	19
TOR1AIP2	163590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	179819995	179819995	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr1:179819995G>A	ENST00000367612.3	-	4	925	c.538C>T	c.(538-540)Cga>Tga	p.R180*	TOR1AIP2_ENST00000609928.1_Nonsense_Mutation_p.R180*	NM_145034.4	NP_659471.1	Q9H496	IFG15_HUMAN	torsin A interacting protein 2	0										cervix(1)|endometrium(3)|large_intestine(1)|lung(10)|ovary(1)|skin(2)	18						GCCAGCAGTCGCCTCCTCAGT	0.542																																																0													88.0	90.0	89.0					1																	179819995		2203	4300	6503	SO:0001587	stop_gained	163590				CCDS1334.1	1q25.2	2012-02-09			ENSG00000169905	ENSG00000169905			24055	protein-coding gene	gene with protein product		614513				15767459	Standard	NM_145034		Approved	LULL1, NET9, IFRG15	uc001gnk.3	Q8NFQ8	OTTHUMG00000035265	ENST00000367612.3:c.538C>T	1.37:g.179819995G>A	ENSP00000356584:p.Arg180*		Q05BU2	Nonsense_Mutation	SNP	ENST00000367612.3	37	CCDS1334.1	.	.	.	.	.	.	.	.	.	.	G	39	7.358017	0.98235	.	.	ENSG00000169905	ENST00000367612	.	.	.	5.11	3.21	0.36854	.	0.482830	0.18523	N	0.138703	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6068	10.6077	0.45404	0.0:0.0:0.652:0.348	.	.	.	.	X	180	.	ENSP00000356584:R180X	R	-	1	2	TOR1AIP2	178086618	0.685000	0.27652	0.955000	0.39395	0.846000	0.48090	1.710000	0.37920	0.696000	0.31696	0.563000	0.77884	CGA		0.542	TOR1AIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085304.1	NM_145034		24	36	24	36
TLK1	9874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	171871388	171871388	+	Missense_Mutation	SNP	T	T	C			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr2:171871388T>C	ENST00000431350.2	-	13	1711	c.1307A>G	c.(1306-1308)aAa>aGa	p.K436R	TLK1_ENST00000360843.3_Missense_Mutation_p.K457R|TLK1_ENST00000442919.2_Missense_Mutation_p.K388R|TLK1_ENST00000521943.1_Missense_Mutation_p.K388R|TLK1_ENST00000434911.2_Missense_Mutation_p.K340R			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	436					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GTTTATTCTTTTCAGCTCACG	0.378																																																0													117.0	114.0	115.0					2																	171871388		2202	4300	6502	SO:0001583	missense	9874			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1307A>G	2.37:g.171871388T>C	ENSP00000411099:p.Lys436Arg		B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.914864	0.92178	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.66099	-0.18;-0.18;-0.19;-0.18;-0.17	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.82268	0.5000	M	0.88450	2.955	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.995	D;D;D	0.76575	0.96;0.988;0.909	D	0.86015	0.1503	10	0.87932	D	0	.	15.7854	0.78297	0.0:0.0:0.0:1.0	.	340;457;436	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	R	388;436;457;388;340	ENSP00000402165:K388R;ENSP00000411099:K436R;ENSP00000354089:K457R;ENSP00000428113:K388R;ENSP00000409222:K340R	ENSP00000354089:K457R	K	-	2	0	TLK1	171579634	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.129000	0.65627	0.533000	0.62120	AAA		0.378	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		8	43	8	43
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			14	22	14	22
ERBB4	2066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	212587211	212587211	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr2:212587211G>C	ENST00000342788.4	-	7	1100	c.790C>G	c.(790-792)Caa>Gaa	p.Q264E	ERBB4_ENST00000436443.1_Missense_Mutation_p.Q264E|ERBB4_ENST00000402597.1_Missense_Mutation_p.Q264E|ERBB4_ENST00000484474.1_5'Flank	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	264	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ACAAAGGTTTGGGGACACTGA	0.383										TSP Lung(8;0.080)																																						0													169.0	155.0	159.0					2																	212587211		2203	4300	6503	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.790C>G	2.37:g.212587211G>C	ENSP00000342235:p.Gln264Glu		B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	G	9.124	1.009763	0.19277	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.28895	1.59;1.59;1.59	5.83	5.83	0.93111	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.35770	0.0943	L	0.34521	1.04	0.58432	D	0.999999	P;B;B;P;P	0.52170	0.94;0.05;0.038;0.94;0.951	P;B;B;P;P	0.49361	0.45;0.034;0.015;0.45;0.608	T	0.01172	-1.1429	10	0.31617	T	0.26	.	20.115	0.97926	0.0:0.0:1.0:0.0	.	264;264;123;264;264	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.;.;.;.;ERBB4_HUMAN	E	264	ENSP00000342235:Q264E;ENSP00000403204:Q264E;ENSP00000385565:Q264E	ENSP00000342235:Q264E	Q	-	1	0	ERBB4	212295456	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.789000	0.99068	2.761000	0.94854	0.650000	0.86243	CAA		0.383	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		14	13	14	13
FEZF2	55079	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	62355877	62355877	+	Missense_Mutation	SNP	T	T	C			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr3:62355877T>C	ENST00000283268.3	-	5	1555	c.1261A>G	c.(1261-1263)Act>Gct	p.T421A	FEZF2_ENST00000486811.1_Missense_Mutation_p.T421A|PTPRG-AS1_ENST00000490916.1_RNA|FEZF2_ENST00000475839.1_Missense_Mutation_p.T421A|PTPRG-AS1_ENST00000495542.1_RNA	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	421					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		TTGCCGCAAGTGGCGCACGTG	0.527																																					NSCLC(170;1772 2053 12525 15604 23984)											0													252.0	229.0	237.0					3																	62355877		2203	4300	6503	SO:0001583	missense	55079			AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"""Zinc fingers, C2H2-type"""	13506	protein-coding gene	gene with protein product		607414	"""zinc finger protein 312"""	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.1261A>G	3.37:g.62355877T>C	ENSP00000283268:p.Thr421Ala		A8K349|Q9BZ91|Q9NWB9	Missense_Mutation	SNP	ENST00000283268.3	37	CCDS2897.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.786123	0.70337	.	.	ENSG00000153266	ENST00000486811;ENST00000283268;ENST00000475839	T;T;T	0.07216	3.21;3.21;3.21	5.86	5.86	0.93980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.09774	0.0240	N	0.25647	0.755	0.80722	D	1	P	0.36909	0.573	B	0.40565	0.333	T	0.17289	-1.0374	10	0.46703	T	0.11	-11.7212	16.2453	0.82441	0.0:0.0:0.0:1.0	.	421	Q8TBJ5	FEZF2_HUMAN	A	421	ENSP00000418589:T421A;ENSP00000283268:T421A;ENSP00000418804:T421A	ENSP00000283268:T421A	T	-	1	0	FEZF2	62330917	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.163000	0.64948	2.241000	0.73720	0.533000	0.62120	ACT		0.527	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		43	68	43	68
FARS2	10667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	5369186	5369186	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr6:5369186G>A	ENST00000324331.6	+	2	719	c.383G>A	c.(382-384)aGc>aAc	p.S128N	FARS2_ENST00000274680.4_Missense_Mutation_p.S128N			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	128					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	AACTTTGACAGCCTGCTCATC	0.557																																																0													74.0	65.0	68.0					6																	5369186		2203	4300	6503	SO:0001583	missense	10667			AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	21062	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 2, mitochondrial"""	611592	"""phenylalanine-tRNA synthetase 1 (mitochondrial)"""	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.383G>A	6.37:g.5369186G>A	ENSP00000316335:p.Ser128Asn		B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	37	CCDS4494.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023815	0.54683	.	.	ENSG00000145982	ENST00000274680;ENST00000324331	T;T	0.63255	-0.03;-0.03	5.38	5.38	0.77491	Phenylalanyl-tRNA synthetase (1);	0.079876	0.85682	D	0.000000	T	0.68128	0.2967	M	0.76938	2.355	0.50039	D	0.999846	D	0.56968	0.978	P	0.57283	0.817	T	0.67745	-0.5591	10	0.36615	T	0.2	-6.2773	13.8469	0.63472	0.0764:0.0:0.9236:0.0	.	128	O95363	SYFM_HUMAN	N	128	ENSP00000274680:S128N;ENSP00000316335:S128N	ENSP00000274680:S128N	S	+	2	0	FARS2	5314185	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.641000	0.83368	2.666000	0.90696	0.655000	0.94253	AGC		0.557	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567		17	18	17	18
SYNJ2	8871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	158516963	158516963	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr6:158516963G>A	ENST00000355585.4	+	27	4133	c.4058G>A	c.(4057-4059)aGc>aAc	p.S1353N	SYNJ2_ENST00000367112.1_Missense_Mutation_p.S438N|SYNJ2_ENST00000367122.2_Missense_Mutation_p.S1308N	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1353					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CAGAGCAACAGCCAGCTTCTC	0.642																																																0													28.0	32.0	30.0					6																	158516963		2203	4300	6503	SO:0001583	missense	8871			AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.4058G>A	6.37:g.158516963G>A	ENSP00000347792:p.Ser1353Asn		Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.518915	0.27211	.	.	ENSG00000078269	ENST00000367122;ENST00000355585;ENST00000367112	D;D;T	0.93659	-3.18;-3.26;0.77	5.79	3.95	0.45737	.	0.701355	0.14568	N	0.311602	T	0.80237	0.4586	L	0.40543	1.245	0.24490	N	0.994307	B;B	0.28760	0.221;0.003	B;B	0.26517	0.07;0.003	T	0.67300	-0.5705	10	0.20519	T	0.43	.	9.7828	0.40658	0.126:0.1163:0.7578:0.0	.	748;1353	B4DLC4;O15056	.;SYNJ2_HUMAN	N	1308;1353;438	ENSP00000356089:S1308N;ENSP00000347792:S1353N;ENSP00000356079:S438N	ENSP00000347792:S1353N	S	+	2	0	SYNJ2	158436951	0.876000	0.30132	0.822000	0.32727	0.492000	0.33523	0.724000	0.25954	0.790000	0.33803	0.650000	0.86243	AGC		0.642	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			9	10	9	10
FGL2	10875	hgsc.bcm.edu;broad.mit.edu	37	7	76826042	76826042	+	Silent	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr7:76826042G>A	ENST00000248598.5	-	2	906	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L	RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	292	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						CTCTTGGTCAGAAGATGAATT	0.408																																																0													126.0	130.0	129.0					7																	76826042		2203	4300	6503	SO:0001819	synonymous_variant	10875			Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"""Fibrinogen C domain containing"""	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.874C>T	7.37:g.76826042G>A				Silent	SNP	ENST00000248598.5	37	CCDS5591.1																																																																																				0.408	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		5	72	5	72
COL1A2	1278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	94056997	94056997	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr7:94056997A>G	ENST00000297268.6	+	49	3797	c.3326A>G	c.(3325-3327)gAc>gGc	p.D1109G		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1109					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GGTGGTTATGACTTTGGTTAC	0.532										HNSCC(75;0.22)																																						0													94.0	97.0	96.0					7																	94056997		2203	4300	6503	SO:0001583	missense	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3326A>G	7.37:g.94056997A>G	ENSP00000297268:p.Asp1109Gly		P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.704790	0.48412	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89746	-2.56	5.85	5.85	0.93711	.	0.100604	0.64402	D	0.000002	D	0.86669	0.5988	N	0.20574	0.59	0.80722	D	1	P	0.37083	0.581	P	0.46825	0.528	D	0.86023	0.1508	10	0.37606	T	0.19	.	16.5479	0.84454	1.0:0.0:0.0:0.0	.	1109	P08123	CO1A2_HUMAN	G	1109;1110	ENSP00000297268:D1109G	ENSP00000297268:D1109G	D	+	2	0	COL1A2	93894933	1.000000	0.71417	0.996000	0.52242	0.113000	0.19764	7.327000	0.79147	2.371000	0.80710	0.533000	0.62120	GAC		0.532	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		34	61	34	61
FAM9B	171483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	8993591	8993591	+	Missense_Mutation	SNP	C	C	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chrX:8993591C>A	ENST00000327220.5	-	8	890	c.526G>T	c.(526-528)Gtt>Ttt	p.V176F	FAM9B_ENST00000362066.3_Missense_Mutation_p.V216F|FAM9B_ENST00000428477.1_Missense_Mutation_p.V176F			Q8IZU0	FAM9B_HUMAN	family with sequence similarity 9, member B	176						nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11		Hepatocellular(5;0.219)				TCGGAAAAAACTCTGTCACAA	0.328																																																0													79.0	76.0	77.0					X																	8993591		2203	4299	6502	SO:0001583	missense	171483				CCDS14132.1	Xp22.31	2014-02-17			ENSG00000177138	ENSG00000177138			18404	protein-coding gene	gene with protein product	"""testis expressed 39B"""	300478				12213195, 21085121, 21998597, 22936694	Standard	XM_005274456		Approved	TEX39B	uc011mhu.2	Q8IZU0	OTTHUMG00000021114	ENST00000327220.5:c.526G>T	X.37:g.8993591C>A	ENSP00000318716:p.Val176Phe		Q0IJ68|Q8N7Z8	Missense_Mutation	SNP	ENST00000327220.5	37	CCDS14132.1	.	.	.	.	.	.	.	.	.	.	C	0.036	-1.307605	0.01342	.	.	ENSG00000177138	ENST00000362066;ENST00000327220;ENST00000428477	.	.	.	0.605	-1.21	0.09524	.	.	.	.	.	T	0.17238	0.0414	N	0.16368	0.405	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.16867	-1.0388	7	0.48119	T	0.1	.	.	.	.	.	176;216	Q8IZU0;Q8N7Z8	FAM9B_HUMAN;.	F	216;176;176	.	ENSP00000318716:V176F	V	-	1	0	FAM9B	8953591	0.206000	0.23470	0.000000	0.03702	0.000000	0.00434	-0.550000	0.06034	-2.361000	0.00609	-2.168000	0.00324	GTT		0.328	FAM9B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055702.2	NM_205849		11	22	11	22
ATRX	546	hgsc.bcm.edu;ucsc.edu	37	X	76907606	76907606	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chrX:76907606C>A	ENST00000373344.5	-	15	4769	c.4555G>T	c.(4555-4557)Gag>Tag	p.E1519*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.E1481*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1519					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTAGTTACCTCTCTCAATTTT	0.438			"""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)	bone(1)											244.0	211.0	222.0					X																	76907606		2203	4300	6503	SO:0001587	stop_gained	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4555G>T	X.37:g.76907606C>A	ENSP00000362441:p.Glu1519*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	46	12.665368	0.99687	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	4.9	4.9	0.64082	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-12.3323	16.8775	0.86056	0.0:1.0:0.0:0.0	.	.	.	.	X	1519;1481	.	ENSP00000362441:E1519X	E	-	1	0	ATRX	76794262	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.301000	0.72782	2.002000	0.58637	0.594000	0.82650	GAG		0.438	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		24	38	24	38
MORC4	79710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	106185949	106185949	+	Silent	SNP	T	T	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chrX:106185949T>A	ENST00000355610.4	-	15	2446	c.2172A>T	c.(2170-2172)gcA>gcT	p.A724A	MORC4_ENST00000255495.7_Silent_p.A724A|MORC4_ENST00000535534.1_Silent_p.A472A	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	724						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						AGGATTCAACTGCTTTTCGTC	0.512																																																0													158.0	144.0	149.0					X																	106185949		2203	4300	6503	SO:0001819	synonymous_variant	79710			AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.2172A>T	X.37:g.106185949T>A			A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Silent	SNP	ENST00000355610.4	37	CCDS14525.2																																																																																				0.512	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657		42	62	42	62
SASH3	54440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	128926408	128926408	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chrX:128926408G>A	ENST00000356892.3	+	5	661	c.547G>A	c.(547-549)Gac>Aac	p.D183N	RP4-753P9.3_ENST00000432513.1_RNA	NM_018990.3	NP_061863.1	O75995	SASH3_HUMAN	SAM and SH3 domain containing 3	183	SH3.				homeostasis of number of cells within a tissue (GO:0048873)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of organ growth (GO:0046622)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tumor necrosis factor production (GO:0032760)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	12						AGTCCACACCGACTTCACTCC	0.622																																																0													114.0	108.0	110.0					X																	128926408		2203	4300	6503	SO:0001583	missense	54440			BC051881	CCDS14614.1	Xq26	2013-01-10	2008-02-18	2008-02-18	ENSG00000122122	ENSG00000122122		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	15975	protein-coding gene	gene with protein product		300441	"""chromosome X open reading frame 9"""	CXorf9		11470164	Standard	NM_018990		Approved	SLY, 753P9, SH3D6C, HACS2	uc004euu.3	O75995	OTTHUMG00000022372	ENST00000356892.3:c.547G>A	X.37:g.128926408G>A	ENSP00000349359:p.Asp183Asn		A6NCH1|A8K7K8|Q5JZ38	Missense_Mutation	SNP	ENST00000356892.3	37	CCDS14614.1	.	.	.	.	.	.	.	.	.	.	G	35	5.585994	0.96578	.	.	ENSG00000122122	ENST00000443760;ENST00000356892	T	0.09911	2.93	5.46	5.46	0.80206	Src homology-3 domain (2);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.35682	0.0940	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.08700	-1.0709	10	0.62326	D	0.03	-39.138	18.0558	0.89364	0.0:0.0:1.0:0.0	.	151;183	B4DKQ0;O75995	.;SASH3_HUMAN	N	151;183	ENSP00000349359:D183N	ENSP00000349359:D183N	D	+	1	0	SASH3	128754089	1.000000	0.71417	0.988000	0.46212	0.990000	0.78478	9.476000	0.97823	2.300000	0.77407	0.523000	0.50628	GAC		0.622	SASH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058208.1	NM_018990		27	169	27	169
SLC9A3	6550	broad.mit.edu;ucsc.edu	37	5	491957	491957	+	Silent	SNP	G	G	A	rs372546363		TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr5:491957G>A	ENST00000264938.3	-	2	450	c.441C>T	c.(439-441)gcC>gcT	p.A147A	SLC9A3_ENST00000514375.1_Silent_p.A147A	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	147					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TACCCACGACGGCGTACAACA	0.642																																																0								G		1,4387		0,1,2193	51.0	36.0	41.0		441	-9.1	0.0	5		41	0,8590		0,0,4295	no	coding-synonymous	SLC9A3	NM_004174.2		0,1,6488	AA,AG,GG		0.0,0.0228,0.0077		147/835	491957	1,12977	2194	4295	6489	SO:0001819	synonymous_variant	6550				CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.441C>T	5.37:g.491957G>A			B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																				0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		4	9	4	9
GNG12	55970	broad.mit.edu;hgsc.bcm.edu	37	1	68171150	68171151	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr1:68171150_68171151insT	ENST00000370982.3	-	4	401_402	c.202_203insA	c.(202-204)actfs	p.T68fs		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	68					cellular response to glucagon stimulus (GO:0071377)|cerebral cortex development (GO:0021987)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			lung(3)	3						GATGATGCAAGTTTTTTTATCC	0.436																																																0																																										SO:0001589	frameshift_variant	55970			AF119663	CCDS30749.1	1p31.2	2008-02-05			ENSG00000172380	ENSG00000172380			19663	protein-coding gene	gene with protein product		615405				10819326	Standard	NM_018841		Approved		uc001dea.2	Q9UBI6	OTTHUMG00000009545	ENST00000370982.3:c.203dupA	1.37:g.68171157_68171157dupT	ENSP00000360021:p.Thr68fs		Q69YP5|Q9BRV5	Frame_Shift_Ins	INS	ENST00000370982.3	37	CCDS30749.1																																																																																				0.436	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2			23	39	23	39
RBM27	54439	broad.mit.edu;hgsc.bcm.edu	37	5	145608531	145608531	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr5:145608531delA	ENST00000265271.5	+	4	492	c.326delA	c.(325-327)gaafs	p.E110fs	RBM27_ENST00000506502.1_Frame_Shift_Del_p.E110fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	110					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCAGCAGAGGAAGAACGAGAT	0.418																																																0													111.0	107.0	108.0					5																	145608531		1568	3582	5150	SO:0001589	frameshift_variant	54439			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.326delA	5.37:g.145608531delA	ENSP00000265271:p.Glu110fs		Q8IYW9	Frame_Shift_Del	DEL	ENST00000265271.5	37	CCDS43378.1																																																																																				0.418	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		27	39	27	39
NETO1	81832	broad.mit.edu;hgsc.bcm.edu	37	18	70526115	70526116	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr18:70526115_70526116insA	ENST00000327305.6	-	4	1071_1072	c.414_415insT	c.(412-417)tttgctfs	p.A139fs	NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000299430.2_Frame_Shift_Ins_p.A138fs|NETO1_ENST00000397929.1_Frame_Shift_Ins_p.A138fs|NETO1_ENST00000583169.1_Frame_Shift_Ins_p.A139fs	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	139	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		TCTCCATCAGCAAAAAATTTAA	0.342																																																0																																										SO:0001589	frameshift_variant	81832			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.415dupT	18.37:g.70526121_70526121dupA	ENSP00000313088:p.Ala139fs		Q86W85|Q8ND78|Q8TDF4	Frame_Shift_Ins	INS	ENST00000327305.6	37	CCDS12000.1																																																																																				0.342	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		14	21	14	21
TP53	7157	broad.mit.edu	37	17	7577143	7577143	+	Silent	SNP	C	C	T			TCGA-DB-A4X9-01A-11D-A26M-08	TCGA-DB-A4X9-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eea26f3f-6798-4b36-8e5c-a1de8c55f666	59d8d896-b937-4a7b-b503-f112f5570356	g.chr17:7577143C>T	ENST00000269305.4	-	8	984	c.795G>A	c.(793-795)ctG>ctA	p.L265L	TP53_ENST00000359597.4_Silent_p.L265L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Silent_p.L265L|TP53_ENST00000445888.2_Silent_p.L265L|TP53_ENST00000455263.2_Silent_p.L265L|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	265	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		L -> M (in sporadic cancers; somatic mutation).|L -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|L -> Q (in sporadic cancers; somatic mutation).|L -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.L265L(2)|p.L265P(1)|p.N263fs*5(1)|p.L265_K305del41(1)|p.G266fs*9(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGTTCCGTCCCAGTAGATTAC	0.522		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"""	24	Whole gene deletion(8)|Deletion - In frame(6)|Unknown(3)|Deletion - Frameshift(3)|Substitution - coding silent(2)|Insertion - Frameshift(1)|Substitution - Missense(1)	bone(4)|haematopoietic_and_lymphoid_tissue(3)|urinary_tract(3)|lung(3)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(2)|stomach(1)|breast(1)|eye(1)|ovary(1)|liver(1)											48.0	43.0	45.0					17																	7577143		2203	4300	6503	SO:0001819	synonymous_variant	7157	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;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.795G>A	17.37:g.7577143C>T			Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		3	0	3	0
