#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	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_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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
FRRS1	391059	hgsc.bcm.edu	37	1	100214268	100214268	+	Silent	SNP	A	A	G			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:100214268A>G	ENST00000414213.1	-	3	658	c.57T>C	c.(55-57)taT>taC	p.Y19Y	FRRS1_ENST00000287474.5_Silent_p.Y19Y			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	19	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AATTAGCCACATAACTAATGT	0.378																																					p.Y19Y		Atlas-SNP	.											.	FRRS1	50	.	0			c.T57C						PASS	.						154.0	132.0	139.0					1																	100214268		2203	4300	6503	SO:0001819	synonymous_variant	391059	exon3			AGCCACATAACTA	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.57T>C	chr1.hg19:g.100214268A>G		112.0	0.0	.		107.0	38.0	.	NM_001013660	A6NLN7	Silent	SNP	ENST00000414213.1	hg19																																																																																				.	.	.	none		0.378	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
ALX3	257	hgsc.bcm.edu	37	1	110604111	110604111	+	Silent	SNP	G	G	T			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:110604111G>T	ENST00000369792.4	-	3	756	c.669C>A	c.(667-669)ccC>ccA	p.P223P	RP4-773N10.4_ENST00000596959.1_RNA|RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	223					embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|pattern specification process (GO:0007389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		CAGCCGTGAAGGGGTTCCGCC	0.622																																					p.P223P		Atlas-SNP	.											.	ALX3	16	.	0			c.C669A						PASS	.						79.0	78.0	78.0					1																	110604111		2203	4300	6503	SO:0001819	synonymous_variant	257	exon3			CGTGAAGGGGTTC	AF008203	CCDS819.1	1p13.3	2014-02-04	2008-11-04		ENSG00000156150	ENSG00000156150		"""Homeoboxes / PRD class"""	449	protein-coding gene	gene with protein product		606014	"""aristaless-like homeobox 3"", ""frontonasal dysplasia"""	FND		15226305, 11807986, 19409524	Standard	NM_006492		Approved		uc001dzb.3	O95076	OTTHUMG00000011650	ENST00000369792.4:c.669C>A	chr1.hg19:g.110604111G>T		106.0	0.0	.		101.0	34.0	.	NM_006492	O95075|Q5T8M4	Silent	SNP	ENST00000369792.4	hg19	CCDS819.1																																																																																			.	.	.	none		0.622	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492	
DSTYK	25778	hgsc.bcm.edu	37	1	205132867	205132867	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:205132867C>G	ENST00000367162.3	-	4	1571	c.1541G>C	c.(1540-1542)aGt>aCt	p.S514T	DSTYK_ENST00000367160.4_Intron|DSTYK_ENST00000367161.3_Missense_Mutation_p.S514T	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	514					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						GAGATAATTACTGGTGATGTG	0.433																																					p.S514T		Atlas-SNP	.											DSTYK_ENST00000367162,colon,carcinoma,0,1	DSTYK	87	.	0			c.G1541C						PASS	.						80.0	72.0	75.0					1																	205132867		2203	4300	6503	SO:0001583	missense	25778	exon4			TAATTACTGGTGA	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"""receptor interacting protein kinase 5"""	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.1541G>C	chr1.hg19:g.205132867C>G	ENSP00000356130:p.Ser514Thr	35.0	0.0	.		31.0	2.0	.	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	hg19	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245935	0.80024	.	.	ENSG00000133059	ENST00000367161;ENST00000367162	T;T	0.81163	-1.41;-1.46	5.8	5.8	0.92144	.	0.090598	0.85682	D	0.000000	D	0.84047	0.5386	L	0.35723	1.085	0.80722	D	1	D;D	0.63880	0.993;0.977	P;P	0.58454	0.839;0.751	D	0.83764	0.0216	10	0.49607	T	0.09	-13.2589	19.6644	0.95887	0.0:1.0:0.0:0.0	.	514;514	Q6XUX3-2;Q6XUX3	.;DUSTY_HUMAN	T	514	ENSP00000356129:S514T;ENSP00000356130:S514T	ENSP00000356129:S514T	S	-	2	0	DSTYK	203399490	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.108000	0.71522	2.758000	0.94735	0.563000	0.77884	AGT	.	.	.	none		0.433	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375	
BIN1	274	hgsc.bcm.edu	37	2	127828371	127828371	+	Missense_Mutation	SNP	T	T	C			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:127828371T>C	ENST00000316724.5	-	3	598	c.187A>G	c.(187-189)Aag>Gag	p.K63E	BIN1_ENST00000393041.3_Missense_Mutation_p.K63E|BIN1_ENST00000351659.3_Missense_Mutation_p.K63E|BIN1_ENST00000348750.4_Missense_Mutation_p.K63E|BIN1_ENST00000357970.3_Missense_Mutation_p.K63E|BIN1_ENST00000352848.3_Missense_Mutation_p.K63E|BIN1_ENST00000346226.3_Missense_Mutation_p.K63E|BIN1_ENST00000409400.1_Missense_Mutation_p.K63E|BIN1_ENST00000393040.3_Missense_Mutation_p.K63E|BIN1_ENST00000259238.4_Missense_Mutation_p.K63E|BIN1_ENST00000376113.2_Missense_Mutation_p.K63E	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	63	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Interaction with BIN2.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CGGAGATCCTTCTGCAGCCGG	0.647																																					p.K63E		Atlas-SNP	.											.	BIN1	85	.	0			c.A187G						PASS	.						45.0	44.0	44.0					2																	127828371		2203	4300	6503	SO:0001583	missense	274	exon3			GATCCTTCTGCAG	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.187A>G	chr2.hg19:g.127828371T>C	ENSP00000316779:p.Lys63Glu	31.0	0.0	.		56.0	24.0	.	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	hg19	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331702	0.81690	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.49	3.3	0.37823	BAR (3);	0.101360	0.64402	D	0.000002	T	0.71558	0.3354	M	0.66939	2.045	0.54753	D	0.999988	P;D;P;P;P;P;P;P;B;P;P;B;P	0.60575	0.947;0.988;0.457;0.942;0.606;0.952;0.938;0.884;0.432;0.837;0.941;0.047;0.929	P;D;B;P;B;P;P;B;B;B;B;B;P	0.65010	0.879;0.931;0.286;0.528;0.286;0.611;0.804;0.346;0.177;0.287;0.357;0.017;0.794	T	0.73697	-0.3901	10	0.87932	D	0	-23.223	8.0196	0.30402	0.0:0.0991:0.0:0.9009	.	63;39;63;63;63;63;63;63;63;63;63;63;63	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	E	63	ENSP00000365281:K63E;ENSP00000350654:K63E;ENSP00000376760:K63E;ENSP00000259237:K63E;ENSP00000259238:K63E;ENSP00000315411:K63E;ENSP00000376761:K63E;ENSP00000315388:K63E;ENSP00000315284:K63E;ENSP00000316779:K63E;ENSP00000386797:K63E	ENSP00000259238:K63E	K	-	1	0	BIN1	127544841	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	4.533000	0.60615	1.884000	0.54569	0.459000	0.35465	AAG	.	.	.	none		0.647	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
NEB	4703	hgsc.bcm.edu	37	2	152512859	152512859	+	Silent	SNP	C	C	T			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:152512859C>T	ENST00000172853.10	-	49	6450	c.6303G>A	c.(6301-6303)gaG>gaA	p.E2101E	NEB_ENST00000427231.2_Silent_p.E2101E|NEB_ENST00000409198.1_Silent_p.E2101E|NEB_ENST00000604864.1_Silent_p.E2101E|NEB_ENST00000603639.1_Silent_p.E2101E|NEB_ENST00000397345.3_Silent_p.E2101E			P20929	NEBU_HUMAN	nebulin	2101					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTTTCTTGTACTCCCGATCAG	0.483																																					p.E2101E		Atlas-SNP	.											.	NEB	1697	.	0			c.G6303A						PASS	.						239.0	236.0	237.0					2																	152512859		2046	4199	6245	SO:0001819	synonymous_variant	4703	exon49			CTTGTACTCCCGA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.6303G>A	chr2.hg19:g.152512859C>T		191.0	0.0	.		155.0	66.0	.	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.	.	none		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
PRKRA	8575	hgsc.bcm.edu	37	2	179306336	179306336	+	Splice_Site	SNP	C	C	T			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:179306336C>T	ENST00000325748.4	-	6	810		c.e6+1		PRKRA_ENST00000432031.2_Splice_Site|PRKRA_ENST00000487082.1_Splice_Site|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000438687.3_Splice_Site	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator						cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			ACATTACTCACTAAAGAAATG	0.353																																					.	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,NS,carcinoma,0,1	PRKRA	56	.	1	Unknown(1)	lung(1)	c.534+1G>A						PASS	.						70.0	74.0	73.0					2																	179306336		2203	4300	6503	SO:0001630	splice_region_variant	8575	exon7			TACTCACTAAAGA	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.609+1G>A	chr2.hg19:g.179306336C>T		61.0	1.0	.		80.0	5.0	.	NM_001139518	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Splice_Site	SNP	ENST00000325748.4	hg19	CCDS2279.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.689950	0.68271	.	.	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5111	0.44862	0.0:0.9114:0.0:0.0886	.	.	.	.	.	-1	.	.	.	-	.	.	PRKRA	179014582	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.492000	0.60334	2.618000	0.88619	0.591000	0.81541	.	.	.	.	none		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	Intron
TTN	7273	hgsc.bcm.edu	37	2	179433843	179433843	+	Nonsense_Mutation	SNP	G	G	C			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:179433843G>C	ENST00000591111.1	-	276	72317	c.72093C>G	c.(72091-72093)taC>taG	p.Y24031*	TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Y16799*|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Y16732*|TTN_ENST00000460472.2_Nonsense_Mutation_p.Y16607*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Y25672*|TTN_ENST00000342992.6_Nonsense_Mutation_p.Y23104*|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24031	Fibronectin type-III 74. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			TGACTCTAAAGTAATAACTGC	0.418																																					p.Y25672X		Atlas-SNP	.											.	TTN	18412	.	0			c.C77016G						PASS	.						171.0	169.0	170.0					2																	179433843		1958	4136	6094	SO:0001587	stop_gained	7273	exon326			TCTAAAGTAATAA	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.72093C>G	chr2.hg19:g.179433843G>C	ENSP00000465570:p.Tyr24031*	200.0	0.0	.		231.0	99.0	.	NM_001267550	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	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	63	76.472557	0.99993	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.5208	0.61566	0.071:0.0:0.929:0.0	.	.	.	.	X	23104;16607;16799;16732;16605	.	ENSP00000340554:Y16799X	Y	-	3	2	TTN	179142089	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.714000	0.68422	2.803000	0.96430	0.650000	0.86243	TAC	.	.	.	none		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RBM6	10180	hgsc.bcm.edu	37	3	50005960	50005960	+	Missense_Mutation	SNP	G	G	T			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr3:50005960G>T	ENST00000266022.4	+	3	1361	c.1102G>T	c.(1102-1104)Gat>Tat	p.D368Y	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.D236Y|RBM6_ENST00000539992.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	368					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TCAAGACCAAGATAAGTCACA	0.463																																					p.D368Y		Atlas-SNP	.											.	RBM6	85	.	0			c.G1102T						PASS	.						80.0	76.0	78.0					3																	50005960		2203	4300	6503	SO:0001583	missense	10180	exon3			GACCAAGATAAGT	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.1102G>T	chr3.hg19:g.50005960G>T	ENSP00000266022:p.Asp368Tyr	72.0	0.0	.		96.0	43.0	.	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	hg19	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043431	0.36085	.	.	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.36878	1.23;1.25	5.85	3.97	0.46021	.	0.614854	0.16479	N	0.212625	T	0.29389	0.0732	N	0.24115	0.695	0.80722	D	1	D	0.59767	0.986	P	0.49752	0.621	T	0.01988	-1.1234	9	.	.	.	-4.7397	7.5857	0.27991	0.1421:0.1365:0.7214:0.0	.	368	P78332	RBM6_HUMAN	Y	368;236	ENSP00000266022:D368Y;ENSP00000396466:D236Y	.	D	+	1	0	RBM6	49980964	1.000000	0.71417	0.999000	0.59377	0.735000	0.41995	2.640000	0.46579	1.495000	0.48549	0.491000	0.48974	GAT	.	.	.	none		0.463	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
GATB	5188	hgsc.bcm.edu	37	4	152592364	152592364	+	Missense_Mutation	SNP	T	T	C			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr4:152592364T>C	ENST00000515812.1	-	12	1529	c.1513A>G	c.(1513-1515)Atg>Gtg	p.M505V	PET112_ENST00000263985.6_Missense_Mutation_p.M546V|RP11-164P12.4_ENST00000508664.1_RNA|PET112_ENST00000507592.1_5'UTR																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						TCCTTTATCATGACTGGATCT	0.483																																					p.M546V		Atlas-SNP	.											.	PET112	43	.	0			c.A1636G						PASS	.						178.0	163.0	168.0					4																	152592364		2203	4300	6503	SO:0001583	missense	5188	exon13			TTATCATGACTGG																												ENST00000515812.1:c.1513A>G	chr4.hg19:g.152592364T>C	ENSP00000426859:p.Met505Val	156.0	0.0	.		187.0	88.0	.	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.061	-1.224008	0.01530	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.39592	1.07;1.08	5.8	-5.06	0.02946	Asn/Gln amidotransferase (2);	0.986159	0.08279	N	0.970181	T	0.13286	0.0322	N	0.02181	-0.65	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39961	-0.9588	10	0.06365	T	0.9	0.2792	10.1442	0.42753	0.0:0.1381:0.5532:0.3086	.	546	O75879	GATB_HUMAN	V	546;505	ENSP00000263985:M546V;ENSP00000426859:M505V	ENSP00000263985:M546V	M	-	1	0	PET112	152811814	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.347000	0.07750	-0.814000	0.04352	-0.904000	0.02843	ATG	.	.	.	none		0.483	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
F12	2161	hgsc.bcm.edu	37	5	176831341	176831341	+	Silent	SNP	G	G	A			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr5:176831341G>A	ENST00000253496.3	-	9	922	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	292	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CACTGTGCCAGGTCGCAGTAC	0.692									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L292L		Atlas-SNP	.											.	F12	35	.	0			c.C874T						PASS	.						17.0	21.0	19.0					5																	176831341		2201	4296	6497	SO:0001819	synonymous_variant	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GTGCCAGGTCGCA	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.874C>T	chr5.hg19:g.176831341G>A		50.0	0.0	.	1934	35.0	15.0	.	NM_000505	P78339	Silent	SNP	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.	.	none		0.692	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1		
VPS37D	155382	hgsc.bcm.edu	37	7	73083798	73083798	+	Missense_Mutation	SNP	C	C	G	rs370705512		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr7:73083798C>G	ENST00000324941.4	+	2	322	c.188C>G	c.(187-189)gCg>gGg	p.A63G	VPS37D_ENST00000451519.1_Intron	NM_001077621.1	NP_001071089.1			vacuolar protein sorting 37 homolog D (S. cerevisiae)											central_nervous_system(1)|ovary(1)	2		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCCAACTACGCGCTGGCCAAG	0.677																																					p.A63G		Atlas-SNP	.											.	VPS37D	10	.	0			c.C188G						PASS	.						7.0	9.0	8.0					7																	73083798		1885	4067	5952	SO:0001583	missense	155382	exon2			ACTACGCGCTGGC	AY081952	CCDS43596.1	7q11.23	2007-07-27	2006-04-04	2005-08-18	ENSG00000176428	ENSG00000176428			18287	protein-coding gene	gene with protein product		610039	"""Williams Beuren syndrome chromosome region 24"", ""vacuolar protein sorting 37D (yeast)"""	WBSCR24		15218037	Standard	NM_001077621		Approved	MGC35352	uc003tyr.3	Q86XT2	OTTHUMG00000157227	ENST00000324941.4:c.188C>G	chr7.hg19:g.73083798C>G	ENSP00000320416:p.Ala63Gly	7.0	0.0	.		10.0	4.0	.	NM_001077621		Missense_Mutation	SNP	ENST00000324941.4	hg19	CCDS43596.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336561	0.41398	.	.	ENSG00000176428	ENST00000324941	T	0.77229	-1.08	4.3	3.41	0.39046	Modifier of rudimentary, Modr (1);	0.335218	0.24041	U	0.042099	T	0.64438	0.2598	N	0.14661	0.345	0.80722	D	1	P	0.49090	0.919	P	0.46172	0.506	T	0.66002	-0.6031	10	0.66056	D	0.02	.	8.0448	0.30542	0.0:0.8859:0.0:0.1141	.	63	Q86XT2	VP37D_HUMAN	G	63	ENSP00000320416:A63G	ENSP00000320416:A63G	A	+	2	0	VPS37D	72721734	0.015000	0.18098	0.868000	0.34077	0.570000	0.35934	1.008000	0.29872	1.024000	0.39682	0.563000	0.77884	GCG	.	.	.	alt		0.677	VPS37D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348064.1	NM_152560	
EDF1	8721	hgsc.bcm.edu	37	9	139757816	139757816	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr9:139757816C>A	ENST00000224073.1	-	3	242	c.215G>T	c.(214-216)aGg>aTg	p.R72M	EDF1_ENST00000371649.1_Missense_Mutation_p.R72M|EDF1_ENST00000371648.4_Missense_Mutation_p.R72M	NM_003792.2	NP_003783.1	O60869	EDF1_HUMAN	endothelial differentiation-related factor 1	72	Interaction with NR5A2, PPARG and NR1H3.|Interaction with TBP and NR5A1.				endothelial cell differentiation (GO:0045446)|multicellular organismal development (GO:0007275)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			lung(1)	1	all_cancers(76;0.0841)|all_epithelial(76;0.217)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CAGGGTCACCCTGTCATGGTG	0.617																																					p.R72M		Atlas-SNP	.											.	EDF1	9	.	0			c.G215T						PASS	.						150.0	112.0	125.0					9																	139757816		2203	4300	6503	SO:0001583	missense	8721	exon3			GTCACCCTGTCAT	AJ005259	CCDS7011.1, CCDS7012.1, CCDS65193.1	9q34.3	2009-11-06			ENSG00000107223	ENSG00000107223			3164	protein-coding gene	gene with protein product	"""multiprotein bridging factor-1"""	605107				9813014, 15112053	Standard	NM_003792		Approved	EDF-1	uc004cjt.1	O60869	OTTHUMG00000020948	ENST00000224073.1:c.215G>T	chr9.hg19:g.139757816C>A	ENSP00000224073:p.Arg72Met	69.0	0.0	.		48.0	19.0	.	NM_003792	Q5T5T2|Q9UIM1	Missense_Mutation	SNP	ENST00000224073.1	hg19	CCDS7011.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.877120	0.91664	.	.	ENSG00000107223	ENST00000371649;ENST00000224073;ENST00000371648	.	.	.	5.79	4.9	0.64082	Lambda repressor-like, DNA-binding (1);Multiprotein bridging factor 1, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76877	0.4049	M	0.80847	2.515	0.80722	D	1	P;P	0.48407	0.897;0.91	P;P	0.57425	0.725;0.82	T	0.80741	-0.1247	9	0.87932	D	0	-10.8624	14.6074	0.68489	0.0:0.9301:0.0:0.0699	.	72;72	O60869-2;O60869	.;EDF1_HUMAN	M	72	.	ENSP00000224073:R72M	R	-	2	0	EDF1	138877637	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.317000	0.79018	1.463000	0.47967	0.655000	0.94253	AGG	.	.	.	none		0.617	EDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055143.1		
RPL6	6128	hgsc.bcm.edu	37	12	112843158	112843158	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:112843158C>T	ENST00000424576.2	-	7	922	c.737G>A	c.(736-738)cGc>cAc	p.R246H	RPL6_ENST00000202773.9_Missense_Mutation_p.R246H	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	246					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|large_intestine(6)|lung(3)	10						ATCAATCTTGCGCTGCTCCGT	0.393																																					p.R246H		Atlas-SNP	.											.	RPL6	20	.	0			c.G737A						PASS	.						23.0	25.0	24.0					12																	112843158		2187	4288	6475	SO:0001583	missense	6128	exon7			ATCTTGCGCTGCT	X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"""L ribosomal proteins"""	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.737G>A	chr12.hg19:g.112843158C>T	ENSP00000403172:p.Arg246His	49.0	0.0	.		59.0	16.0	.	NM_001024662	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	hg19	CCDS9162.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.498413	0.64298	.	.	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.34072	1.38;1.38	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.66297	2.02	0.80722	D	1	B	0.30439	0.279	B	0.29524	0.103	T	0.40572	-0.9556	10	0.62326	D	0.03	.	16.8348	0.85954	0.0:1.0:0.0:0.0	.	246	Q02878	RL6_HUMAN	H	246;246;186	ENSP00000202773:R246H;ENSP00000403172:R246H	ENSP00000202773:R246H	R	-	2	0	RPL6	111327541	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.919000	0.75793	2.408000	0.81797	0.591000	0.81541	CGC	.	.	.	none		0.393	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1		
CHD2	1106	hgsc.bcm.edu	37	15	93567925	93567925	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr15:93567925G>A	ENST00000394196.4	+	39	6545	c.5477G>A	c.(5476-5478)cGg>cAg	p.R1826Q		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1826					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TGGAATGTTCGGAAAACATAA	0.428																																					p.R1826Q		Atlas-SNP	.											CHD2_ENST00000394196,NS,carcinoma,0,1	CHD2	280	.	0			c.G5477A						PASS	.						50.0	47.0	48.0					15																	93567925		1887	4107	5994	SO:0001583	missense	1106	exon39			ATGTTCGGAAAAC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.5477G>A	chr15.hg19:g.93567925G>A	ENSP00000377747:p.Arg1826Gln	59.0	0.0	.		44.0	4.0	.	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	36	5.643949	0.96704	.	.	ENSG00000173575	ENST00000394196	D	0.92647	-3.08	5.56	5.56	0.83823	.	.	.	.	.	D	0.93485	0.7921	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.94151	0.7405	9	0.72032	D	0.01	-0.1389	19.8965	0.96963	0.0:0.0:1.0:0.0	.	1826	O14647	CHD2_HUMAN	Q	1826	ENSP00000377747:R1826Q	ENSP00000377747:R1826Q	R	+	2	0	CHD2	91368929	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.932000	0.75869	2.771000	0.95319	0.563000	0.77884	CGG	.	.	.	none		0.428	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67315014	67315014	+	Missense_Mutation	SNP	G	G	C			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:67315014G>C	ENST00000360461.5	+	4	3275	c.740G>C	c.(739-741)gGa>gCa	p.G247A	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.G247A|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.G247A|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.G166A	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	247							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CAGGCACTGGGACTGACAGTG	0.552																																					p.G247A		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.G740C						PASS	.						138.0	123.0	128.0					16																	67315014		2198	4300	6498	SO:0001583	missense	25894	exon5			CACTGGGACTGAC	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.740G>C	chr16.hg19:g.67315014G>C	ENSP00000353646:p.Gly247Ala	155.0	0.0	.		118.0	62.0	.	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	hg19	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	34	5.393426	0.96009	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.71	5.71	0.89125	.	0.000000	0.32802	N	0.005631	T	0.66366	0.2782	M	0.88570	2.965	0.35318	D	0.78447	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.78059	-0.2352	10	0.62326	D	0.03	.	15.3559	0.74425	0.0:0.0:1.0:0.0	.	166;54;247	Q58EX7-2;B4E3H4;Q58EX7	.;.;PKHG4_HUMAN	A	247;247;247;166	ENSP00000353646:G247A;ENSP00000401118:G247A;ENSP00000368649:G247A;ENSP00000398030:G166A	ENSP00000353646:G247A	G	+	2	0	PLEKHG4	65872515	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.887000	0.69751	2.688000	0.91661	0.591000	0.81541	GGA	.	.	.	none		0.552	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
ABR	29	hgsc.bcm.edu	37	17	975901	975901	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:975901C>A	ENST00000302538.5	-	8	993	c.847G>T	c.(847-849)Gag>Tag	p.E283*	ABR_ENST00000574437.1_Nonsense_Mutation_p.E237*|ABR_ENST00000536794.2_Nonsense_Mutation_p.E65*|ABR_ENST00000544583.2_Nonsense_Mutation_p.E237*|ABR_ENST00000291107.2_Nonsense_Mutation_p.E246*	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	283	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E283K(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TCGATGTCCTCGTTGATGCTG	0.642																																					p.E283X	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											ABR,NS,carcinoma,0,1	ABR	119	.	1	Substitution - Missense(1)	breast(1)	c.G847T						PASS	.						99.0	78.0	85.0					17																	975901		2203	4300	6503	SO:0001587	stop_gained	29	exon8			TGTCCTCGTTGAT	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.847G>T	chr17.hg19:g.975901C>A	ENSP00000303909:p.Glu283*	41.0	0.0	.		30.0	2.0	.	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Nonsense_Mutation	SNP	ENST00000302538.5	hg19	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	C	37	6.326444	0.97476	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000382259	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	19.0001	0.92830	0.0:1.0:0.0:0.0	.	.	.	.	X	283;237;246;65;167	.	ENSP00000291107:E246X	E	-	1	0	ABR	922651	1.000000	0.71417	0.987000	0.45799	0.996000	0.88848	7.751000	0.85126	2.712000	0.92718	0.650000	0.86243	GAG	.	.	.	none		0.642	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
CDK12	51755	hgsc.bcm.edu	37	17	37627488	37627488	+	Missense_Mutation	SNP	T	T	A			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:37627488T>A	ENST00000447079.4	+	2	1436	c.1403T>A	c.(1402-1404)cTa>cAa	p.L468Q	CDK12_ENST00000430627.2_Missense_Mutation_p.L468Q	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	468					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						GTAACACATCTAAACACAGAG	0.383			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																											p.L468Q		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.T1403A						PASS	.						98.0	103.0	101.0					17																	37627488		2203	4300	6503	SO:0001583	missense	51755	exon2			CACATCTAAACAC	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.1403T>A	chr17.hg19:g.37627488T>A	ENSP00000398880:p.Leu468Gln	159.0	0.0	.		187.0	50.0	.	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	hg19	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.939975	0.34283	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.39787	1.06;1.06	5.76	3.58	0.41010	.	0.608641	0.12825	N	0.436065	T	0.22589	0.0545	N	0.14661	0.345	0.21220	N	0.99976	B;B;B	0.16603	0.01;0.01;0.018	B;B;B	0.25291	0.026;0.026;0.059	T	0.18967	-1.0320	10	0.25106	T	0.35	-0.9823	2.5375	0.04717	0.2138:0.3455:0.0:0.4407	.	467;468;468	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	Q	468	ENSP00000407720:L468Q;ENSP00000398880:L468Q	ENSP00000407720:L468Q	L	+	2	0	CDK12	34881014	0.002000	0.14202	1.000000	0.80357	0.998000	0.95712	0.584000	0.23864	1.076000	0.40961	0.528000	0.53228	CTA	.	.	.	none		0.383	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
JUP	3728	hgsc.bcm.edu	37	17	39914006	39914006	+	Missense_Mutation	SNP	G	G	T	rs199511559		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:39914006G>T	ENST00000393931.3	-	11	1922	c.1804C>A	c.(1804-1806)Cgc>Agc	p.R602S	JUP_ENST00000540235.1_Intron|JUP_ENST00000393930.1_Missense_Mutation_p.R602S|JUP_ENST00000310706.5_Missense_Mutation_p.R602S	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	602	Interaction with DSC1.				adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)	p.R602C(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GCAGCCACGCGCTGGATGTTC	0.667																																					p.R602S	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											JUP,NS,carcinoma,0,1	JUP	64	.	1	Substitution - Missense(1)	endometrium(1)	c.C1804A						PASS	.						25.0	24.0	25.0					17																	39914006		2203	4297	6500	SO:0001583	missense	3728	exon11			CCACGCGCTGGAT	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"""Armadillo repeat containing"""	6207	protein-coding gene	gene with protein product		173325	"""catenin (cadherin-associated protein), gamma 80kDa"""	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.1804C>A	chr17.hg19:g.39914006G>T	ENSP00000377508:p.Arg602Ser	47.0	0.0	.		56.0	4.0	.	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	hg19	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.128863	0.77549	.	.	ENSG00000173801	ENST00000393930;ENST00000310706;ENST00000393931	T;T;T	0.70869	-0.52;-0.52;-0.52	4.83	4.83	0.62350	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80899	0.4712	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82339	-0.0506	10	0.87932	D	0	-13.1972	12.2188	0.54423	0.0:0.0:0.83:0.17	.	602	P14923	PLAK_HUMAN	S	602	ENSP00000377507:R602S;ENSP00000311113:R602S;ENSP00000377508:R602S	ENSP00000311113:R602S	R	-	1	0	JUP	37167532	1.000000	0.71417	0.998000	0.56505	0.634000	0.38068	4.360000	0.59455	2.518000	0.84900	0.561000	0.74099	CGC	.	.	.	alt		0.667	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1		
CDC27	996	hgsc.bcm.edu	37	17	45214661	45214661	+	Silent	SNP	G	G	A	rs111322439		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:45214661G>A	ENST00000066544.3	-	14	1863	c.1770C>T	c.(1768-1770)ttC>ttT	p.F590F	CDC27_ENST00000531206.1_Silent_p.F596F|CDC27_ENST00000527547.1_Silent_p.F589F|CDC27_ENST00000446365.2_Silent_p.F529F	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	590					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAGCTCTCTGGAAGAATTTAA	0.383																																					p.F596F		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,4	CDC27	337	.	0			c.C1788T						PASS	.						58.0	61.0	60.0					17																	45214661		2203	4300	6503	SO:0001819	synonymous_variant	996	exon14			TCTCTGGAAGAAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1770C>T	chr17.hg19:g.45214661G>A		81.0	1.0	.		117.0	9.0	.	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	G|0.500;A|0.500	0.500	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
CLTC	1213	hgsc.bcm.edu	37	17	57754485	57754485	+	Missense_Mutation	SNP	A	A	G			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:57754485A>G	ENST00000269122.3	+	17	3006	c.2732A>G	c.(2731-2733)aAg>aGg	p.K911R	CLTC_ENST00000393043.1_Missense_Mutation_p.K911R|CLTC_ENST00000579815.1_3'UTR|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	911	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TATTGTGAGAAGAGAGATCCA	0.423			T	"""ALK, TFE3"""	"""ALCL, renal """																																p.K911R		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	.	CLTC	124	.	0			c.A2732G						PASS	.						118.0	116.0	116.0					17																	57754485		2203	4300	6503	SO:0001583	missense	1213	exon17			GTGAGAAGAGAGA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2732A>G	chr17.hg19:g.57754485A>G	ENSP00000269122:p.Lys911Arg	82.0	0.0	.		127.0	82.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	34	5.330051	0.95733	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.23552	1.9;1.9	5.69	5.69	0.88448	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56156	0.1966	M	0.85945	2.785	0.80722	D	1	D;B	0.69078	0.997;0.139	D;B	0.83275	0.996;0.394	T	0.60707	-0.7210	10	0.48119	T	0.1	.	15.9483	0.79809	1.0:0.0:0.0:0.0	.	911;911	Q00610;Q00610-2	CLH1_HUMAN;.	R	911	ENSP00000269122:K911R;ENSP00000376763:K911R	ENSP00000269122:K911R	K	+	2	0	CLTC	55109267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.228000	0.95250	2.168000	0.68352	0.455000	0.32223	AAG	.	.	.	none		0.423	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
SLC16A6	9120	hgsc.bcm.edu	37	17	66267173	66267173	+	Silent	SNP	A	A	G			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:66267173A>G	ENST00000327268.4	-	6	1292	c.1128T>C	c.(1126-1128)ttT>ttC	p.F376F	SLC16A6_ENST00000580666.1_Silent_p.F376F|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	376					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	TAGCAAAAGTAAAGGCAAACA	0.443																																					p.F376F		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T1128C						PASS	.						120.0	112.0	115.0					17																	66267173		2203	4300	6503	SO:0001819	synonymous_variant	9120	exon6			AAAAGTAAAGGCA	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.1128T>C	chr17.hg19:g.66267173A>G		94.0	0.0	.		130.0	85.0	.	NM_001174166	Q6P1X3	Silent	SNP	ENST00000327268.4	hg19	CCDS11675.1																																																																																			.	.	.	none		0.443	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
FBXO7	25793	hgsc.bcm.edu	37	22	32889131	32889131	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr22:32889131C>A	ENST00000266087.7	+	7	1334	c.1007C>A	c.(1006-1008)cCa>cAa	p.P336Q	FBXO7_ENST00000397426.1_Missense_Mutation_p.P222Q|FBXO7_ENST00000382058.3_Missense_Mutation_p.P257Q	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	336	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTCGTCCTCCCATTGGAACTG	0.438																																					p.P336Q		Atlas-SNP	.											.	FBXO7	131	.	0			c.C1007A						PASS	.						371.0	310.0	330.0					22																	32889131		2203	4300	6503	SO:0001583	missense	25793	exon7			TCCTCCCATTGGA	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.1007C>A	chr22.hg19:g.32889131C>A	ENSP00000266087:p.Pro336Gln	270.0	1.0	.		278.0	111.0	.	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	hg19	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.192232	0.78902	.	.	ENSG00000100225	ENST00000266087;ENST00000382058;ENST00000397426	D;D;D	0.99709	-6.48;-6.48;-6.48	6.08	6.08	0.98989	F-box domain, cyclin-like (3);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;1.0	D	0.97617	1.0133	10	0.87932	D	0	-17.0815	20.6634	0.99662	0.0:1.0:0.0:0.0	.	336;257;336	A8K7F7;Q9Y3I1-2;Q9Y3I1	.;.;FBX7_HUMAN	Q	336;257;222	ENSP00000266087:P336Q;ENSP00000371490:P257Q;ENSP00000380571:P222Q	ENSP00000266087:P336Q	P	+	2	0	FBXO7	31219131	1.000000	0.71417	0.815000	0.32552	0.630000	0.37929	5.980000	0.70516	2.894000	0.99253	0.655000	0.94253	CCA	.	.	.	none		0.438	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
INF2	64423	hgsc.bcm.edu	37	14	105174895	105174896	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr14:105174895_105174896insC	ENST00000392634.4	+	9	1970_1971	c.1858_1859insC	c.(1858-1860)gccfs	p.A620fs	INF2_ENST00000330634.7_Frame_Shift_Ins_p.A620fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	620	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CACCATGGTGGCCCCCCGGGCC	0.703											OREG0022959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A620fs		Atlas-INDEL	.											.	INF2	148	.	0			c.1858_1859insC						PASS	.																																			SO:0001589	frameshift_variant	64423	exon9			.	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1864dupC	chr14.hg19:g.105174901_105174901dupC	ENSP00000376410:p.Ala620fs	44.0	0.0	0	1387	43.0	22.0	0.511628	NM_001031714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Ins	INS	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.	.	none		0.703	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
FGGY	55277	hgsc.bcm.edu	37	1	60133071	60133091	+	Splice_Site	DEL	TACTGGTAAGTCTGGGAAAGA	TACTGGTAAGTCTGGGAAAGA	-	rs115318188	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	TACTGGTAAGTCTGGGAAAGA	TACTGGTAAGTCTGGGAAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:60133071_60133091delTACTGGTAAGTCTGGGAAAGA	ENST00000303721.7	+	13	1587_1591	c.1413_1417delTACTGGTAAGTCTGGGAAAGA	c.(1411-1419)attactggt>atgt	p.471_473ITG>M	FGGY_ENST00000371218.4_Splice_Site_p.495_497ITG>M|FGGY_ENST00000371210.1_Splice_Site_p.172_174ITG>M|FGGY_ENST00000371212.1_Splice_Site_p.383_385ITG>M	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	471					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.G361C(1)|p.G473C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					ATGCGGACATTACTGGTAAGTCTGGGAAAGAGGAGAGAAGG	0.466																																					p.495_497del		Atlas-INDEL	.											.	FGGY	99	.	2	Substitution - Missense(2)	lung(2)	c.1484_1489del						PASS	.																																			SO:0001630	splice_region_variant	55277	exon14			.		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1417+1TACTGGTAAGTCTGGGAAAGA>-	chr1.hg19:g.60133071_60133091delTACTGGTAAGTCTGGGAAAGA		252.0	0.0	0		119.0	19.0	0.159664	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	In_Frame_Del	DEL	ENST00000303721.7	hg19	CCDS611.2																																																																																			.	.	.	none		0.466	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	In_Frame_Del
PPP6R3	55291	hgsc.bcm.edu	37	11	68318634	68318637	+	Frame_Shift_Del	DEL	CATC	CATC	-			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	CATC	CATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:68318634_68318637delCATC	ENST00000393800.2	+	6	852_855	c.598_601delCATC	c.(598-603)catccafs	p.HP200fs	PPP6R3_ENST00000527403.2_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000534534.1_Intron|PPP6R3_ENST00000265636.5_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000393799.2_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000393801.3_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000529710.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000524904.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000265637.4_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000524845.1_Frame_Shift_Del_p.HP200fs	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	200					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGAAATAGTTCATCCATCGCAAGA	0.348																																					p.199_200del		Atlas-INDEL	.											.	PPP6R3	159	.	0			c.597_600del						PASS	.																																			SO:0001589	frameshift_variant	55291	exon6			.	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.598_601delCATC	chr11.hg19:g.68318638_68318641delCATC	ENSP00000377389:p.His200fs	79.0	0.0	0		55.0	25.0	0.454545	NM_001164161	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Frame_Shift_Del	DEL	ENST00000393800.2	hg19	CCDS53672.1																																																																																			.	.	.	none		0.348	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
OR52H1	390067	hgsc.bcm.edu	37	11	5566652	5566652	+	Frame_Shift_Del	DEL	C	C	-	rs565760908		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:5566652delC	ENST00000322653.4	-	1	127	c.102delG	c.(100-102)tggfs	p.W34fs	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	34						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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAATTCCAATCCACACATGGA	0.473																																					p.I35fs		Atlas-INDEL	.											.	OR52H1	46	.	0			c.103delA						PASS	.						88.0	80.0	83.0					11																	5566652		2201	4297	6498	SO:0001589	frameshift_variant	390067	exon1			.	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.102delG	chr11.hg19:g.5566652delC	ENSP00000326259:p.Trp34fs	99.0	0.0	0		72.0	27.0	0.375	NM_001005289	B9EH26|Q6IF79	Frame_Shift_Del	DEL	ENST00000322653.4	hg19	CCDS31386.1																																																																																			.	.	.	none		0.473	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
SBNO1	55206	hgsc.bcm.edu	37	12	123801801	123801802	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:123801801_123801802insT	ENST00000602398.1	-	21	3028_3029	c.2901_2902insA	c.(2899-2904)ttacctfs	p.P968fs	SBNO1_ENST00000420886.2_Frame_Shift_Ins_p.P968fs|SBNO1_ENST00000267176.4_Frame_Shift_Ins_p.P967fs|SBNO1_ENST00000602750.1_Frame_Shift_Ins_p.P967fs			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	968					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GCGCTCCAAGGTAATTCTAAAG	0.396																																					p.P968fs		Atlas-INDEL	.											.	SBNO1	138	.	0			c.2902_2903insA						PASS	.																																			SO:0001589	frameshift_variant	55206	exon20			.	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2902dupA	chr12.hg19:g.123801802_123801802dupT	ENSP00000473665:p.Pro968fs	91.0	0.0	0		115.0	36.0	0.313043	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Frame_Shift_Ins	INS	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	.	.	none		0.396	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
NCOA3	8202	hgsc.bcm.edu	37	20	46252817	46252817	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:46252817delA	ENST00000371998.3	+	4	437	c.246delA	c.(244-246)atafs	p.I82fs	NCOA3_ENST00000341724.6_Frame_Shift_Del_p.I82fs|NCOA3_ENST00000372004.3_Frame_Shift_Del_p.I82fs|NCOA3_ENST00000371997.3_Frame_Shift_Del_p.I82fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	82	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TACGTCAAATAAAAGAGCAAG	0.378																																					p.I82fs		Atlas-INDEL	.											.	NCOA3	156	.	0			c.245delT						PASS	.						61.0	58.0	59.0					20																	46252817		2203	4300	6503	SO:0001589	frameshift_variant	8202	exon4			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.246delA	chr20.hg19:g.46252817delA	ENSP00000361066:p.Ile82fs	38.0	0.0	0		89.0	17.0	0.191011	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.	.	none		0.378	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
