#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
TMX2	51075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	57480129	57480129	+	Silent	SNP	G	G	A			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr11:57480129G>A	ENST00000278422.4	+	1	51	c.39G>A	c.(37-39)tcG>tcA	p.S13S	TMX2-CTNND1_ENST00000528395.1_Silent_p.S13S|MED19_ENST00000431606.2_5'Flank|TMX2_ENST00000378312.4_Silent_p.S13S|MED19_ENST00000337672.2_5'Flank	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	13					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						TCGTGTATTCGGTGCCGCGAC	0.627																																																0													90.0	72.0	78.0					11																	57480129		2201	4296	6497	SO:0001819	synonymous_variant	51075			AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"""Protein disulfide isomerases"""	30739	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 12"""		"""thioredoxin domain containing 14"""	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.39G>A	11.37:g.57480129G>A			B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	Silent	SNP	ENST00000278422.4	37	CCDS7967.1																																																																																				0.627	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959		7	40	7	40
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	39884880	39884880	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr15:39884880C>T	ENST00000260356.5	+	17	2809	c.2644C>T	c.(2644-2646)Cag>Tag	p.Q882*	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	882					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CAATGCCAACCAGGCTGACCA	0.502																																																0													135.0	95.0	108.0					15																	39884880		2200	4297	6497	SO:0001587	stop_gained	7057				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2644C>T	15.37:g.39884880C>T	ENSP00000260356:p.Gln882*		A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Nonsense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	41	8.886990	0.98990	.	.	ENSG00000137801	ENST00000260356	.	.	.	5.3	5.3	0.74995	.	0.000000	0.34178	N	0.004196	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.6107	14.5347	0.67953	0.0:0.8535:0.1465:0.0	.	.	.	.	X	882	.	ENSP00000260356:Q882X	Q	+	1	0	THBS1	37672172	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.474000	0.83562	0.655000	0.94253	CAG		0.502	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		18	36	18	36
SPINT1	6692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	41146276	41146276	+	Missense_Mutation	SNP	G	G	A	rs138167951		TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr15:41146276G>A	ENST00000344051.4	+	6	1214	c.980G>A	c.(979-981)cGc>cAc	p.R327H	SPINT1_ENST00000431806.1_Missense_Mutation_p.R311H|SPINT1_ENST00000562057.1_Missense_Mutation_p.R311H			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	327					branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		ATGGAAAGGCGCCATCCAGGT	0.592																																																0								G	HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	107.0	108.0	108.0		932,932,980	1.0	0.7	15	dbSNP_134	108	0,8600		0,0,4300	no	missense,missense,missense	SPINT1	NM_001032367.1,NM_003710.3,NM_181642.2	29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign	311/514,311/514,327/530	41146276	1,13005	2203	4300	6503	SO:0001583	missense	6692				CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"""serine protease inhibitor, Kunitz type 1"""				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.980G>A	15.37:g.41146276G>A	ENSP00000342098:p.Arg327His		Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	37	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	G	3.591	-0.083572	0.07141	2.27E-4	0.0	ENSG00000166145	ENST00000344051;ENST00000536281;ENST00000431806	D;D	0.95622	-3.7;-3.76	4.59	0.986	0.19784	.	1.291370	0.04602	N	0.398660	D	0.88559	0.6469	N	0.08118	0	0.18873	N	0.999989	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.78254	-0.2275	10	0.28530	T	0.3	-8.3304	7.4557	0.27266	0.7285:0.0:0.2715:0.0	.	311;327	O43278-2;O43278	.;SPIT1_HUMAN	H	327;294;311	ENSP00000342098:R327H;ENSP00000409935:R311H	ENSP00000342098:R327H	R	+	2	0	SPINT1	38933568	0.968000	0.33430	0.663000	0.29738	0.821000	0.46438	1.898000	0.39809	0.010000	0.14839	-1.671000	0.00744	CGC		0.592	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		52	126	52	126
ANKRD13B	124930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	27939276	27939276	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr17:27939276T>G	ENST00000394859.3	+	11	1397	c.1243T>G	c.(1243-1245)Ttc>Gtc	p.F415V	RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	415						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						GCCTCCTGGCTTCCCAGTTAA	0.622																																																0													86.0	84.0	85.0					17																	27939276		2203	4300	6503	SO:0001583	missense	124930			AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"""Ankyrin repeat domain containing"""	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.1243T>G	17.37:g.27939276T>G	ENSP00000378328:p.Phe415Val		Q8N7S9	Missense_Mutation	SNP	ENST00000394859.3	37	CCDS11251.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.506837	0.85282	.	.	ENSG00000198720	ENST00000394859	T	0.69306	-0.39	5.83	5.83	0.93111	.	0.044919	0.85682	D	0.000000	D	0.86184	0.5872	M	0.93720	3.45	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	D	0.89794	0.3970	10	0.87932	D	0	-23.9562	15.8671	0.79074	0.0:0.0:0.0:1.0	.	415	Q86YJ7	AN13B_HUMAN	V	415	ENSP00000378328:F415V	ENSP00000378328:F415V	F	+	1	0	ANKRD13B	24963402	1.000000	0.71417	0.992000	0.48379	0.620000	0.37586	7.962000	0.87912	2.220000	0.72140	0.533000	0.62120	TTC		0.622	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345		32	86	32	86
ABCA9	10350	hgsc.bcm.edu;broad.mit.edu	37	17	66982397	66982397	+	Silent	SNP	C	C	T			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr17:66982397C>T	ENST00000340001.4	-	32	4327	c.4116G>A	c.(4114-4116)gcG>gcA	p.A1372A	ABCA9_ENST00000453985.2_Silent_p.A1334A|ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000370732.2_Silent_p.A1372A	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1372	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TGGGCCACAGCGCATTCTCCT	0.547																																																0													129.0	105.0	113.0					17																	66982397		2203	4300	6503	SO:0001819	synonymous_variant	10350			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4116G>A	17.37:g.66982397C>T			Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	37	CCDS11681.1																																																																																				0.547	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		8	119	8	119
DSG2	1829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	29126141	29126141	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr18:29126141G>C	ENST00000261590.8	+	15	3001	c.2792G>C	c.(2791-2793)aGa>aCa	p.R931T	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	931					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			ATGGCTTCTAGAAATGTGATA	0.473																																																0													92.0	91.0	91.0					18																	29126141		1957	4157	6114	SO:0001583	missense	1829			Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.2792G>C	18.37:g.29126141G>C	ENSP00000261590:p.Arg931Thr		Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	G	4.033	0.003645	0.07866	.	.	ENSG00000046604	ENST00000261590	T	0.75367	-0.93	4.9	3.11	0.35812	.	0.967056	0.08537	N	0.931086	T	0.55162	0.1903	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.46965	-0.9153	10	0.52906	T	0.07	.	7.8193	0.29278	0.1524:0.1341:0.7134:0.0	.	931	Q14126	DSG2_HUMAN	T	931	ENSP00000261590:R931T	ENSP00000261590:R931T	R	+	2	0	DSG2	27380139	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.874000	0.28065	0.776000	0.33473	-0.140000	0.14226	AGA		0.473	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		66	78	66	78
RTTN	25914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	67695981	67695981	+	Silent	SNP	A	A	C			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr18:67695981A>C	ENST00000255674.6	-	43	6088	c.5802T>G	c.(5800-5802)ctT>ctG	p.L1934L	RTTN_ENST00000579986.1_5'UTR|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1934				L -> P (in Ref. 4; AAH46222). {ECO:0000305}.	determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CATTTTGATAAAGACAGTTTC	0.308																																																0													80.0	74.0	76.0					18																	67695981		1829	4083	5912	SO:0001819	synonymous_variant	25914			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.5802T>G	18.37:g.67695981A>C			Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	37	CCDS42443.1																																																																																				0.308	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		5	20	5	20
PRODH2	58510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	36293163	36293163	+	Silent	SNP	G	G	T			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr19:36293163G>T	ENST00000301175.3	-	10	1373	c.1356C>A	c.(1354-1356)ggC>ggA	p.G452G		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	452					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCAGAGGAATGCCCAGCTCCC	0.542																																																0													210.0	159.0	176.0					19																	36293163		2203	4300	6503	SO:0001819	synonymous_variant	58510			U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.1356C>A	19.37:g.36293163G>T				Silent	SNP	ENST00000301175.3	37	CCDS12478.1																																																																																				0.542	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232		13	148	13	148
KCNA7	3743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	49573516	49573516	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr19:49573516A>G	ENST00000221444.1	-	2	1530	c.1175T>C	c.(1174-1176)gTc>gCc	p.V392A		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	392					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GGAGACAATGACGGGCACTGG	0.567																																					Colon(74;686 1235 3793 23366 48562)											0													72.0	65.0	68.0					19																	49573516		2203	4300	6503	SO:0001583	missense	3743			AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1175T>C	19.37:g.49573516A>G	ENSP00000221444:p.Val392Ala		A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.360125	0.82353	.	.	ENSG00000104848	ENST00000221444	D	0.99089	-5.41	4.65	4.65	0.58169	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99296	0.9754	M	0.90483	3.12	0.58432	D	0.999995	D	0.54397	0.966	D	0.67548	0.952	D	0.98928	1.0786	10	0.87932	D	0	.	13.3495	0.60593	1.0:0.0:0.0:0.0	.	392	Q96RP8	KCNA7_HUMAN	A	392	ENSP00000221444:V392A	ENSP00000221444:V392A	V	-	2	0	KCNA7	54265328	1.000000	0.71417	0.989000	0.46669	0.953000	0.61014	9.332000	0.96446	1.880000	0.54463	0.402000	0.26972	GTC		0.567	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886		26	43	26	43
PRR12	57479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	50123629	50123629	+	Silent	SNP	C	C	T			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr19:50123629C>T	ENST00000418929.2	+	10	5530	c.5518C>T	c.(5518-5520)Ctg>Ttg	p.L1840L		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	1019							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		ACCTGGGCGTCTGCTCAAAAC	0.567																																																0													46.0	50.0	49.0					19																	50123629		2106	4226	6332	SO:0001819	synonymous_variant	57479			AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.5518C>T	19.37:g.50123629C>T			E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																				0.567	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		7	16	7	16
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	179453926	179453926	+	Silent	SNP	A	A	G			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr2:179453926A>G	ENST00000591111.1	-	254	57827	c.57603T>C	c.(57601-57603)taT>taC	p.Y19201Y	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Silent_p.Y20842Y|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.Y18274Y|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Y11969Y|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.Y11902Y|TTN_ENST00000460472.2_Silent_p.Y11777Y|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19201	Ig-like 108.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCGTAACTACATATTTACCCC	0.413																																																0													115.0	115.0	115.0					2																	179453926		1900	4126	6026	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.57603T>C	2.37:g.179453926A>G			A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		54	67	54	67
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	179579894	179579894	+	Silent	SNP	G	G	A	rs370266918	byFrequency	TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr2:179579894G>A	ENST00000591111.1	-	88	25292	c.25068C>T	c.(25066-25068)caC>caT	p.H8356H	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.H8673H|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.H7429H|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12530	Ig-like 66.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCAAGAAACGTGAAATGGGG	0.443													g|||	4	0.000798722	0.003	0.0	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0															0								A	,,,	1,3749		0,1,1874	231.0	214.0	219.0		,22287,,	-1.2	1.0	2		219	0,8214		0,0,4107	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,5981	AA,AG,GG		0.0,0.0267,0.0084	,,,	,7429/33424,,	179579894	1,11963	1875	4107	5982	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25068C>T	2.37:g.179579894G>A			A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		62	105	62	105
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	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			16	51	16	51
CCDC54	84692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	107096617	107096617	+	Silent	SNP	C	C	T	rs144553244	byFrequency	TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr3:107096617C>T	ENST00000261058.1	+	1	430	c.183C>T	c.(181-183)gaC>gaT	p.D61D		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	61								p.D61D(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						ATAGTTATGACGGAAAAATGA	0.363													C|||	2	0.000399361	0.0015	0.0	5008	,	,		21297	0.0		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	prostate(1)											132.0	127.0	129.0					3																	107096617		2203	4300	6503	SO:0001819	synonymous_variant	84692			AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.183C>T	3.37:g.107096617C>T			Q96A43	Silent	SNP	ENST00000261058.1	37	CCDS2949.1																																																																																				0.363	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600		29	85	29	85
CAPN11	11131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	44143857	44143857	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr6:44143857G>A	ENST00000398776.1	+	8	922	c.884G>A	c.(883-885)gGg>gAg	p.G295E	CAPN11_ENST00000542245.1_Missense_Mutation_p.G295E	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	295	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTGGTGAGAGGGCACGCTTAC	0.557																																																0													78.0	79.0	78.0					6																	44143857		2148	4253	6401	SO:0001583	missense	11131			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.884G>A	6.37:g.44143857G>A	ENSP00000381758:p.Gly295Glu		B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.484468	0.84854	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.97976	-4.64;-4.64	3.56	3.56	0.40772	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.47093	D	0.000252	D	0.99146	0.9705	H	0.97131	3.945	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.98725	1.0710	10	0.87932	D	0	.	15.3933	0.74767	0.0:0.0:1.0:0.0	.	295	Q9UMQ6	CAN11_HUMAN	E	295	ENSP00000381758:G295E;ENSP00000441078:G295E	ENSP00000381758:G295E	G	+	2	0	CAPN11	44251835	1.000000	0.71417	0.748000	0.31131	0.268000	0.26511	9.556000	0.98127	2.317000	0.78254	0.462000	0.41574	GGG		0.557	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			8	28	8	28
MAGEB4	4115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	30260295	30260295	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chrX:30260295C>T	ENST00000378982.2	+	1	239	c.43C>T	c.(43-45)Cgc>Tgc	p.R15C	MAGEB1_ENST00000378981.3_5'Flank|MAGEB1_ENST00000397550.1_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	15										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						CCGTGAGAAACGCCAGCGGAC	0.567																																																0													99.0	79.0	86.0					X																	30260295		2202	4300	6502	SO:0001583	missense	4115				CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"""melanoma-associated antigen B4"", ""cancer/testis antigen family 3, member 6"""	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.43C>T	X.37:g.30260295C>T	ENSP00000368266:p.Arg15Cys		B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	37	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126557	0.37533	.	.	ENSG00000120289	ENST00000378982	T	0.06933	3.24	3.22	-1.76	0.08006	Melanoma associated antigen, MAGE, N-terminal (1);	1.576910	0.05036	U	0.475533	T	0.21062	0.0507	M	0.76574	2.34	0.09310	N	1	D	0.57257	0.979	P	0.56865	0.808	T	0.27706	-1.0066	10	0.44086	T	0.13	.	7.626	0.28212	0.0:0.3504:0.0:0.6496	.	15	O15481	MAGB4_HUMAN	C	15	ENSP00000368266:R15C	ENSP00000368266:R15C	R	+	1	0	MAGEB4	30170216	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.801000	0.01743	-0.647000	0.05444	-0.268000	0.10319	CGC		0.567	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		16	52	16	52
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76939697	76939697	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chrX:76939697C>A	ENST00000373344.5	-	9	1265	c.1051G>T	c.(1051-1053)Gag>Tag	p.E351*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.E313*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	351					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						TTAATCATCTCTTTGGGCACA	0.353			"""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)											81.0	78.0	79.0					X																	76939697		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.1051G>T	X.37:g.76939697C>A	ENSP00000362441:p.Glu351*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	c	38	6.875248	0.97904	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	.	.	.	5.3	4.44	0.53790	.	0.196705	0.43579	D	0.000553	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-1.1203	13.1753	0.59624	0.0:0.9208:0.0:0.0792	.	.	.	.	X	351;313;307	.	ENSP00000362441:E351X	E	-	1	0	ATRX	76826353	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	7.481000	0.81124	1.014000	0.39417	0.502000	0.49764	GAG		0.353	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		39	71	39	71
RGAG1	57529	hgsc.bcm.edu;broad.mit.edu	37	X	109694050	109694050	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chrX:109694050C>G	ENST00000465301.2	+	3	451	c.205C>G	c.(205-207)Cca>Gca	p.P69A	RGAG1_ENST00000540313.1_Missense_Mutation_p.P69A	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	69										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						GATGACATCTCCAGTCTTTGA	0.517											OREG0019909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													240.0	208.0	219.0					X																	109694050		2203	4300	6503	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.205C>G	X.37:g.109694050C>G	ENSP00000419786:p.Pro69Ala	1421	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	C	7.197	0.592668	0.13875	.	.	ENSG00000243978	ENST00000520821;ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.66099	-0.19;-0.19	4.16	1.38	0.22167	.	0.459089	0.16314	N	0.219845	T	0.41789	0.1174	L	0.29908	0.895	0.09310	N	1	B	0.25563	0.129	B	0.23419	0.046	T	0.17258	-1.0375	9	.	.	.	-3.9455	3.7088	0.08411	0.0:0.5612:0.2023:0.2365	.	69	Q8NET4	RGAG1_HUMAN	A	69	ENSP00000419786:P69A;ENSP00000441452:P69A	.	P	+	1	0	RGAG1	109580706	0.001000	0.12720	0.058000	0.19502	0.086000	0.17979	-0.052000	0.11865	0.147000	0.19030	-0.208000	0.12717	CCA		0.517	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		26	316	26	316
MCF2	4168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	138711938	138711938	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chrX:138711938T>A	ENST00000370576.4	-	4	563	c.354A>T	c.(352-354)gaA>gaT	p.E118D	MCF2_ENST00000370573.4_Missense_Mutation_p.E118D|MCF2_ENST00000338585.6_Missense_Mutation_p.E118D|MCF2_ENST00000519895.1_Missense_Mutation_p.E178D|MCF2_ENST00000370578.4_Missense_Mutation_p.E263D|MCF2_ENST00000536274.1_Missense_Mutation_p.E79D|MCF2_ENST00000520602.1_Missense_Mutation_p.E178D|MCF2_ENST00000414978.1_Missense_Mutation_p.E178D	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	118					apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					TCTCAGCCAGTTCAGTTCCAA	0.398																																																0													194.0	187.0	189.0					X																	138711938		2203	4300	6503	SO:0001583	missense	4168				CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"""Rho guanine nucleotide exchange factors"""	6940	protein-coding gene	gene with protein product	"""Oncogene MCF2 (oncogene DBL)"""	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.354A>T	X.37:g.138711938T>A	ENSP00000359608:p.Glu118Asp		B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317726	0.60524	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T;T	0.43294	1.19;1.13;0.95;1.19;1.19;1.24;1.16;1.2	5.17	2.29	0.28610	.	0.000000	0.85682	D	0.000000	T	0.54046	0.1834	M	0.62016	1.91	0.31052	N	0.715116	B;D;B;B;B;B;D;B	0.89917	0.204;0.999;0.307;0.353;0.307;0.204;1.0;0.204	B;D;B;B;B;B;D;B	0.91635	0.1;0.996;0.204;0.188;0.204;0.1;0.999;0.134	T	0.53947	-0.8366	10	0.30854	T	0.27	.	7.4139	0.27034	0.0:0.3172:0.0:0.6828	.	178;263;79;118;118;263;118;118	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;.;.;MCF2_HUMAN	D	178;118;79;263;178;178;118;118	ENSP00000427745:E178D;ENSP00000359608:E118D;ENSP00000438155:E79D;ENSP00000359610:E263D;ENSP00000397055:E178D;ENSP00000430276:E178D;ENSP00000359605:E118D;ENSP00000342204:E118D	ENSP00000342204:E118D	E	-	3	2	MCF2	138539604	0.995000	0.38212	0.997000	0.53966	0.997000	0.91878	0.306000	0.19279	0.580000	0.29522	0.425000	0.28330	GAA		0.398	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		82	147	82	147
CD99L2	83692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	149938823	149938823	+	Silent	SNP	G	G	A	rs147156476	byFrequency	TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chrX:149938823G>A	ENST00000370377.3	-	10	792	c.675C>T	c.(673-675)taC>taT	p.Y225Y	CD99L2_ENST00000437787.2_Silent_p.Y152Y|CD99L2_ENST00000466436.1_Silent_p.Y176Y|CD99L2_ENST00000346693.4_5'UTR|CD99L2_ENST00000355149.3_Silent_p.Y153Y	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN	CD99 molecule-like 2	225					cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CTCCCTTCACGTAGTCTGCGT	0.537																																																0								G	,,,,	2,3833		0,1,1,1631,570	202.0	120.0	148.0		456,705,675,459,528	-2.9	1.0	X	dbSNP_134	148	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD99L2	NM_001184808.1,NM_001242614.1,NM_031462.3,NM_134445.3,NM_134446.3	,,,,	0,1,1,4059,2442	AA,AG,A,GG,G		0.0,0.0522,0.0189	,,,,	152/190,235/273,225/263,153/191,176/214	149938823	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	83692			BC030536	CCDS14697.1, CCDS14698.1, CCDS35427.1, CCDS55527.1, CCDS76044.1	Xq28	2007-12-04	2006-03-28	2003-02-14	ENSG00000102181	ENSG00000102181			18237	protein-coding gene	gene with protein product		300846	"""MIC2 like 1"", ""CD99 antigen-like 2"""	MIC2L1			Standard	NM_001184808		Approved	CD99B	uc004fek.3	Q8TCZ2	OTTHUMG00000024247	ENST00000370377.3:c.675C>T	X.37:g.149938823G>A			A8K2D5|A8K5R0|B3KWG2|B4DDL7|E7EMK5|E9PD27|Q8TAW2|Q8TCZ0|Q8TCZ1|Q9BQG9	Silent	SNP	ENST00000370377.3	37	CCDS35427.1																																																																																				0.537	CD99L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061199.1	NM_031462		20	39	20	39
HMGB3	3149	hgsc.bcm.edu;broad.mit.edu	37	X	150156360	150156360	+	Silent	SNP	G	G	A			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chrX:150156360G>A	ENST00000325307.7	+	5	672	c.576G>A	c.(574-576)gaG>gaA	p.E192E	HMGB3_ENST00000448905.2_Silent_p.E192E	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	192	Asp/Glu-rich (acidic).				DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.E192E(1)		endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					aggaagaagaggaggaggagg	0.443																																																1	Substitution - coding silent(1)	large_intestine(1)											50.0	48.0	49.0					X																	150156360		2202	4299	6501	SO:0001819	synonymous_variant	3149			AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"""High-mobility group / Canonical"""	5004	protein-coding gene	gene with protein product	"""non-histone chromosomal protein"""	300193	"""high-mobility group (nonhistone chromosomal) protein 4"", ""high-mobility group box 3"""	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.576G>A	X.37:g.150156360G>A			O95556|Q6NS40	Silent	SNP	ENST00000325307.7	37	CCDS35428.1																																																																																				0.443	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342		5	62	5	62
KIAA1324	57535	broad.mit.edu;ucsc.edu	37	1	109741239	109741239	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr1:109741239C>G	ENST00000369939.3	+	18	2627	c.2444C>G	c.(2443-2445)aCc>aGc	p.T815S	KIAA1324_ENST00000529753.1_Missense_Mutation_p.T728S|KIAA1324_ENST00000369938.1_3'UTR	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	815					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		AGATCAACCACCATCCGCGTC	0.532																																																0													86.0	65.0	72.0					1																	109741239		2203	4300	6503	SO:0001583	missense	57535			AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.2444C>G	1.37:g.109741239C>G	ENSP00000358955:p.Thr815Ser		Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	37	CCDS794.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.084008	0.55861	.	.	ENSG00000116299	ENST00000369939;ENST00000457623;ENST00000529753	T;T;T	0.03951	3.75;3.75;3.75	5.64	5.64	0.86602	Mannose-6-phosphate receptor, binding (1);	0.152885	0.56097	D	0.000024	T	0.01730	0.0055	N	0.16656	0.425	0.37414	D	0.913359	B;P;B;B	0.39181	0.254;0.663;0.254;0.254	B;B;B;B	0.37198	0.06;0.243;0.06;0.06	T	0.63328	-0.6662	10	0.21540	T	0.41	-26.7023	16.6354	0.85058	0.0:1.0:0.0:0.0	.	815;728;815;815	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	S	815;765;728	ENSP00000358955:T815S;ENSP00000393964:T765S;ENSP00000434595:T728S	ENSP00000358955:T815S	T	+	2	0	KIAA1324	109542762	0.927000	0.31430	1.000000	0.80357	0.927000	0.56198	2.087000	0.41653	2.659000	0.90383	0.655000	0.94253	ACC		0.532	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		3	17	3	17
CCAR1	55749	broad.mit.edu;hgsc.bcm.edu	37	10	70513778	70513779	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HT-A616-01A-11D-A29Q-08	TCGA-HT-A616-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e41fcb0-82bf-4e09-99ba-ff6f56d6f18c	eb5310fc-1426-4b59-b41b-47302c259a6a	g.chr10:70513778_70513779insA	ENST00000265872.6	+	11	1407_1408	c.1288_1289insA	c.(1288-1290)gaafs	p.E430fs	CCAR1_ENST00000543719.1_Frame_Shift_Ins_p.E415fs|CCAR1_ENST00000535016.1_Frame_Shift_Ins_p.E415fs|SNORD98_ENST00000408255.1_RNA	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	430					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						AGAGTCCTTAGAAAAAAATATG	0.381																																																0																																										SO:0001589	frameshift_variant	55749			AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.1295dupA	10.37:g.70513785_70513785dupA	ENSP00000265872:p.Glu430fs		A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Frame_Shift_Ins	INS	ENST00000265872.6	37	CCDS7282.1																																																																																				0.381	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		32	69	32	69
