#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
C2CD3	26005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	73829328	73829328	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:73829328C>G	ENST00000334126.7	-	9	1691	c.1465G>C	c.(1465-1467)Gtt>Ctt	p.V489L	C2CD3_ENST00000313663.7_Missense_Mutation_p.V489L			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	489					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GACTCCAGAACCTTAGATGAT	0.413																																																0													115.0	109.0	111.0					11																	73829328		2200	4293	6493	SO:0001583	missense	26005			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1465G>C	11.37:g.73829328C>G	ENSP00000334379:p.Val489Leu		C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	C	3.942	-0.013973	0.07681	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.09817	2.94;2.95	6.02	3.15	0.36227	.	0.711905	0.14175	N	0.336426	T	0.09468	0.0233	L	0.57536	1.79	0.19300	N	0.999979	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.44982	-0.9292	10	0.10377	T	0.69	0.0823	4.754	0.13075	0.1247:0.6185:0.1207:0.1361	.	489;489	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	L	489	ENSP00000334379:V489L;ENSP00000323339:V489L	ENSP00000323339:V489L	V	-	1	0	C2CD3	73506976	0.000000	0.05858	0.051000	0.19133	0.529000	0.34654	-0.880000	0.04183	0.428000	0.26173	-0.156000	0.13503	GTT		0.413	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		50	75	50	75
HOXC13	3229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	54338833	54338833	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr12:54338833G>A	ENST00000243056.3	+	2	942	c.786G>A	c.(784-786)aaG>aaA	p.K262K		NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN	homeobox C13	262					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|hair follicle development (GO:0001942)|nail development (GO:0035878)|tongue morphogenesis (GO:0043587)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(1)|skin(1)	3						GCGGGCGCAAGAAACGCGTGC	0.612			T	NUP98	AML																																		Dom	yes		12	12q13.3	3229	homeo box C13		L	0													75.0	83.0	80.0					12																	54338833		2203	4300	6503	SO:0001819	synonymous_variant	3229				CCDS8865.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123364	ENSG00000123364		"""Homeoboxes / ANTP class : HOXL subclass"""	5125	protein-coding gene	gene with protein product		142976	"""homeo box C13"""	HOX3, HOX3G		1973146, 1358459	Standard	NM_017410		Approved		uc001sei.3	P31276	OTTHUMG00000160008	ENST00000243056.3:c.786G>A	12.37:g.54338833G>A			Q5BL02|Q96J32|Q9NR24|Q9NYD5	Silent	SNP	ENST00000243056.3	37	CCDS8865.1																																																																																				0.612	HOXC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358865.2			86	144	86	144
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:7578190T>C	ENST00000269305.4	-	6	848	c.659A>G	c.(658-660)tAt>tGt	p.Y220C	TP53_ENST00000455263.2_Missense_Mutation_p.Y220C|TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.Y220C	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	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and 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.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(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)	AGGCGGCTCATAGGGCACCAC	0.557		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"""	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	GRCh37	CM015378|CM951227	TP53	M	rs121912666						102.0	94.0	97.0					17																	7578190		2203	4300	6503	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.659A>G	17.37:g.7578190T>C	ENSP00000269305:p.Tyr220Cys		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	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248510	0.80024	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99840	-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.996;1.0;0.999;0.998;1.0	D	0.96735	0.9542	10	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220C;ENSP00000352610:Y220C;ENSP00000269305:Y220C;ENSP00000398846:Y220C;ENSP00000391127:Y220C;ENSP00000391478:Y220C;ENSP00000425104:Y88C;ENSP00000423862:Y127C	ENSP00000269305:Y220C	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		45	8	45	8
DDX5	1655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	62498302	62498302	+	Missense_Mutation	SNP	T	T	G	rs372537624		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:62498302T>G	ENST00000225792.5	-	10	1535	c.1134A>C	c.(1132-1134)caA>caC	p.Q378H	DDX5_ENST00000578804.1_Missense_Mutation_p.Q378H|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000580026.1_5'Flank|MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000450599.2_Missense_Mutation_p.Q299H	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	378	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			AGTCACGCTCTTGTTGACTCT	0.378			T	ETV4	prostate																																NSCLC(22;406 813 4871 19580 40307)		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	0													62.0	58.0	60.0					17																	62498302		2203	4300	6503	SO:0001583	missense	1655			AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1134A>C	17.37:g.62498302T>G	ENSP00000225792:p.Gln378His		B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	37	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.347019	0.41599	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	6.17	4.2	0.49525	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.51736	0.1692	L	0.38649	1.16	0.80722	D	1	B;B;B	0.30664	0.126;0.159;0.289	B;B;B	0.37304	0.246;0.159;0.159	T	0.52419	-0.8578	9	0.56958	D	0.05	-7.3255	12.3973	0.55393	0.0:0.8631:0.0:0.1369	.	299;378;378	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	H	378;308;367	.	ENSP00000225792:Q367H	Q	-	3	2	DDX5	59928764	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.478000	0.35442	0.926000	0.37118	-0.242000	0.12053	CAA		0.378	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		13	53	13	53
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	39070725	39070725	+	Missense_Mutation	SNP	C	C	T	rs148540135		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:39070725C>T	ENST00000359596.3	+	100	14468	c.14468C>T	c.(14467-14469)aCg>aTg	p.T4823M	RYR1_ENST00000355481.4_Missense_Mutation_p.T4818M|RYR1_ENST00000360985.3_Missense_Mutation_p.T4818M			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4823					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGGGTCAAGACGCTGCGCACC	0.597																																																0			GRCh37	CM083554	RYR1	M	rs148540135	C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	122.0	85.0	98.0		14468,14453	4.6	1.0	19	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	RYR1	NM_000540.2,NM_001042723.1	81,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	4823/5039,4818/5034	39070725	1,13005	2203	4300	6503	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14468C>T	19.37:g.39070725C>T	ENSP00000352608:p.Thr4823Met		Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.746556	0.49257	2.27E-4	0.0	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98617	-5.03;-5.03;-5.03	4.57	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000001	D	0.99026	0.9667	M	0.80422	2.495	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99342	1.0912	10	0.36615	T	0.2	.	17.129	0.86722	0.0:1.0:0.0:0.0	.	4818;4823	P21817-2;P21817	.;RYR1_HUMAN	M	4823;4818;4818	ENSP00000352608:T4823M;ENSP00000347667:T4818M;ENSP00000354254:T4818M	ENSP00000347667:T4818M	T	+	2	0	RYR1	43762565	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.617000	0.83032	2.357000	0.79964	0.462000	0.41574	ACG		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			44	56	44	56
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	39071043	39071043	+	Missense_Mutation	SNP	G	G	T	rs118192168		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:39071043G>T	ENST00000359596.3	+	101	14545	c.14545G>T	c.(14545-14547)Gtc>Ttc	p.V4849F	RYR1_ENST00000355481.4_Missense_Mutation_p.V4844F|RYR1_ENST00000360985.3_Missense_Mutation_p.V4844F			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4849			V -> I (in MHS1 and CCD; autosomal recessive form). {ECO:0000269|PubMed:12136074, ECO:0000269|PubMed:16163667, ECO:0000269|PubMed:17226826, ECO:0000269|PubMed:18253926}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCGGTGGTCGTCTACCTGTA	0.602																																																0			GRCh37	CM021677	RYR1	M	rs118192168						152.0	116.0	128.0					19																	39071043		2203	4300	6503	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14545G>T	19.37:g.39071043G>T	ENSP00000352608:p.Val4849Phe		Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974553	0.53720	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98313	-4.86;-4.86;-4.86	4.57	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000014	D	0.99013	0.9663	M	0.87097	2.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99659	1.0993	10	0.87932	D	0	.	17.129	0.86722	0.0:0.0:1.0:0.0	.	4844;4849	P21817-2;P21817	.;RYR1_HUMAN	F	4849;4844;4844	ENSP00000352608:V4849F;ENSP00000347667:V4844F;ENSP00000354254:V4844F	ENSP00000347667:V4844F	V	+	1	0	RYR1	43762883	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.776000	0.85560	2.357000	0.79964	0.462000	0.41574	GTC		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			22	25	22	25
GBP1	2633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	89520410	89520410	+	Silent	SNP	G	G	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:89520410G>C	ENST00000370473.4	-	10	1839	c.1620C>G	c.(1618-1620)gtC>gtG	p.V540V	GBP1_ENST00000484970.1_5'UTR	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	540					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		TCAGCAACTGGACCCTGTCGT	0.433																																																0													271.0	272.0	272.0					1																	89520410		2203	4300	6503	SO:0001819	synonymous_variant	2633			BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.1620C>G	1.37:g.89520410G>C			D3DT26|Q5T8M1	Silent	SNP	ENST00000370473.4	37	CCDS718.1																																																																																				0.433	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053		86	281	86	281
RSBN1	54665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	114310931	114310931	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:114310931C>G	ENST00000261441.5	-	5	1802	c.1739G>C	c.(1738-1740)aGa>aCa	p.R580T	RSBN1_ENST00000369581.2_5'Flank	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	580						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		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)		AGCATGAGCTCTAGTCCTATC	0.433																																																0													130.0	124.0	126.0					1																	114310931		2203	4300	6503	SO:0001583	missense	54665			AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.1739G>C	1.37:g.114310931C>G	ENSP00000261441:p.Arg580Thr		A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	37	CCDS862.1	.	.	.	.	.	.	.	.	.	.	C	33	5.199348	0.94997	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.7	5.7	0.88788	.	0.044125	0.85682	D	0.000000	T	0.72598	0.3480	L	0.54323	1.7	0.80722	D	1	D	0.61080	0.989	D	0.75020	0.985	T	0.73107	-0.4087	9	0.62326	D	0.03	-9.9448	19.8336	0.96646	0.0:1.0:0.0:0.0	.	580	Q5VWQ0	RSBN1_HUMAN	T	580	.	ENSP00000261441:R580T	R	-	2	0	RSBN1	114112454	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.073000	0.71245	2.692000	0.91855	0.655000	0.94253	AGA		0.433	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		45	67	45	67
USP25	29761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	17238647	17238647	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr21:17238647A>G	ENST00000285679.6	+	20	2948	c.2579A>G	c.(2578-2580)aAc>aGc	p.N860S	USP25_ENST00000285681.2_Missense_Mutation_p.N892S|USP25_ENST00000400183.2_Missense_Mutation_p.N930S|USP25_ENST00000351097.5_Intron	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	860					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		GAAGAAGTAAACTTGGAGGAA	0.358																																																0													122.0	127.0	125.0					21																	17238647		2203	4299	6502	SO:0001583	missense	29761			AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2579A>G	21.37:g.17238647A>G	ENSP00000285679:p.Asn860Ser		C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.35|15.35	2.807202|2.807202	0.50421|0.50421	.|.	.|.	ENSG00000155313|ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183|ENST00000449491	T;T;T|.	0.25414|.	1.85;1.87;1.8|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.163089|.	0.64402|.	D|.	0.000003|.	T|T	0.71290|0.71290	0.3322|0.3322	L|L	0.59436|0.59436	1.845|1.845	0.48571|0.48571	D|D	0.999675|0.999675	P;P;B|.	0.44309|.	0.832;0.534;0.058|.	P;B;B|.	0.49421|.	0.61;0.127;0.022|.	T|T	0.69397|0.69397	-0.5156|-0.5156	10|5	0.62326|.	D|.	0.03|.	.|.	16.3839|16.3839	0.83495|0.83495	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	930;892;860|.	Q9UHP3-3;Q9UHP3-1;Q9UHP3|.	.;.;UBP25_HUMAN|.	S|A	892;860;930|159	ENSP00000285681:N892S;ENSP00000285679:N860S;ENSP00000383044:N930S|.	ENSP00000285679:N860S|.	N|T	+|+	2|1	0|0	USP25|USP25	16160518|16160518	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.387000|0.387000	0.30353|0.30353	6.822000|6.822000	0.75277|0.75277	2.258000|2.258000	0.74832|0.74832	0.533000|0.533000	0.62120|0.62120	AAC|ACT		0.358	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			17	51	17	51
FBXO7	25793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	32879927	32879927	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:32879927A>G	ENST00000266087.7	+	3	788	c.461A>G	c.(460-462)aAt>aGt	p.N154S	FBXO7_ENST00000382058.3_Missense_Mutation_p.N75S|FBXO7_ENST00000397426.1_Missense_Mutation_p.N40S	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	154	Important for interaction with CDK6.			N -> S (in Ref. 4; BAG63187). {ECO:0000305}.	cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ATTCAAGATAATGCGCATATG	0.383																																																0													123.0	115.0	117.0					22																	32879927		2203	4300	6503	SO:0001583	missense	25793			AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.461A>G	22.37:g.32879927A>G	ENSP00000266087:p.Asn154Ser		B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	A	0.077	-1.190721	0.01607	.	.	ENSG00000100225	ENST00000266087;ENST00000452138;ENST00000382058;ENST00000397426;ENST00000444207	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.45	0.0432	0.14221	.	0.837211	0.10750	N	0.638487	T	0.19805	0.0476	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17592	-1.0364	10	0.51188	T	0.08	-2.9948	4.3432	0.11120	0.4929:0.2935:0.0:0.2136	.	75;154;40	Q9Y3I1-2;Q9Y3I1;Q5TI86	.;FBX7_HUMAN;.	S	154;75;75;40;40	ENSP00000266087:N154S;ENSP00000388547:N75S;ENSP00000371490:N75S;ENSP00000380571:N40S;ENSP00000404388:N40S	ENSP00000266087:N154S	N	+	2	0	FBXO7	31209927	0.103000	0.21917	0.057000	0.19452	0.147000	0.21601	0.379000	0.20585	0.051000	0.15978	-0.580000	0.04137	AAT		0.383	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			26	47	26	47
ROCK2	9475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	11355517	11355517	+	Missense_Mutation	SNP	A	A	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:11355517A>T	ENST00000315872.6	-	15	2067	c.1619T>A	c.(1618-1620)cTt>cAt	p.L540H	ROCK2_ENST00000401753.1_Missense_Mutation_p.L297H	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	540	Interaction with PPP1R12A.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CAAATCTTCAAGTTGATCTTT	0.308																																																0													109.0	94.0	99.0					2																	11355517		1810	4072	5882	SO:0001583	missense	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.1619T>A	2.37:g.11355517A>T	ENSP00000317985:p.Leu540His		Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314831	0.81358	.	.	ENSG00000134318	ENST00000315872;ENST00000401753	D;D	0.85484	-1.99;-1.99	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.91099	0.7198	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.91965	0.5582	10	0.66056	D	0.02	.	15.0145	0.71573	1.0:0.0:0.0:0.0	.	540	O75116	ROCK2_HUMAN	H	540;297	ENSP00000317985:L540H;ENSP00000385509:L297H	ENSP00000317985:L540H	L	-	2	0	ROCK2	11272968	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.486000	0.81215	1.955000	0.56771	0.533000	0.62120	CTT		0.308	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			33	40	33	40
LIMS2	55679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	128399630	128399630	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:128399630G>A	ENST00000355119.4	-	6	819	c.654C>T	c.(652-654)caC>caT	p.H218H	LIMS2_ENST00000409455.1_Silent_p.H213H|LIMS2_ENST00000410038.1_Silent_p.H66H|LIMS2_ENST00000410011.1_Silent_p.H213H|LIMS2_ENST00000494613.1_5'Flank|LIMS2_ENST00000409808.2_Silent_p.H213H|LIMS2_ENST00000409754.1_Silent_p.H66H|LIMS2_ENST00000409286.1_Silent_p.H66H|LIMS2_ENST00000545738.2_Silent_p.H240H|LIMS2_ENST00000409254.1_Silent_p.H66H|LIMS2_ENST00000324938.5_Silent_p.H242H	NM_001161403.1	NP_001154875.1	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	218	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.H242H(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)		TCACCTCCACGTGCCACTGCT	0.677																																																1	Substitution - coding silent(1)	endometrium(1)											23.0	25.0	24.0					2																	128399630		2202	4298	6500	SO:0001819	synonymous_variant	55679			AF520987	CCDS2147.1, CCDS54394.1, CCDS54395.1, CCDS54396.1, CCDS58725.1	2q21.1	2008-02-05			ENSG00000072163	ENSG00000072163			16084	protein-coding gene	gene with protein product		607908					Standard	NM_017980		Approved		uc002tox.3	Q7Z4I7	OTTHUMG00000131529	ENST00000355119.4:c.654C>T	2.37:g.128399630G>A			A6NLH0|B4DMV1|F5H6E6|Q7Z4I2|Q7Z4I6|Q7Z4I8|Q8NFE7|Q9HA13	Silent	SNP	ENST00000355119.4	37	CCDS54395.1	.	.	.	.	.	.	.	.	.	.	g	11.15	1.554027	0.27739	.	.	ENSG00000072163	ENST00000426981	.	.	.	5.27	-7.07	0.01563	.	.	.	.	.	T	0.64394	0.2594	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68284	-0.5449	4	.	.	.	.	16.6731	0.85271	0.34:0.0:0.66:0.0	.	.	.	.	M	26	.	.	T	-	2	0	LIMS2	128116100	0.616000	0.27035	0.697000	0.30258	0.982000	0.71751	-0.289000	0.08365	-1.855000	0.01162	-0.783000	0.03347	ACG		0.677	LIMS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331133.2	NM_017980		15	26	15	26
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_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			41	48	41	48
KCNH8	131096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	19575087	19575087	+	Silent	SNP	C	C	T	rs151258565	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:19575087C>T	ENST00000328405.2	+	16	3086	c.2820C>T	c.(2818-2820)ggC>ggT	p.G940G		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	940					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						TGCAAACAGGCGGGGCTGCTT	0.542													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		18580	0.0		0.001	False		,,,				2504	0.0				NSCLC(124;1625 1765 8018 24930 42026)											0								C		2,4404	4.2+/-10.8	0,2,2201	81.0	79.0	79.0		2820	-7.2	0.0	3	dbSNP_134	79	0,8600		0,0,4300	no	coding-synonymous	KCNH8	NM_144633.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		940/1108	19575087	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2820C>T	3.37:g.19575087C>T			B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																				0.542	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		50	84	50	84
CP	1356	hgsc.bcm.edu;broad.mit.edu	37	3	148930358	148930358	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:148930358A>G	ENST00000264613.6	-	2	536	c.274T>C	c.(274-276)Ttt>Ctt	p.F92L		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	92	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GGGCCTAAAAACCCAAGCCAG	0.398																																																0													104.0	103.0	103.0					3																	148930358		2203	4300	6503	SO:0001583	missense	1356			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.274T>C	3.37:g.148930358A>G	ENSP00000264613:p.Phe92Leu		Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.633539	0.47049	.	.	ENSG00000047457	ENST00000264613;ENST00000455472	D;D	0.99462	-5.94;-5.94	5.42	2.99	0.34606	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.174928	0.52532	N	0.000065	D	0.97427	0.9158	L	0.42245	1.32	0.35600	D	0.807809	B;B	0.19583	0.037;0.037	B;B	0.25405	0.04;0.06	D	0.95640	0.8697	10	0.09338	T	0.73	-14.7078	8.2842	0.31920	0.7108:0.0:0.2892:0.0	.	92;92	A8K5A4;P00450	.;CERU_HUMAN	L	92;132	ENSP00000264613:F92L;ENSP00000426888:F132L	ENSP00000264613:F92L	F	-	1	0	CP	150413048	0.994000	0.37717	0.980000	0.43619	0.689000	0.40095	3.486000	0.53215	0.478000	0.27488	0.460000	0.39030	TTT		0.398	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		6	94	6	94
LVRN	206338	hgsc.bcm.edu;broad.mit.edu	37	5	115351039	115351039	+	Silent	SNP	T	T	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr5:115351039T>C	ENST00000357872.4	+	17	2665	c.2541T>C	c.(2539-2541)acT>acC	p.T847T	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		847						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										ATACTTACACTAATACAACAA	0.348																																																0													107.0	107.0	107.0					5																	115351039		2202	4300	6502	SO:0001819	synonymous_variant	206338																														ENST00000357872.4:c.2541T>C	5.37:g.115351039T>C			A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																				0.348	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			6	91	6	91
NKAIN2	154215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	124979504	124979504	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr6:124979504C>T	ENST00000368417.1	+	4	506	c.446C>T	c.(445-447)gCt>gTt	p.A149V	NKAIN2_ENST00000368416.1_Missense_Mutation_p.A149V|NKAIN2_ENST00000545433.1_Missense_Mutation_p.A134V|NKAIN2_ENST00000546092.1_Intron	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		ATAGAAGTGGCTCATAGTTCC	0.542																																																0													161.0	113.0	130.0					6																	124979504		2203	4300	6503	SO:0001583	missense	154215			AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"""Na+/K+ transporting ATPase interacting"""	16443	protein-coding gene	gene with protein product		609758	"""T-cell lymphoma breakpoint associated target 1"""	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.446C>T	6.37:g.124979504C>T	ENSP00000357402:p.Ala149Val		Q8IYR4|Q8TF67	Missense_Mutation	SNP	ENST00000368417.1	37	CCDS34526.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564238	0.86335	.	.	ENSG00000188580	ENST00000368416;ENST00000368417;ENST00000539866;ENST00000545433	T;T;T	0.13196	2.61;2.61;2.61	5.72	4.85	0.62838	.	0.105591	0.64402	D	0.000004	T	0.08891	0.0220	N	0.22421	0.69	0.45899	D	0.998749	P;B;P;B	0.51240	0.943;0.004;0.943;0.095	P;B;P;B	0.53912	0.737;0.007;0.737;0.058	T	0.29212	-1.0019	10	0.24483	T	0.36	-2.9332	14.6114	0.68519	0.0:0.9303:0.0:0.0697	.	134;148;149;149	B3KNZ0;Q5VXU1-3;Q5VXU1;Q5VXU1-2	.;.;NKAI2_HUMAN;.	V	149;149;148;134	ENSP00000357401:A149V;ENSP00000357402:A149V;ENSP00000437798:A134V	ENSP00000357401:A149V	A	+	2	0	NKAIN2	125021203	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.433000	0.80362	1.433000	0.47394	0.650000	0.86243	GCT		0.542	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214		38	50	38	50
EIF3B	8662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	2404028	2404028	+	Missense_Mutation	SNP	C	C	T	rs368514580		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr7:2404028C>T	ENST00000360876.4	+	6	1077	c.1021C>T	c.(1021-1023)Cgt>Tgt	p.R341C	EIF3B_ENST00000397011.2_Missense_Mutation_p.R341C	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B											breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		GACGTATGTGCGTTGGTCTCC	0.458																																																0								C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	135.0	138.0	137.0		1021,1021	5.9	1.0	7		137	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EIF3B	NM_001037283.1,NM_003751.3	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	341/815,341/815	2404028	1,13005	2203	4300	6503	SO:0001583	missense	8662			U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"""RNA binding motif (RRM) containing"""	3280	protein-coding gene	gene with protein product		603917	"""eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"""	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1021C>T	7.37:g.2404028C>T	ENSP00000354125:p.Arg341Cys			Missense_Mutation	SNP	ENST00000360876.4	37	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	C	35	5.581538	0.96565	0.0	1.16E-4	ENSG00000106263	ENST00000431643;ENST00000314800;ENST00000360876;ENST00000413917;ENST00000397011;ENST00000489558	T;T;T;T	0.57595	0.91;0.91;0.39;0.91	5.93	5.93	0.95920	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63094	0.2482	L	0.52266	1.64	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.53146	0.676;0.719	T	0.64390	-0.6419	10	0.87932	D	0	-25.5779	20.3437	0.98782	0.0:1.0:0.0:0.0	.	302;341	A4D210;P55884	.;EIF3B_HUMAN	C	69;341;341;302;341;265	ENSP00000408062:R69C;ENSP00000354125:R341C;ENSP00000407785:R302C;ENSP00000380206:R341C	ENSP00000316638:R341C	R	+	1	0	EIF3B	2370554	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.381000	0.79718	2.815000	0.96918	0.561000	0.74099	CGT		0.458	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			88	107	88	107
NUP214	8021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	134073213	134073213	+	Silent	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:134073213A>G	ENST00000359428.5	+	29	4476	c.4332A>G	c.(4330-4332)caA>caG	p.Q1444Q	NUP214_ENST00000411637.2_Silent_p.Q1434Q|NUP214_ENST00000483497.2_Silent_p.Q270Q|NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000451030.1_Silent_p.Q1445Q			P35658	NU214_HUMAN	nucleoporin 214kDa	1444	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTGGAAGCCAACAGACCAATA	0.522			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	0													129.0	119.0	122.0					9																	134073213		2203	4300	6503	SO:0001819	synonymous_variant	8021			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4332A>G	9.37:g.134073213A>G			A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	CCDS6940.1																																																																																				0.522	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		20	98	20	98
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76829760	76829760	+	Nonsense_Mutation	SNP	G	G	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrX:76829760G>C	ENST00000373344.5	-	28	6495	c.6281C>G	c.(6280-6282)tCa>tGa	p.S2094*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.S2056*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2094	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				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						CTTCTTCCTTGACTGTGCAGT	0.313			"""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)											139.0	125.0	130.0					X																	76829760		2203	4296	6499	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.6281C>G	X.37:g.76829760G>C	ENSP00000362441:p.Ser2094*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	-	49	15.142353	0.99824	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	5.45	5.45	0.79879	.	0.093852	0.45867	U	0.000331	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-4.7825	18.0086	0.89216	0.0:0.0:1.0:0.0	.	.	.	.	X	2094;2056	.	ENSP00000362441:S2094X	S	-	2	0	ATRX	76716416	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.949000	0.93012	2.288000	0.76882	0.540000	0.68198	TCA		0.313	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		75	12	75	12
CALCRL	10203	broad.mit.edu;ucsc.edu	37	2	188225389	188225389	+	Silent	SNP	T	T	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:188225389T>G	ENST00000409998.1	-	11	1498	c.717A>C	c.(715-717)acA>acC	p.T239T	CALCRL_ENST00000392370.3_Silent_p.T239T|AC007319.1_ENST00000453517.1_RNA|AC007319.1_ENST00000412276.1_RNA|CALCRL_ENST00000410068.1_Silent_p.T239T			Q16602	CALRL_HUMAN	calcitonin receptor-like	239					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			CCACAATGAGTGTGTGTAGGT	0.403																																																0													96.0	85.0	88.0					2																	188225389		2203	4300	6503	SO:0001819	synonymous_variant	10203			U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.717A>C	2.37:g.188225389T>G			A8K6G5|A8KAD3|Q53S02|Q53TS5	Silent	SNP	ENST00000409998.1	37	CCDS2293.1																																																																																				0.403	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		29	40	29	40
RSPH14	27156	broad.mit.edu;ucsc.edu	37	22	23404005	23404005	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:23404005C>T	ENST00000216036.4	-	6	968	c.772G>A	c.(772-774)Gcc>Acc	p.A258T		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		258										breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		ATCACTGTGGCGAACATCAGG	0.587																																																0													89.0	68.0	75.0					22																	23404005		2203	4300	6503	SO:0001583	missense	27156																														ENST00000216036.4:c.772G>A	22.37:g.23404005C>T	ENSP00000216036:p.Ala258Thr			Missense_Mutation	SNP	ENST00000216036.4	37	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	C	3.695	-0.062667	0.07273	.	.	ENSG00000100218	ENST00000216036	T	0.48836	0.8	4.77	3.72	0.42706	Armadillo-like helical (1);Armadillo-type fold (1);	0.444604	0.22403	N	0.060514	T	0.34454	0.0898	L	0.59436	1.845	0.21147	N	0.999775	P	0.43578	0.811	B	0.28849	0.095	T	0.30475	-0.9977	10	0.40728	T	0.16	-12.2163	7.9737	0.30143	0.0:0.8749:0.0:0.1251	.	258	Q9UHP6	RTDR1_HUMAN	T	258	ENSP00000216036:A258T	ENSP00000216036:A258T	A	-	1	0	RTDR1	21734005	0.945000	0.32115	0.014000	0.15608	0.007000	0.05969	2.613000	0.46351	1.076000	0.40961	0.462000	0.41574	GCC		0.587	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1			11	25	11	25
TBC1D4	9882	broad.mit.edu;ucsc.edu	37	13	75873512	75873512	+	Missense_Mutation	SNP	T	T	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr13:75873512T>A	ENST00000377636.3	-	17	3456	c.3110A>T	c.(3109-3111)gAc>gTc	p.D1037V	TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000425511.1_Missense_Mutation_p.D201V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.D1029V|TBC1D4_ENST00000377625.2_Missense_Mutation_p.D974V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1037	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GAAGCCGAGGTCATACATGAG	0.512																																																0													67.0	75.0	73.0					13																	75873512		2024	4180	6204	SO:0001583	missense	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3110A>T	13.37:g.75873512T>A	ENSP00000366863:p.Asp1037Val		A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.441196	0.83993	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.63	5.63	0.86233	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000001	T	0.36524	0.0970	M	0.81497	2.545	0.80722	D	1	P;P;D;D	0.89917	0.504;0.825;0.957;1.0	B;B;P;D	0.87578	0.226;0.353;0.838;0.998	T	0.17349	-1.0372	10	0.62326	D	0.03	-30.0041	15.8391	0.78831	0.0:0.0:0.0:1.0	.	201;974;1029;1037	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	V	1037;1029;974;201	ENSP00000366863:D1037V;ENSP00000395986:D1029V;ENSP00000366852:D974V;ENSP00000390654:D201V	ENSP00000366852:D974V	D	-	2	0	TBC1D4	74771513	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.698000	0.84413	2.134000	0.65973	0.482000	0.46254	GAC		0.512	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		3	40	3	40
ALS2	57679	broad.mit.edu;ucsc.edu	37	2	202609063	202609063	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:202609063G>A	ENST00000264276.6	-	10	2460	c.2088C>T	c.(2086-2088)caC>caT	p.H696H	ALS2_ENST00000457679.2_Silent_p.H8H	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	696	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TAGCTAACTCGTGGAGACTGG	0.398																																																0													138.0	129.0	132.0					2																	202609063		1865	4114	5979	SO:0001819	synonymous_variant	57679			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2088C>T	2.37:g.202609063G>A			Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	37	CCDS42800.1																																																																																				0.398	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		28	32	28	32
WNK2	65268	broad.mit.edu;ucsc.edu	37	9	96080327	96080327	+	3'UTR	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:96080327G>A	ENST00000297954.4	+	0	6912				WNK2_ENST00000356055.3_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000427277.2_Missense_Mutation_p.A1828T|WNK2_ENST00000349097.3_Intron|WNK2_ENST00000395475.2_Intron|WNK2_ENST00000395477.2_Intron	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2						intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TGGTCCACGCGCCGTCTCCAC	0.582																																																0													122.0	112.0	115.0					9																	96080327		876	1991	2867	SO:0001624	3_prime_UTR_variant	65268			AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.*18G>A	9.37:g.96080327G>A			Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.	.	.	.	.	.	.	.	.	.	G	16.36	3.101685	0.56183	.	.	ENSG00000165238	ENST00000427277	T	0.59772	0.24	4.63	-3.61	0.04556	.	.	.	.	.	T	0.26048	0.0635	.	.	.	0.09310	N	1	B	0.28584	0.216	B	0.21546	0.035	T	0.19353	-1.0308	8	0.11485	T	0.65	.	1.953	0.03370	0.3421:0.1198:0.4153:0.1228	.	2216	Q9Y3S1-2	.	T	1828	ENSP00000411181:A1828T	ENSP00000411181:A1828T	A	+	1	0	WNK2	95120148	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.046000	0.14035	-1.131000	0.02910	-1.113000	0.02065	GCC		0.582	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		9	103	9	103
ROS1	6098	broad.mit.edu;ucsc.edu	37	6	117609712	117609712	+	Silent	SNP	A	A	G	rs375228224		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr6:117609712A>G	ENST00000368508.3	-	43	7185	c.6987T>C	c.(6985-6987)ccT>ccC	p.P2329P	ROS1_ENST00000368507.3_Silent_p.P2323P	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2329					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TCAGGCCTTCAGGCTTGCCAG	0.438			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	0													109.0	104.0	106.0					6																	117609712		2203	4300	6503	SO:0001819	synonymous_variant	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6987T>C	6.37:g.117609712A>G			Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																				0.438	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			40	64	40	64
GLYAT	10249	broad.mit.edu;ucsc.edu	37	11	58477535	58477535	+	Missense_Mutation	SNP	G	G	A	rs138125182	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:58477535G>A	ENST00000344743.3	-	6	736	c.595C>T	c.(595-597)Cgc>Tgc	p.R199C	GLYAT_ENST00000529732.1_Missense_Mutation_p.R199C	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	199					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TGAATGCAGCGCTCAATGAAT	0.502													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19262	0.001		0.0	False		,,,				2504	0.0															0								G	CYS/ARG	0,4402		0,0,2201	78.0	79.0	79.0		595	5.2	0.0	11	dbSNP_134	79	2,8588	2.2+/-6.3	0,2,4293	yes	missense	GLYAT	NM_201648.2	180	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	199/297	58477535	2,12990	2201	4295	6496	SO:0001583	missense	10249			AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.595C>T	11.37:g.58477535G>A	ENSP00000340200:p.Arg199Cys		O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	37	CCDS7970.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.43	1.935409	0.34189	0.0	2.33E-4	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.19938	2.11;2.11	6.06	5.16	0.70880	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, N-terminal (1);	0.304112	0.36338	N	0.002658	T	0.52354	0.1729	M	0.91717	3.235	0.22292	N	0.999225	D	0.89917	1.0	D	0.74674	0.984	T	0.55879	-0.8071	10	0.62326	D	0.03	-10.1399	11.4349	0.50062	0.0825:0.0:0.9175:0.0	.	199	Q6IB77	GLYAT_HUMAN	C	199	ENSP00000340200:R199C;ENSP00000431688:R199C	ENSP00000340200:R199C	R	-	1	0	GLYAT	58234111	0.978000	0.34361	0.027000	0.17364	0.054000	0.15201	2.344000	0.44010	1.578000	0.49821	0.650000	0.86243	CGC		0.502	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			60	79	60	79
DOC2A	8448	broad.mit.edu;hgsc.bcm.edu	37	16	30018527	30018529	+	In_Frame_Del	DEL	CTT	CTT	-	rs139431507		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr16:30018527_30018529delCTT	ENST00000350119.4	-	6	809_811	c.619_621delAAG	c.(619-621)aagdel	p.K207del	DOC2A_ENST00000564944.1_In_Frame_Del_p.K207del|DOC2A_ENST00000564979.1_In_Frame_Del_p.K207del	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	207					nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						TGTTAAAATGCTTCTTCTGCGAA	0.635																																																0																																										SO:0001651	inframe_deletion	8448			D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.619_621delAAG	16.37:g.30018530_30018532delCTT	ENSP00000340017:p.Lys207del		B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	In_Frame_Del	DEL	ENST00000350119.4	37	CCDS10666.1																																																																																				0.635	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		45	74	45	74
CDKN2A	1029	broad.mit.edu	37	9	21974684	21974684	+	Missense_Mutation	SNP	G	G	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:21974684G>C	ENST00000304494.5	-	1	413	c.143C>G	c.(142-144)cCg>cGg	p.P48R	CDKN2A_ENST00000579755.1_Intron|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000579122.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000446177.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000498124.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000494262.1_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	48			P -> L (in CMM2 and a head and neck tumor; somatic mutation). {ECO:0000269|PubMed:10651484}.		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(25)|p.P48L(8)|p.P48R(1)|p.0(1)|p.V28_V51del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CACCTGGATCGGCCTCCGACC	0.677		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																						1351	Whole gene deletion(1316)|Unknown(25)|Substitution - Missense(9)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(278)|skin(173)|central_nervous_system(163)|lung(148)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(52)|oesophagus(50)|upper_aerodigestive_tract(49)|ovary(35)|kidney(31)|breast(30)|pancreas(29)|thyroid(14)|biliary_tract(14)|NS(12)|stomach(12)|large_intestine(7)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	GRCh37	CM970251	CDKN2A	M							76.0	90.0	85.0					9																	21974684		2203	4300	6503	SO:0001583	missense	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.143C>G	9.37:g.21974684G>C	ENSP00000307101:p.Pro48Arg		A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	37	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.022727	0.54683	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	D;D	0.94576	-3.46;-3.46	4.89	4.89	0.63831	Ankyrin repeat-containing domain (3);	.	.	.	.	D	0.96861	0.8975	M	0.86268	2.805	0.80722	D	1	D;D	0.76494	0.999;0.99	D;P	0.63877	0.919;0.842	D	0.96994	0.9724	9	0.87932	D	0	.	13.1018	0.59224	0.0:0.1617:0.8383:0.0	.	48;48	P42771;G3XAG3	CD2A1_HUMAN;.	R	48	ENSP00000307101:P48R;ENSP00000394932:P48R	ENSP00000307101:P48R	P	-	2	0	CDKN2A	21964684	0.979000	0.34478	0.971000	0.41717	0.119000	0.20118	4.091000	0.57700	2.681000	0.91329	0.655000	0.94253	CCG		0.677	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		10	21	10	21
ATRX	546	broad.mit.edu	37	X	76938044	76938044	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrX:76938044delT	ENST00000373344.5	-	9	2918	c.2704delA	c.(2704-2706)atgfs	p.M902fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.M864fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	902					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						CTTAATTCCATGATGGTCGTG	0.428			"""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)											199.0	185.0	190.0					X																	76938044		2203	4296	6499	SO:0001589	frameshift_variant	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.2704delA	X.37:g.76938044delT	ENSP00000362441:p.Met902fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.428	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		7	207	7	207
TP53	7157	broad.mit.edu	37	17	7577548	7577548	+	Missense_Mutation	SNP	C	C	T	rs28934575|rs397516437		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:7577548C>T	ENST00000269305.4	-	7	922	c.733G>A	c.(733-735)Ggc>Agc	p.G245S	TP53_ENST00000455263.2_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S|TP53_ENST00000445888.2_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.G245S	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	245	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1978757}.|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2259385}.|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575). {ECO:0000269|PubMed:8829627}.|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		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.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(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)	CGGTTCATGCCGCCCATGCAG	0.577	G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN)	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"""	420	Substitution - Missense(390)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)|Insertion - Frameshift(1)	large_intestine(119)|lung(51)|breast(38)|ovary(29)|central_nervous_system(27)|upper_aerodigestive_tract(25)|stomach(25)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(22)|urinary_tract(14)|skin(9)|liver(7)|prostate(7)|biliary_tract(5)|bone(5)|pancreas(4)|soft_tissue(3)|vulva(2)|endometrium(2)|kidney(1)|cervix(1)|salivary_gland(1)	GRCh37	CM010463|CM900210|CM920674	TP53	M	rs28934575	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	149.0	112.0	125.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	733,733,733,733,337,337,337	4.6	1.0	17	dbSNP_125	125	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	56,56,56,56,56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	245/394,245/394,245/347,245/342,113/262,113/210,113/215	7577548	1,13005	2203	4300	6503	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.733G>A	17.37:g.7577548C>T	ENSP00000269305:p.Gly245Ser		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	.	.	.	.	.	.	.	.	.	.	C	33	5.259904	0.95368	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99894	-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99878	0.9942	M	0.84585	2.705	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.976;0.992;0.999;0.999;1.0	D	0.96039	0.9023	10	0.87932	D	0	-19.4293	15.3618	0.74483	0.0:1.0:0.0:0.0	rs28934575	245;245;152;245;245;245	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	245;245;245;245;245;245;234;152;113;152	ENSP00000410739:G245S;ENSP00000352610:G245S;ENSP00000269305:G245S;ENSP00000398846:G245S;ENSP00000391127:G245S;ENSP00000391478:G245S;ENSP00000425104:G113S;ENSP00000423862:G152S	ENSP00000269305:G245S	G	-	1	0	TP53	7518273	1.000000	0.71417	0.965000	0.40720	0.974000	0.67602	7.609000	0.82925	2.564000	0.86499	0.462000	0.41574	GGC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		4	90	4	90
