#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
OPN4	94233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	88418275	88418275	+	Silent	SNP	T	T	C			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr10:88418275T>C	ENST00000241891.5	+	4	626	c.459T>C	c.(457-459)ttT>ttC	p.F153F	OPN4_ENST00000372071.2_Silent_p.F164F	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	153					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GAGCTCTCTTTGGCATTTCCT	0.617																																																0													103.0	86.0	92.0					10																	88418275		2203	4300	6503	SO:0001819	synonymous_variant	94233			AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.459T>C	10.37:g.88418275T>C			B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	37	CCDS7376.1																																																																																				0.617	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		18	44	18	44
OR52A5	390054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	5153482	5153482	+	Missense_Mutation	SNP	G	G	T			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr11:5153482G>T	ENST00000307388.1	-	1	390	c.391C>A	c.(391-393)Ccc>Acc	p.P131T		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	131					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		TGTCTCAAGGGGATACAGATG	0.473																																																0													73.0	63.0	66.0					11																	5153482		2201	4298	6499	SO:0001583	missense	390054			BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"""GPCR / Class A : Olfactory receptors"""	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.391C>A	11.37:g.5153482G>T	ENSP00000303469:p.Pro131Thr			Missense_Mutation	SNP	ENST00000307388.1	37	CCDS31373.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593204	0.46214	.	.	ENSG00000171944	ENST00000307388	T	0.01887	4.58	5.22	4.31	0.51392	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000211	T	0.25606	0.0623	H	0.99545	4.62	0.48341	D	0.999631	D	0.89917	1.0	D	0.97110	1.0	T	0.51371	-0.8714	10	0.87932	D	0	.	12.5783	0.56375	0.0802:0.0:0.9198:0.0	.	131	Q9H2C5	O52A5_HUMAN	T	131	ENSP00000303469:P131T	ENSP00000303469:P131T	P	-	1	0	OR52A5	5110058	1.000000	0.71417	0.526000	0.27913	0.048000	0.14542	7.292000	0.78731	1.433000	0.47394	0.655000	0.94253	CCC		0.473	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160		12	15	12	15
ANO1	55107	hgsc.bcm.edu;broad.mit.edu	37	11	69934117	69934117	+	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr11:69934117A>G	ENST00000355303.5	+	2	673	c.368A>G	c.(367-369)gAc>gGc	p.D123G	ANO1_ENST00000538023.1_Missense_Mutation_p.D123G|ANO1_ENST00000530676.1_Missense_Mutation_p.D7G|ANO1_ENST00000398543.2_Missense_Mutation_p.D7G|ANO1_ENST00000316296.5_Missense_Mutation_p.D95G	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	123					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CACGAGGATGACAAGCGCTTC	0.672																																																0													13.0	17.0	16.0					11																	69934117		1975	4145	6120	SO:0001583	missense	55107			BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.368A>G	11.37:g.69934117A>G	ENSP00000347454:p.Asp123Gly		A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	37	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.932601	0.73442	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000531604;ENST00000316296;ENST00000530676	T;T;T;T;T;T	0.70869	-0.22;-0.22;-0.52;1.52;-0.22;-0.52	4.21	4.21	0.49690	.	0.212263	0.39615	N	0.001320	T	0.79879	0.4522	M	0.72118	2.19	0.47778	D	0.999517	D;P	0.62365	0.991;0.945	P;P	0.61800	0.894;0.468	T	0.80578	-0.1320	9	.	.	.	.	12.4818	0.55847	1.0:0.0:0.0:0.0	.	95;123	Q5XXA6-3;Q5XXA6	.;ANO1_HUMAN	G	123;123;7;123;95;7	ENSP00000347454:D123G;ENSP00000444689:D123G;ENSP00000381551:D7G;ENSP00000436392:D123G;ENSP00000319477:D95G;ENSP00000435797:D7G	.	D	+	2	0	ANO1	69611765	1.000000	0.71417	0.991000	0.47740	0.628000	0.37860	5.387000	0.66243	1.520000	0.48965	0.459000	0.35465	GAC		0.672	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		4	17	4	17
TPTE2	93492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	20025343	20025343	+	Missense_Mutation	SNP	T	T	C			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr13:20025343T>C	ENST00000400230.2	-	11	808	c.764A>G	c.(763-765)aAg>aGg	p.K255R	TPTE2_ENST00000457266.2_Missense_Mutation_p.K144R|TPTE2_ENST00000382978.1_Missense_Mutation_p.K215R|TPTE2_ENST00000400103.2_Missense_Mutation_p.K144R|TPTE2_ENST00000382975.4_Missense_Mutation_p.K215R|TPTE2_ENST00000390680.2_Missense_Mutation_p.K178R|TPTE2_ENST00000255310.6_Missense_Mutation_p.K178R|TPTE2_ENST00000382977.4_Missense_Mutation_p.K255R			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	255	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TCGATGTTTCTTATCTAGAAA	0.363																																																0													124.0	110.0	115.0					13																	20025343		2203	4299	6502	SO:0001583	missense	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.764A>G	13.37:g.20025343T>C	ENSP00000383089:p.Lys255Arg		A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	t	5.911	0.352075	0.11182	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	T;T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	2.63	1.74	0.24563	Phosphatase tensin type (1);	0.344519	0.30293	N	0.009953	T	0.13756	0.0333	N	0.12569	0.235	0.21675	N	0.999593	B;B;B	0.10296	0.002;0.003;0.003	B;B;B	0.12156	0.007;0.004;0.007	T	0.23226	-1.0194	9	.	.	.	-4.094	6.5787	0.22581	0.0:0.0:0.7054:0.2946	.	144;178;255	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	R	215;144;255;178;178;255;215;144;255;124	ENSP00000372438:K215R;ENSP00000382974:K144R;ENSP00000383089:K255R;ENSP00000255310:K178R;ENSP00000375098:K178R;ENSP00000372437:K255R;ENSP00000372435:K215R;ENSP00000442218:K144R	.	K	-	2	0	TPTE2	18923343	0.873000	0.30073	0.358000	0.25811	0.184000	0.23303	3.249000	0.51437	0.646000	0.30693	0.163000	0.16589	AAG		0.363	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		9	27	9	27
CHMP1A	5119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	89720317	89720317	+	Silent	SNP	A	A	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr16:89720317A>G	ENST00000397901.3	-	2	278	c.22T>C	c.(22-24)Ttg>Ctg	p.L8L	CHMP1A_ENST00000253475.5_Intron|CHMP1A_ENST00000547614.1_Intron|CHMP1A_ENST00000535997.2_Intron|CHMP1A_ENST00000550102.1_Silent_p.L8L	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	8					cytokinesis (GO:0000910)|gene silencing (GO:0016458)|mitotic chromosome condensation (GO:0007076)|negative regulation of transcription by glucose (GO:0045014)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|proteolysis (GO:0006508)|transcription, DNA-templated (GO:0006351)|vesicle-mediated transport (GO:0016192)	condensed nuclear chromosome (GO:0000794)|early endosome (GO:0005769)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|nuclear matrix (GO:0016363)	metallopeptidase activity (GO:0008237)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|ovary(1)	3		all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.048)		CATACCTTCAACTGGAACAGG	0.502																																																0													148.0	146.0	147.0					16																	89720317		2000	4158	6158	SO:0001819	synonymous_variant	5119			U58048	CCDS45552.1	16q24.3	2011-09-21	2011-09-21	2007-03-20	ENSG00000131165	ENSG00000131165		"""Charged multivesicular body proteins"""	8740	protein-coding gene	gene with protein product		164010	"""procollagen (type III) N-endopeptidase"", ""chromatin modifying protein 1A"""	PRSM1, PCOLN3		11559748, 11559747	Standard	NM_002768		Approved	KIAA0047, CHMP1, Vps46A	uc002fnu.4	Q9HD42	OTTHUMG00000169521	ENST00000397901.3:c.22T>C	16.37:g.89720317A>G			A2RU09|Q14468|Q15779|Q96G31	Silent	SNP	ENST00000397901.3	37	CCDS45552.1																																																																																				0.502	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		36	73	36	73
EPG5	57724	hgsc.bcm.edu;broad.mit.edu	37	18	43505774	43505774	+	Missense_Mutation	SNP	T	T	C			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr18:43505774T>C	ENST00000282041.5	-	14	2682	c.2648A>G	c.(2647-2649)aAc>aGc	p.N883S		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	883					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CACTGTCAGGTTGTAATTCAA	0.403																																																0													141.0	126.0	131.0					18																	43505774		1865	4104	5969	SO:0001583	missense	57724			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.2648A>G	18.37:g.43505774T>C	ENSP00000282041:p.Asn883Ser		A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	9.408	1.079868	0.20309	.	.	ENSG00000152223	ENST00000282041	T	0.08458	3.09	5.47	1.51	0.23008	.	0.959553	0.08751	N	0.899104	T	0.05868	0.0153	L	0.29908	0.895	0.30855	N	0.734183	B;B	0.16603	0.018;0.018	B;B	0.16722	0.016;0.011	T	0.43212	-0.9405	10	0.12103	T	0.63	-9.6051	5.8046	0.18432	0.0:0.2303:0.1329:0.6368	.	883;883	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	S	883	ENSP00000282041:N883S	ENSP00000282041:N883S	N	-	2	0	EPG5	41759772	0.535000	0.26370	0.990000	0.47175	0.995000	0.86356	0.150000	0.16263	0.467000	0.27218	0.529000	0.55759	AAC		0.403	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		6	57	6	57
ATP9A	10079	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	50314007	50314007	+	Missense_Mutation	SNP	T	T	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr20:50314007T>G	ENST00000338821.5	-	5	715	c.451A>C	c.(451-453)Aag>Cag	p.K151Q	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	151					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTAGAACTCTTCACCTTCACT	0.443																																																0													246.0	225.0	232.0					20																	50314007		2203	4300	6503	SO:0001583	missense	10079			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.451A>C	20.37:g.50314007T>G	ENSP00000342481:p.Lys151Gln		E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	T	15.27	2.785227	0.49997	.	.	ENSG00000054793	ENST00000338821	D	0.90676	-2.71	5.04	5.04	0.67666	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.044153	0.85682	D	0.000000	D	0.86100	0.5852	L	0.37561	1.115	0.80722	D	1	B	0.14438	0.01	B	0.15870	0.014	T	0.82072	-0.0638	10	0.36615	T	0.2	-40.298	14.7939	0.69863	0.0:0.0:0.0:1.0	.	151	O75110	ATP9A_HUMAN	Q	151	ENSP00000342481:K151Q	ENSP00000342481:K151Q	K	-	1	0	ATP9A	49747414	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.449000	0.80643	1.889000	0.54706	0.533000	0.62120	AAG		0.443	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		40	70	40	70
TMEM17	200728	hgsc.bcm.edu;broad.mit.edu	37	2	62729687	62729687	+	Splice_Site	SNP	T	T	C			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr2:62729687T>C	ENST00000335390.5	-	3	416		c.e3-2			NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17						cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GATTGAATACTAAAAGAAAAG	0.308																																																0													71.0	71.0	71.0					2																	62729687		2203	4300	6503	SO:0001630	splice_region_variant	200728				CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.205-2A>G	2.37:g.62729687T>C			Q53QP7|Q53R98	Splice_Site	SNP	ENST00000335390.5	37	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.945783	0.53079	.	.	ENSG00000186889	ENST00000335390	.	.	.	6.07	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.354	0.49605	0.1352:0.0:0.0:0.8647	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM17	62583191	1.000000	0.71417	0.924000	0.36721	0.788000	0.44548	7.253000	0.78320	1.076000	0.40961	0.533000	0.62120	.		0.308	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	Intron	6	18	6	18
RPIA	22934	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	89037526	89037526	+	Silent	SNP	C	C	T			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr2:89037526C>T	ENST00000283646.4	+	8	826	c.771C>T	c.(769-771)atC>atT	p.I257I		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	257					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				GGAATTTTATCTTGGACTGGA	0.433																																																0													143.0	134.0	137.0					2																	89037526		1900	4118	6018	SO:0001819	synonymous_variant	22934			L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"""ribose 5-phosphate epimerase"""	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.771C>T	2.37:g.89037526C>T			Q541P9|Q96BJ6	Silent	SNP	ENST00000283646.4	37	CCDS2004.2																																																																																				0.433	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2			19	40	19	40
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	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			14	21	14	21
ALPP	250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	233245025	233245025	+	Missense_Mutation	SNP	C	C	T	rs201259070		TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr2:233245025C>T	ENST00000392027.2	+	6	1056	c.787C>T	c.(787-789)Cgc>Tgc	p.R263C	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	263			R -> H (in dbSNP:rs2853378). {ECO:0000269|PubMed:3461452}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)	p.R263C(1)		NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GCTGGCGAAGCGCCAGGTGAT	0.667																																																1	Substitution - Missense(1)	kidney(1)											73.0	75.0	74.0					2																	233245025		2203	4300	6503	SO:0001583	missense	250			M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.787C>T	2.37:g.233245025C>T	ENSP00000375881:p.Arg263Cys		P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	.	9.825	1.186738	0.21870	.	.	ENSG00000163283	ENST00000392027	D	0.96802	-4.13	2.31	0.0197	0.14122	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	1.003840	0.08014	N	0.990937	D	0.96065	0.8718	M	0.79258	2.445	0.09310	N	1	D	0.76494	0.999	P	0.52672	0.706	D	0.88532	0.3103	10	0.51188	T	0.08	.	3.4481	0.07487	0.3001:0.4479:0.0:0.252	.	263	P05187	PPB1_HUMAN	C	263	ENSP00000375881:R263C	ENSP00000375881:R263C	R	+	1	0	ALPP	232953269	0.000000	0.05858	0.953000	0.39169	0.172000	0.22775	-0.022000	0.12480	0.295000	0.22570	0.298000	0.19748	CGC		0.667	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		25	193	25	193
SETMAR	6419	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	4355172	4355172	+	Silent	SNP	C	C	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr3:4355172C>G	ENST00000358065.4	+	2	814	c.747C>G	c.(745-747)gcC>gcG	p.A249A	SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000425863.1_Intron|SETMAR_ENST00000430981.1_Silent_p.A249A	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	249	Histone-lysine N-methyltransferase.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		TTTTTGCAGCCAAAGATATTG	0.373								Chromatin Structure																																								0													71.0	72.0	72.0					3																	4355172		2203	4300	6503	SO:0001819	synonymous_variant	6419			U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.747C>G	3.37:g.4355172C>G			B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Silent	SNP	ENST00000358065.4	37	CCDS2563.2																																																																																				0.373	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		7	34	7	34
FLNB	2317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	58120353	58120353	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr3:58120353G>A	ENST00000295956.4	+	27	4690	c.4525G>A	c.(4525-4527)Gtc>Atc	p.V1509I	FLNB_ENST00000490882.1_Missense_Mutation_p.V1540I|FLNB_ENST00000493452.1_Missense_Mutation_p.V1340I|FLNB_ENST00000358537.3_Missense_Mutation_p.V1509I|FLNB_ENST00000357272.4_Missense_Mutation_p.V1509I|FLNB_ENST00000348383.5_Missense_Mutation_p.V1509I|FLNB_ENST00000429972.2_Missense_Mutation_p.V1509I|FLNB_ENST00000419752.2_Missense_Mutation_p.V1340I	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1509	Interaction with FBLP1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TCCCTTCAAGGTCAAGGTCCT	0.488																																																0													193.0	182.0	186.0					3																	58120353		2203	4300	6503	SO:0001583	missense	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4525G>A	3.37:g.58120353G>A	ENSP00000295956:p.Val1509Ile		B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.121538	0.37436	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	T;T;D;T;T;T;D;T	0.92647	-0.8;-0.8;-3.08;-0.8;-0.8;-0.8;-3.08;-0.8	5.81	4.93	0.64822	Immunoglobulin E-set (2);Immunoglobulin-like fold (1);	0.231260	0.44483	D	0.000447	D	0.88448	0.6439	L	0.41710	1.295	0.51767	D	0.999934	B;B;B;B;B;B	0.22003	0.004;0.063;0.0;0.001;0.002;0.002	B;B;B;B;B;B	0.29942	0.012;0.109;0.001;0.014;0.005;0.005	T	0.83231	-0.0063	10	0.21014	T	0.42	.	14.3104	0.66413	0.0707:0.0:0.9293:0.0	.	1509;1540;1340;1340;1509;1509	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	I	1509;1540;1509;1509;1509;1509;1340;1340	ENSP00000295956:V1509I;ENSP00000420213:V1540I;ENSP00000351339:V1509I;ENSP00000415599:V1509I;ENSP00000232447:V1509I;ENSP00000349819:V1509I;ENSP00000418510:V1340I;ENSP00000414532:V1340I	ENSP00000295956:V1509I	V	+	1	0	FLNB	58095393	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.509000	0.45459	2.738000	0.93877	0.655000	0.94253	GTC		0.488	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		17	133	17	133
FGF5	2250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	81207567	81207567	+	Missense_Mutation	SNP	A	A	T			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr4:81207567A>T	ENST00000312465.7	+	3	774	c.548A>T	c.(547-549)aAa>aTa	p.K183I	FGF5_ENST00000456523.3_3'UTR|FGF5_ENST00000503413.1_3'UTR	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	183					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						AGAACTGAAAAAACAGGGCGG	0.468																																																0													95.0	108.0	104.0					4																	81207567		2203	4300	6503	SO:0001583	missense	2250			M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"""Endogenous ligands"""	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.548A>T	4.37:g.81207567A>T	ENSP00000311697:p.Lys183Ile		B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	37	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.575072	0.28092	.	.	ENSG00000138675	ENST00000312465	T	0.67865	-0.29	5.82	0.437	0.16555	.	0.749481	0.13420	N	0.389234	T	0.64616	0.2614	L	0.42245	1.32	0.09310	N	1	B	0.31599	0.33	P	0.46419	0.516	T	0.60767	-0.7198	10	0.52906	T	0.07	.	5.5107	0.16878	0.5303:0.2472:0.2226:0.0	.	183	P12034	FGF5_HUMAN	I	183	ENSP00000311697:K183I	ENSP00000311697:K183I	K	+	2	0	FGF5	81426591	0.402000	0.25311	0.000000	0.03702	0.038000	0.13279	1.646000	0.37249	-0.118000	0.11851	-0.323000	0.08544	AAA		0.468	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			28	65	28	65
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	82833311	82833311	+	Missense_Mutation	SNP	G	G	C			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr5:82833311G>C	ENST00000265077.3	+	8	5054	c.4489G>C	c.(4489-4491)Gag>Cag	p.E1497Q	VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.E510Q|VCAN-AS1_ENST00000512090.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1497	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TTCAGGTGGTGAGCCTGATGT	0.438																																																0													77.0	74.0	75.0					5																	82833311		2203	4300	6503	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4489G>C	5.37:g.82833311G>C	ENSP00000265077:p.Glu1497Gln		P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390630	0.82902	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.93906	-3.31;-3.25;1.77	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000004	D	0.96156	0.8747	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.982;0.989	D	0.95885	0.8902	10	0.66056	D	0.02	.	13.5937	0.61975	0.0704:0.0:0.9296:0.0	.	510;1497	P13611-2;P13611	.;CSPG2_HUMAN	Q	1497;510;510	ENSP00000265077:E1497Q;ENSP00000340062:E510Q;ENSP00000426251:E510Q	ENSP00000265077:E1497Q	E	+	1	0	VCAN	82869067	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.877000	0.63086	2.832000	0.97577	0.655000	0.94253	GAG		0.438	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		12	26	12	26
C6orf15	29113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	31079466	31079466	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr6:31079466C>T	ENST00000259870.3	-	2	673	c.670G>A	c.(670-672)Ggg>Agg	p.G224R		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	224	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CAACCAGTCCCAGGGCCTCCA	0.587																																																0													36.0	36.0	36.0					6																	31079466		1713	3311	5024	SO:0001583	missense	0			AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.670G>A	6.37:g.31079466C>T	ENSP00000259870:p.Gly224Arg		B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985914	0.74589	.	.	ENSG00000204542	ENST00000259870	T	0.19669	2.13	4.4	4.4	0.53042	.	0.000000	0.48767	D	0.000175	T	0.36580	0.0972	M	0.69823	2.125	0.37145	D	0.901895	D	0.89917	1.0	D	0.97110	1.0	T	0.32079	-0.9920	10	0.87932	D	0	-9.8524	14.4911	0.67651	0.0:1.0:0.0:0.0	.	224	Q6UXA7	CF015_HUMAN	R	224	ENSP00000259870:G224R	ENSP00000259870:G224R	G	-	1	0	C6orf15	31187445	0.755000	0.28372	0.998000	0.56505	0.914000	0.54420	3.254000	0.51477	2.266000	0.75297	0.643000	0.83706	GGG		0.587	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070		14	40	14	40
AMER1	139285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	63412447	63412447	+	Silent	SNP	A	A	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chrX:63412447A>G	ENST00000330258.3	-	2	992	c.720T>C	c.(718-720)tcT>tcC	p.S240S	AMER1_ENST00000403336.1_Silent_p.S240S|AMER1_ENST00000374869.3_Silent_p.S240S	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	240					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CTGGTGTTGGAGAAACTTTTG	0.537																																																67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)											96.0	95.0	95.0					X																	63412447		2203	4297	6500	SO:0001819	synonymous_variant	139285			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.720T>C	X.37:g.63412447A>G			A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																				0.537	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		28	97	28	97
PCDH19	57526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	99662601	99662601	+	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chrX:99662601A>G	ENST00000373034.4	-	1	2670	c.995T>C	c.(994-996)gTc>gCc	p.V332A	PCDH19_ENST00000255531.7_Missense_Mutation_p.V332A|PCDH19_ENST00000420881.2_Missense_Mutation_p.V332A	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	332	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GCTGACGGTGACCTTGCAGTG	0.602																																																0													46.0	51.0	49.0					X																	99662601		2194	4276	6470	SO:0001583	missense	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.995T>C	X.37:g.99662601A>G	ENSP00000362125:p.Val332Ala		B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.760508	0.69763	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.60920	0.15;0.15;0.15	5.65	5.65	0.86999	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.80454	0.4626	M	0.90145	3.09	0.80722	D	1	D;D;D	0.76494	0.999;0.996;0.997	D;D;D	0.83275	0.996;0.954;0.973	D	0.84862	0.0820	10	0.87932	D	0	.	15.0094	0.71539	1.0:0.0:0.0:0.0	.	332;332;332	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	A	332	ENSP00000400327:V332A;ENSP00000362125:V332A;ENSP00000255531:V332A	ENSP00000255531:V332A	V	-	2	0	PCDH19	99549257	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.287000	0.95975	1.995000	0.58328	0.417000	0.27973	GTC		0.602	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		20	53	20	53
BSG	682	broad.mit.edu;ucsc.edu	37	19	581456	581456	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr19:581456G>A	ENST00000333511.3	+	6	1004	c.934G>A	c.(934-936)Gcc>Acc	p.A312T	BSG_ENST00000545507.2_Missense_Mutation_p.A103T|BSG_ENST00000353555.4_Missense_Mutation_p.A196T|BSG_ENST00000346916.4_Missense_Mutation_p.A132T	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	312	Ig-like V-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCGACCAGGCCATCATCAC	0.647																																																0													33.0	32.0	32.0					19																	581456		2196	4298	6494	SO:0001583	missense	682			L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.934G>A	19.37:g.581456G>A	ENSP00000333769:p.Ala312Thr		A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Missense_Mutation	SNP	ENST00000333511.3	37	CCDS12033.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476481	0.44044	.	.	ENSG00000172270	ENST00000346916;ENST00000545507;ENST00000333511;ENST00000353555	T;T;T	0.68624	-0.34;-0.34;-0.34	4.15	2.03	0.26663	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.132015	0.49916	D	0.000132	T	0.72415	0.3457	M	0.69185	2.1	0.29431	N	0.859887	D;D;D;D;D	0.71674	0.998;0.998;0.998;0.998;0.997	P;D;D;D;P	0.65233	0.89;0.91;0.933;0.91;0.871	T	0.65730	-0.6097	10	0.13853	T	0.58	-34.2781	9.192	0.37204	0.1771:0.0:0.8229:0.0	.	196;312;196;312;132	P35613-2;B4DNE1;Q54A51;P35613;A6NJW1	.;.;.;BASI_HUMAN;.	T	132;103;312;196	ENSP00000344707:A132T;ENSP00000333769:A312T;ENSP00000343809:A196T	ENSP00000333769:A312T	A	+	1	0	BSG	532456	0.996000	0.38824	0.003000	0.11579	0.003000	0.03518	5.054000	0.64275	0.428000	0.26173	-0.251000	0.11542	GCC		0.647	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728		8	12	8	12
HSD3B7	80270	broad.mit.edu;ucsc.edu	37	16	30998231	30998231	+	Missense_Mutation	SNP	T	T	G			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr16:30998231T>G	ENST00000297679.5	+	6	695	c.602T>G	c.(601-603)aTc>aGc	p.I201S	AC135048.1_ENST00000602217.1_5'Flank|HSD3B7_ENST00000262520.6_Intron|HSD3B7_ENST00000353250.5_Intron	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	201					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GGCCACCAGATCATGAGGGAC	0.662																																																0													58.0	57.0	58.0					16																	30998231		2197	4300	6497	SO:0001583	missense	80270			AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	18324	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 3"""	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.602T>G	16.37:g.30998231T>G	ENSP00000297679:p.Ile201Ser		Q96M28|Q9BSN9	Missense_Mutation	SNP	ENST00000297679.5	37	CCDS10698.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.358920	0.82353	.	.	ENSG00000099377	ENST00000297679	T	0.63255	-0.03	5.65	5.65	0.86999	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.233174	0.44902	D	0.000412	T	0.50633	0.1627	L	0.28192	0.835	0.80722	D	1	P	0.34699	0.464	B	0.32928	0.155	T	0.56438	-0.7979	10	0.72032	D	0.01	-24.259	14.8591	0.70366	0.0:0.0:0.0:1.0	.	201	Q9H2F3	3BHS7_HUMAN	S	201	ENSP00000297679:I201S	ENSP00000297679:I201S	I	+	2	0	HSD3B7	30905732	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.469000	0.60169	2.154000	0.67381	0.459000	0.35465	ATC		0.662	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2			13	46	13	46
TP53	7157	broad.mit.edu;hgsc.bcm.edu	37	17	7573991	7573992	+	Frame_Shift_Ins	INS	-	-	A			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chr17:7573991_7573992insA	ENST00000269305.4	-	10	1224_1225	c.1035_1036insT	c.(1033-1038)aatgagfs	p.E346fs	TP53_ENST00000445888.2_Frame_Shift_Ins_p.E346fs|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000359597.4_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	346	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		E -> A (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.L344fs*23(2)|p.E346*(2)|p.L344fs*22(1)|p.?(1)|p.R342_N345delRELN(1)|p.I332fs*5(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)	TCCAAGGCCTCATTCAGCTCTC	0.579		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"""	16	Whole gene deletion(8)|Deletion - Frameshift(4)|Substitution - Nonsense(2)|Unknown(1)|Deletion - In frame(1)	bone(4)|upper_aerodigestive_tract(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|adrenal_gland(1)|large_intestine(1)|stomach(1)|urinary_tract(1)|lung(1)|breast(1)																																								SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1036dupT	17.37:g.7573992_7573992dupA	ENSP00000269305:p.Glu346fs		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	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.579	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		16	9	16	9
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76918915	76918915	+	Frame_Shift_Del	DEL	T	T	-			TCGA-QH-A65S-01A-11D-A29Q-08	TCGA-QH-A65S-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05be7524-29b3-47c4-95bd-eecb53e97770	f3762aaf-0169-420b-93dd-2ebd5afe4412	g.chrX:76918915delT	ENST00000373344.5	-	12	4290	c.4076delA	c.(4075-4077)aagfs	p.K1359fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.K1321fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1359					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						CTCTTTAGGCTTTGTCTTTTT	0.383			"""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)											176.0	146.0	156.0					X																	76918915		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.4076delA	X.37:g.76918915delT	ENSP00000362441:p.Lys1359fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.383	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		17	28	17	28
