#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
MYO3A	53904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	26432481	26432481	+	Silent	SNP	A	A	G			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr10:26432481A>G	ENST00000265944.5	+	21	2533	c.2367A>G	c.(2365-2367)ctA>ctG	p.L789L	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	789	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TACTTTCCCTACTTGATGAAG	0.403																																																0													130.0	123.0	126.0					10																	26432481		2203	4300	6503	SO:0001819	synonymous_variant	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2367A>G	10.37:g.26432481A>G			Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																				0.403	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		29	35	29	35
SPDYC	387778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	64939962	64939962	+	Silent	SNP	A	A	G			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr11:64939962A>G	ENST00000377185.2	+	5	484	c.402A>G	c.(400-402)ccA>ccG	p.P134P	AP003068.18_ENST00000534819.1_RNA	NM_001008778.1	NP_001008778.1			speedy/RINGO cell cycle regulator family member C											breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)	16						AGATTTTTCCATGGGCCCTGG	0.562																																																0													101.0	103.0	102.0					11																	64939962		2201	4297	6498	SO:0001819	synonymous_variant	387778			AY820305	CCDS31606.1	11q13.1	2013-05-08	2013-05-08		ENSG00000204710	ENSG00000204710		"""Speedy homologs"""	32681	protein-coding gene	gene with protein product		614030	"""speedy homolog C (Xenopus laevis)"""			15611625	Standard	NM_001008778		Approved	Ringo2	uc010rnz.2	Q5MJ68	OTTHUMG00000165611	ENST00000377185.2:c.402A>G	11.37:g.64939962A>G				Silent	SNP	ENST00000377185.2	37	CCDS31606.1																																																																																				0.562	SPDYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385299.1	NM_001008778		56	99	56	99
MTNR1B	4544	hgsc.bcm.edu;broad.mit.edu	37	11	92714797	92714797	+	Silent	SNP	T	T	C			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr11:92714797T>C	ENST00000257068.2	+	2	414	c.408T>C	c.(406-408)atT>atC	p.I136I		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	136					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CCATCGCCATTAACCGCTACT	0.607																																																0													134.0	118.0	123.0					11																	92714797		2201	4298	6499	SO:0001819	synonymous_variant	4544			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"""GPCR / Class A : Melatonin receptors"""	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.408T>C	11.37:g.92714797T>C				Silent	SNP	ENST00000257068.2	37	CCDS8290.1																																																																																				0.607	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			6	63	6	63
EML5	161436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	89093251	89093251	+	Missense_Mutation	SNP	G	G	C			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr14:89093251G>C	ENST00000380664.5	-	33	4646	c.4647C>G	c.(4645-4647)agC>agG	p.S1549R	EML5_ENST00000553320.1_5'UTR|EML5_ENST00000352093.5_Missense_Mutation_p.S1511R|EML5_ENST00000554922.1_Missense_Mutation_p.S1557R			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1549						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GCCCTTTTTTGCTAAGAAGAG	0.463																																																0													118.0	117.0	117.0					14																	89093251		1950	4143	6093	SO:0001583	missense	161436			AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.4647C>G	14.37:g.89093251G>C	ENSP00000370039:p.Ser1549Arg		B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.903214	0.33628	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.41758	0.99;0.99;0.99	5.04	4.07	0.47477	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.192785	0.52532	D	0.000063	T	0.26666	0.0652	L	0.28649	0.875	0.45490	D	0.998456	B;B	0.20164	0.035;0.042	B;B	0.30716	0.119;0.04	T	0.13845	-1.0494	10	0.15066	T	0.55	-13.2601	4.092	0.09973	0.3014:0.0:0.6986:0.0	.	1557;1549	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	R	1557;1511;1549	ENSP00000451998:S1557R;ENSP00000298315:S1511R;ENSP00000370039:S1549R	ENSP00000298315:S1511R	S	-	3	2	EML5	88163004	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.460000	0.60108	2.641000	0.89580	0.655000	0.94253	AGC		0.463	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			18	33	18	33
ARHGAP11A	9824	hgsc.bcm.edu;broad.mit.edu	37	15	32917835	32917835	+	Splice_Site	SNP	G	G	C			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr15:32917835G>C	ENST00000361627.3	+	6	1584		c.e6+1		ARHGAP11A_ENST00000563864.1_Splice_Site|ARHGAP11A_ENST00000567348.1_Splice_Site|ARHGAP11A_ENST00000565905.1_Splice_Site|ARHGAP11A_ENST00000543522.1_Splice_Site	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AGTGTAGGAGGTAAGTGGCGG	0.408																																					Colon(45;757 1134 30003 36652)											0													154.0	152.0	152.0					15																	32917835		2201	4300	6501	SO:0001630	splice_region_variant	9824			D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.862+1G>C	15.37:g.32917835G>C			B4DZN9|Q6PI96|Q9Y3S6	Splice_Site	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	22.3	4.273284	0.80580	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4746	0.90788	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGAP11A	30705127	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.278000	0.89899	2.426000	0.82243	0.655000	0.94253	.		0.408	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	Intron	9	105	9	105
CAPN15	6650	hgsc.bcm.edu;broad.mit.edu	37	16	598068	598068	+	Silent	SNP	C	C	T			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr16:598068C>T	ENST00000219611.2	+	4	1593	c.1230C>T	c.(1228-1230)ccC>ccT	p.P410P	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	410					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCGTCCTGCCCGAGCGCCCGG	0.751																																																0													3.0	4.0	4.0					16																	598068		1817	3693	5510	SO:0001819	synonymous_variant	6650			U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1230C>T	16.37:g.598068C>T			B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																				0.751	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		9	14	9	14
SF3B3	23450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	70594469	70594469	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr16:70594469G>A	ENST00000302516.5	+	16	2319	c.2108G>A	c.(2107-2109)cGa>cAa	p.R703Q		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	703					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				AAGCTCTTCCGAGTCCGAATG	0.522																																																0													110.0	98.0	102.0					16																	70594469		2198	4300	6498	SO:0001583	missense	23450			AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"""splicing factor 3b, subunit 3, 130kD"""			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2108G>A	16.37:g.70594469G>A	ENSP00000305790:p.Arg703Gln		Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	37	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.026851	0.75390	.	.	ENSG00000189091	ENST00000302516	T	0.31510	1.49	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.29914	0.0748	L	0.42744	1.35	0.80722	D	1	B	0.20550	0.046	B	0.13407	0.009	T	0.05733	-1.0867	10	0.19590	T	0.45	.	20.0953	0.97838	0.0:0.0:1.0:0.0	.	703	Q15393	SF3B3_HUMAN	Q	703	ENSP00000305790:R703Q	ENSP00000305790:R703Q	R	+	2	0	SF3B3	69151970	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	9.807000	0.99171	2.767000	0.95098	0.655000	0.94253	CGA		0.522	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		5	93	5	93
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7579350	7579350	+	Missense_Mutation	SNP	A	A	C	rs587781642		TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr17:7579350A>C	ENST00000269305.4	-	4	526	c.337T>G	c.(337-339)Ttc>Gtc	p.F113V	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.F113V|TP53_ENST00000359597.4_Missense_Mutation_p.F113V|TP53_ENST00000445888.2_Missense_Mutation_p.F113V|TP53_ENST00000413465.2_Missense_Mutation_p.F113V|TP53_ENST00000420246.2_Missense_Mutation_p.F113V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	113	Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		F -> C (in sporadic cancers; somatic mutation).|F -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|F -> I (in a sporadic cancer; somatic mutation).|F -> L (in sporadic cancers; somatic mutation).|F -> S (in sporadic cancers; somatic mutation).|F -> V (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.F113V(7)|p.G59fs*23(3)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.G112fs*9(1)|p.Y107fs*44(1)|p.G112_S116delGFLHS(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GAATGCAAGAAGCCCAGACGG	0.607		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	26	Whole gene deletion(8)|Deletion - Frameshift(8)|Substitution - Missense(7)|Deletion - In frame(3)	upper_aerodigestive_tract(5)|bone(4)|breast(4)|central_nervous_system(3)|lung(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|stomach(1)|urinary_tract(1)|liver(1)|oesophagus(1)											65.0	61.0	62.0					17																	7579350		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.337T>G	17.37:g.7579350A>C	ENSP00000269305:p.Phe113Val		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552094	0.86127	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99859	-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23;-7.23	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.76433	2.335	0.54753	D	0.999983	D;D;D;P;D;D;D	0.89917	1.0;1.0;1.0;0.474;1.0;1.0;1.0	D;D;D;B;D;D;D	0.97110	1.0;1.0;1.0;0.425;1.0;1.0;1.0	D	0.96597	0.9442	10	0.87932	D	0	-31.6488	12.5363	0.56144	1.0:0.0:0.0:0.0	.	74;113;113;113;113;113;113	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	V	113	ENSP00000410739:F113V;ENSP00000352610:F113V;ENSP00000269305:F113V;ENSP00000398846:F113V;ENSP00000391127:F113V;ENSP00000391478:F113V;ENSP00000424104:F113V;ENSP00000426252:F113V	ENSP00000269305:F113V	F	-	1	0	TP53	7520075	1.000000	0.71417	0.981000	0.43875	0.964000	0.63967	7.389000	0.79806	2.125000	0.65367	0.533000	0.62120	TTC		0.607	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		68	36	68	36
MFAP4	4239	hgsc.bcm.edu;broad.mit.edu	37	17	19290401	19290401	+	Intron	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr17:19290401G>A	ENST00000299610.4	-	1	91				MFAP4_ENST00000497081.2_5'Flank|MFAP4_ENST00000574313.2_5'Flank|MFAP4_ENST00000395592.2_Silent_p.L11L	NM_002404.2	NP_002395.1	P55083	MFAP4_HUMAN	microfibrillar-associated protein 4						cell adhesion (GO:0007155)|cellular response to UV-B (GO:0071493)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|regulation of collagen metabolic process (GO:0010712)|UV protection (GO:0009650)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)				large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	10	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					TCTGTGGCCAGGGGCCTCTGG	0.597																																																0																																										SO:0001627	intron_variant	4239			L38486	CCDS11208.1, CCDS56023.1	17p11.2	2013-02-06			ENSG00000166482	ENSG00000166482		"""Fibrinogen C domain containing"""	7035	protein-coding gene	gene with protein product	"""microfibril-associated glycoprotein 4"""	600596				7633408	Standard	NM_001198695		Approved		uc002gvs.3	P55083	OTTHUMG00000059585	ENST00000299610.4:c.6+61C>T	17.37:g.19290401G>A			A8KAJ1|A8MVM2|B4E317|Q6P680	Silent	SNP	ENST00000299610.4	37	CCDS11208.1																																																																																				0.597	MFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132493.2	NM_002404		14	19	14	19
GPATCH8	23131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	42483311	42483311	+	Missense_Mutation	SNP	C	C	G			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr17:42483311C>G	ENST00000591680.1	-	7	631	c.601G>C	c.(601-603)Gag>Cag	p.E201Q	GPATCH8_ENST00000434000.1_Missense_Mutation_p.E123Q	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	201							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		TTTCTTTGCTCTGCCAACTCA	0.368																																																0													77.0	81.0	80.0					17																	42483311		2203	4300	6503	SO:0001583	missense	23131			AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.601G>C	17.37:g.42483311C>G	ENSP00000467556:p.Glu201Gln		B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608268	0.66558	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.23552	1.9	5.59	5.59	0.84812	.	0.049959	0.85682	D	0.000000	T	0.46190	0.1380	L	0.60455	1.87	0.58432	D	0.999995	D	0.71674	0.998	P	0.59115	0.852	T	0.36744	-0.9735	10	0.66056	D	0.02	-19.7201	19.597	0.95544	0.0:1.0:0.0:0.0	.	201	Q9UKJ3	GPTC8_HUMAN	Q	201;123	ENSP00000395016:E123Q	ENSP00000335486:E201Q	E	-	1	0	GPATCH8	39838837	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.818000	0.86416	2.639000	0.89480	0.655000	0.94253	GAG		0.368	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		11	85	11	85
PRKCA	5578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	64738870	64738870	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr17:64738870G>A	ENST00000413366.3	+	13	1542	c.1516G>A	c.(1516-1518)Gcc>Acc	p.A506T		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	506	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	AGATTATATCGCCCCAGAGGT	0.488																																																0													86.0	80.0	82.0					17																	64738870		2203	4300	6503	SO:0001583	missense	5578				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1516G>A	17.37:g.64738870G>A	ENSP00000408695:p.Ala506Thr		B5BU22|Q15137|Q32M72|Q96RE4	Missense_Mutation	SNP	ENST00000413366.3	37	CCDS11664.1	.	.	.	.	.	.	.	.	.	.	G	33	5.193777	0.94960	.	.	ENSG00000154229	ENST00000413366;ENST00000284384	T	0.53640	0.61	5.6	5.6	0.85130	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79058	0.4382	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.84752	0.0757	10	0.87932	D	0	.	19.6224	0.95663	0.0:0.0:1.0:0.0	.	506;417	P17252;Q59FI5	KPCA_HUMAN;.	T	506;413	ENSP00000408695:A506T	ENSP00000284384:A413T	A	+	1	0	PRKCA	62169332	1.000000	0.71417	0.996000	0.52242	0.677000	0.39632	9.814000	0.99346	2.630000	0.89119	0.655000	0.94253	GCC		0.488	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1			9	23	9	23
KLHL14	57565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	30322013	30322013	+	Splice_Site	SNP	C	C	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr18:30322013C>A	ENST00000359358.4	-	3	1386		c.e3-1		KLHL14_ENST00000358095.4_Splice_Site	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14							endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						AGAGCGAATTCTTCACCCAAA	0.433																																																0													94.0	90.0	91.0					18																	30322013		2203	4300	6503	SO:0001630	splice_region_variant	57565			AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.948-1G>T	18.37:g.30322013C>A			A6NNW1|B4DHA0|Q8WU41	Splice_Site	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.491771	0.64074	.	.	ENSG00000197705	ENST00000359358;ENST00000358095	.	.	.	6.11	6.11	0.99139	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KLHL14	28576011	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.298000	0.78815	2.906000	0.99361	0.655000	0.94253	.		0.433	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		Intron	12	80	12	80
ZNF761	388561	hgsc.bcm.edu;broad.mit.edu	37	19	53958931	53958931	+	RNA	SNP	C	C	G			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr19:53958931C>G	ENST00000454407.1	+	0	1623							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GTGGCAAGACCTTTAGTCACA	0.408																																																0													153.0	154.0	154.0					19																	53958931		2203	4300	6503			388561			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958931C>G			Q6ZNB9	RNA	SNP	ENST00000454407.1	37																																																																																					0.408	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		15	165	15	165
ZMYM6	9204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	35476495	35476495	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr1:35476495C>T	ENST00000357182.4	-	9	1432	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H	ZMYM6_ENST00000487874.1_Missense_Mutation_p.R402H|ZMYM6_ENST00000373340.2_Missense_Mutation_p.R402H|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	402					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				AGCAGAGCCACGGATGGAGCT	0.547																																																0													76.0	78.0	78.0					1																	35476495		2203	4300	6503	SO:0001583	missense	9204			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.1205G>A	1.37:g.35476495C>T	ENSP00000349708:p.Arg402His		B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	C	6.947	0.544543	0.13312	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	T;T	0.22945	1.93;3.1	5.2	1.19	0.21007	.	2.757490	0.00923	N	0.002618	T	0.12817	0.0311	N	0.03608	-0.345	0.09310	N	1	B;P;B	0.37276	0.0;0.589;0.001	B;B;B	0.32583	0.0;0.148;0.006	T	0.20874	-1.0262	10	0.56958	D	0.05	-0.6684	7.3011	0.26422	0.0:0.6738:0.1223:0.2039	.	305;402;402	B4DWC0;O95789;O95789-1	.;ZMYM6_HUMAN;.	H	402	ENSP00000362437:R402H;ENSP00000349708:R402H	ENSP00000349708:R402H	R	-	2	0	ZMYM6	35249082	0.106000	0.21978	0.001000	0.08648	0.005000	0.04900	0.693000	0.25497	0.137000	0.18759	-0.150000	0.13652	CGT		0.547	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		9	83	9	83
SEC16B	89866	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	177909803	177909803	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr1:177909803C>T	ENST00000308284.6	-	17	2158	c.2069G>A	c.(2068-2070)cGc>cAc	p.R690H	RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	690					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GTCTCCACTGCGTCTTTCTAA	0.562																																																0													53.0	61.0	58.0					1																	177909803		2106	4223	6329	SO:0001583	missense	89866			AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2069G>A	1.37:g.177909803C>T	ENSP00000308339:p.Arg690His		A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787628	0.49997	.	.	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.15017	2.46	5.64	-0.913	0.10500	.	0.393150	0.24869	N	0.034947	T	0.24160	0.0585	L	0.54323	1.7	0.09310	N	0.999999	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.73380	0.953;0.98;0.953;0.98	T	0.23868	-1.0176	10	0.13108	T	0.6	-1.7289	4.9936	0.14228	0.0:0.433:0.1467:0.4203	.	245;691;690;387	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	H	690;374;405	ENSP00000308339:R690H	ENSP00000239472:R405H	R	-	2	0	AL359075.1	176176426	0.697000	0.27767	0.000000	0.03702	0.001000	0.01503	-0.078000	0.11375	-0.130000	0.11599	-0.793000	0.03317	CGC		0.562	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		29	32	29	32
NID1	4811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	236144995	236144995	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr1:236144995G>A	ENST00000264187.6	-	16	3225	c.3143C>T	c.(3142-3144)gCg>gTg	p.A1048V	NID1_ENST00000366595.3_Missense_Mutation_p.A915V	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1048					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GTCCAGCTTCGCCACTTCTAT	0.498																																																0													84.0	80.0	82.0					1																	236144995		2203	4300	6503	SO:0001583	missense	4811			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3143C>T	1.37:g.236144995G>A	ENSP00000264187:p.Ala1048Val		Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.352853	0.82132	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.27256	1.68;1.68	5.88	5.88	0.94601	Six-bladed beta-propeller, TolB-like (1);	0.094778	0.64402	D	0.000001	T	0.58977	0.2160	M	0.84846	2.72	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	P;D	0.80764	0.763;0.994	T	0.62618	-0.6816	10	0.72032	D	0.01	.	20.2265	0.98340	0.0:0.0:1.0:0.0	.	915;1048	P14543-2;P14543	.;NID1_HUMAN	V	1048;915	ENSP00000264187:A1048V;ENSP00000355554:A915V	ENSP00000264187:A1048V	A	-	2	0	NID1	234211618	1.000000	0.71417	0.058000	0.19502	0.121000	0.20230	9.802000	0.99131	2.769000	0.95229	0.655000	0.94253	GCG		0.498	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		30	52	30	52
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	237754205	237754205	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr1:237754205G>A	ENST00000366574.2	+	31	4390	c.4073G>A	c.(4072-4074)cGt>cAt	p.R1358H	RYR2_ENST00000360064.6_Missense_Mutation_p.R1356H|RYR2_ENST00000542537.1_Missense_Mutation_p.R1342H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1358	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTGCCCGATCGTGTTGACAAA	0.428																																																0													70.0	66.0	67.0					1																	237754205		1898	4122	6020	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4073G>A	1.37:g.237754205G>A	ENSP00000355533:p.Arg1358His		Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	g	14.26	2.482403	0.44147	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96685	-4.09;-4.05;-4.08	5.34	5.34	0.76211	B30.2/SPRY domain (1);	0.094683	0.41605	D	0.000852	D	0.90287	0.6962	N	0.14661	0.345	0.25752	N	0.98504	P	0.48764	0.915	B	0.35182	0.197	D	0.86159	0.1592	10	0.59425	D	0.04	.	15.1195	0.72432	0.0:0.1408:0.8591:0.0	.	1358	Q92736	RYR2_HUMAN	H	1358;1356;1342	ENSP00000355533:R1358H;ENSP00000353174:R1356H;ENSP00000443798:R1342H	ENSP00000353174:R1356H	R	+	2	0	RYR2	235820828	1.000000	0.71417	0.726000	0.30738	0.964000	0.63967	8.543000	0.90651	2.937000	0.99478	0.650000	0.86243	CGT		0.428	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		9	31	9	31
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	141607789	141607789	+	Silent	SNP	G	G	A	rs372242789		TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr2:141607789G>A	ENST00000389484.3	-	29	5792	c.4821C>T	c.(4819-4821)gaC>gaT	p.D1607D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1607					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.D1607D(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCACAGTAACGTCATCAATAT	0.368										TSP Lung(27;0.18)			G|||	1	0.000199681	0.0008	0.0	5008	,	,		15391	0.0		0.0	False		,,,				2504	0.0				Colon(99;50 2074 2507 20106)											1	Substitution - coding silent(1)	central_nervous_system(1)						G		1,4405	2.1+/-5.4	0,1,2202	167.0	158.0	161.0		4821	-4.2	1.0	2		161	0,8600		0,0,4300	no	coding-synonymous	LRP1B	NM_018557.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1607/4600	141607789	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4821C>T	2.37:g.141607789G>A			Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.368	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		12	60	12	60
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	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			32	59	32	59
SNX18	112574	hgsc.bcm.edu;broad.mit.edu	37	5	53815358	53815358	+	Missense_Mutation	SNP	C	C	G			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr5:53815358C>G	ENST00000326277.3	+	1	1766	c.1576C>G	c.(1576-1578)Cag>Gag	p.Q526E	SNX18_ENST00000381410.4_Missense_Mutation_p.Q526E|SNX18_ENST00000343017.6_Missense_Mutation_p.Q526E	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	526	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				AGCGCTGTATCAGGGGCATCT	0.557																																																0													126.0	117.0	120.0					5																	53815358		2203	4300	6503	SO:0001583	missense	112574			AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1576C>G	5.37:g.53815358C>G	ENSP00000317332:p.Gln526Glu		B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	37	CCDS3962.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.981299	0.74474	.	.	ENSG00000178996	ENST00000343017;ENST00000381410;ENST00000326277	T;T;T	0.14266	2.68;2.52;2.86	4.64	4.64	0.57946	Sorting nexin protein, WASP-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.26231	0.0640	M	0.71581	2.175	0.58432	D	0.999999	P;P	0.52842	0.956;0.745	P;P	0.48304	0.573;0.503	T	0.07597	-1.0764	10	0.72032	D	0.01	-27.7909	17.7087	0.88316	0.0:1.0:0.0:0.0	.	526;526	Q96RF0;Q96RF0-2	SNX18_HUMAN;.	E	526	ENSP00000342276:Q526E;ENSP00000370817:Q526E;ENSP00000317332:Q526E	ENSP00000317332:Q526E	Q	+	1	0	SNX18	53851115	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.645000	0.83430	2.421000	0.82119	0.561000	0.74099	CAG		0.557	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2			8	140	8	140
NKX3-1	4824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	23539038	23539038	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr8:23539038G>A	ENST00000380871.4	-	2	438	c.401C>T	c.(400-402)aCt>aTt	p.T134I	NKX3-1_ENST00000523261.1_Missense_Mutation_p.T59I	NM_006167.3	NP_006158.2	Q99801	NKX31_HUMAN	NK3 homeobox 1	134					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|androgen receptor signaling pathway (GO:0030521)|branching involved in prostate gland morphogenesis (GO:0060442)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to steroid hormone stimulus (GO:0071383)|cellular response to tumor necrosis factor (GO:0071356)|dorsal aorta development (GO:0035907)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|heart development (GO:0007507)|male gonad development (GO:0008584)|metanephros development (GO:0001656)|mitotic cell cycle arrest (GO:0071850)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of transcription, DNA-templated (GO:0045892)|pharyngeal system development (GO:0060037)|positive regulation of androgen secretion (GO:2000836)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell death (GO:0010942)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein kinase B signaling (GO:0043491)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|salivary gland development (GO:0007431)|somitogenesis (GO:0001756)|steroid hormone mediated signaling pathway (GO:0043401)	intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|core promoter binding (GO:0001047)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|histone deacetylase binding (GO:0042826)|protein kinase activator activity (GO:0030295)|protein self-association (GO:0043621)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(3)|lung(4)|prostate(5)|skin(2)	14		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		GATCACCTGAGTGTGGGAGAA	0.577																																																0													109.0	114.0	112.0					8																	23539038		2203	4300	6503	SO:0001583	missense	4824				CCDS6042.1, CCDS59095.1	8p21.2	2012-03-09	2007-07-09	2002-10-04	ENSG00000167034	ENSG00000167034		"""Homeoboxes / ANTP class : NKL subclass"""	7838	protein-coding gene	gene with protein product		602041	"""NK homeobox (Drosophila), family 3, A"", ""NK3 transcription factor related, locus 1 (Drosophila)"""	NKX3A		9226374	Standard	NM_006167		Approved	NKX3.1, BAPX2	uc011kzx.2	Q99801	OTTHUMG00000097851	ENST00000380871.4:c.401C>T	8.37:g.23539038G>A	ENSP00000370253:p.Thr134Ile		O15465|Q9H2P4|Q9H2P5|Q9H2P6|Q9H2P7|Q9HBG0	Missense_Mutation	SNP	ENST00000380871.4	37	CCDS6042.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.485695	0.63962	.	.	ENSG00000167034	ENST00000380871;ENST00000300332;ENST00000523261	D;D	0.96265	-3.96;-3.96	6.17	5.3	0.74995	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.142970	0.45361	D	0.000362	D	0.94896	0.8350	L	0.29908	0.895	0.33407	D	0.578161	P	0.47191	0.891	P	0.49999	0.628	D	0.97412	1.0003	10	0.59425	D	0.04	.	14.9109	0.70755	0.0:0.0:0.8559:0.1441	.	134	Q99801	NKX31_HUMAN	I	134;90;59	ENSP00000370253:T134I;ENSP00000429729:T59I	ENSP00000300332:T90I	T	-	2	0	NKX3-1	23594983	0.850000	0.29656	1.000000	0.80357	0.759000	0.43091	1.425000	0.34859	1.623000	0.50342	0.655000	0.94253	ACT		0.577	NKX3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215141.2			17	142	17	142
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76909629	76909629	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chrX:76909629G>A	ENST00000373344.5	-	14	4490	c.4276C>T	c.(4276-4278)Cga>Tga	p.R1426*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1388*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1426					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.R1426*(1)|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						TTAATACGTCGCCTTTTCTTT	0.328			"""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	2	Substitution - Nonsense(1)|Unknown(1)	central_nervous_system(1)|bone(1)											236.0	201.0	213.0					X																	76909629		2203	4295	6498	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.4276C>T	X.37:g.76909629G>A	ENSP00000362441:p.Arg1426*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	g	44	11.200502	0.99530	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	5.41	3.6	0.41247	.	0.079753	0.50627	D	0.000111	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.8333	13.0038	0.58692	0.0:0.0:0.397:0.603	.	.	.	.	X	1426;1388	.	ENSP00000362441:R1426X	R	-	1	2	ATRX	76796285	0.991000	0.36638	0.982000	0.44146	0.683000	0.39861	1.747000	0.38298	0.544000	0.28883	0.502000	0.49764	CGA		0.328	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		42	14	42	14
IBTK	25998	broad.mit.edu;ucsc.edu	37	6	82912294	82912294	+	Missense_Mutation	SNP	A	A	G			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr6:82912294A>G	ENST00000306270.7	-	18	3229	c.2680T>C	c.(2680-2682)Tct>Cct	p.S894P	IBTK_ENST00000510291.1_Missense_Mutation_p.S894P|IBTK_ENST00000503631.1_Missense_Mutation_p.S693P	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	894					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TGTAAACAAGACAGTTTCAAC	0.343																																																0													131.0	132.0	132.0					6																	82912294		2203	4300	6503	SO:0001583	missense	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2680T>C	6.37:g.82912294A>G	ENSP00000305721:p.Ser894Pro		Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.497131	0.64186	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.31247	1.85;1.5;1.84	5.56	5.56	0.83823	.	0.053219	0.85682	D	0.000000	T	0.44767	0.1309	M	0.74881	2.28	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.995;0.997;0.998	D;P;D;D	0.67382	0.948;0.9;0.951;0.927	T	0.43702	-0.9375	10	0.45353	T	0.12	-16.2132	14.2866	0.66249	1.0:0.0:0.0:0.0	.	693;894;894;894	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	P	894;693;894	ENSP00000305721:S894P;ENSP00000422762:S693P;ENSP00000426405:S894P	ENSP00000305721:S894P	S	-	1	0	IBTK	82969013	1.000000	0.71417	1.000000	0.80357	0.352000	0.29268	8.893000	0.92498	2.105000	0.64084	0.477000	0.44152	TCT		0.343	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		15	126	15	126
PSG1	5669	broad.mit.edu;ucsc.edu	37	19	43382350	43382350	+	Missense_Mutation	SNP	T	T	C			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr19:43382350T>C	ENST00000436291.2	-	2	261	c.145A>G	c.(145-147)Aag>Gag	p.K49E	PSG1_ENST00000244296.2_Missense_Mutation_p.K49E|PSG1_ENST00000595356.1_Missense_Mutation_p.K49E|PSG1_ENST00000403380.3_Missense_Mutation_p.K49E|PSG1_ENST00000595124.1_Missense_Mutation_p.K49E|PSG1_ENST00000312439.6_Missense_Mutation_p.K49E|PSG1_ENST00000601073.1_5'UTR	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	49	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				AGAACATCCTTCCCCTCGGAA	0.473																																																0													155.0	171.0	166.0					19																	43382350		2203	4299	6502	SO:0001583	missense	5669				CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.145A>G	19.37:g.43382350T>C	ENSP00000413041:p.Lys49Glu		O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	7.852	0.724289	0.15439	.	.	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.01406	4.93;4.93;4.93;4.93	1.64	-3.08	0.05347	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03608	0.0103	L	0.51853	1.615	0.09310	N	1	D;B;P;B;P;B;P;P;B	0.89917	1.0;0.0;0.934;0.006;0.823;0.001;0.668;0.956;0.007	D;B;P;B;P;B;P;P;B	0.97110	1.0;0.006;0.705;0.063;0.662;0.01;0.708;0.905;0.034	T	0.30357	-0.9981	9	0.66056	D	0.02	.	2.1195	0.03723	0.4809:0.1818:0.0:0.3373	.	49;49;49;49;49;49;49;49;49	O75238;P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.;.	E	49	ENSP00000413041:K49E;ENSP00000385386:K49E;ENSP00000308970:K49E;ENSP00000244296:K49E	ENSP00000244296:K49E	K	-	1	0	PSG1	48074190	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.895000	0.01606	-0.946000	0.03677	0.155000	0.16302	AAG		0.473	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			37	301	37	301
FAM189A2	9413	broad.mit.edu;ucsc.edu	37	9	72000864	72000864	+	Splice_Site	SNP	G	G	T			TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr9:72000864G>T	ENST00000257515.8	+	9	1276		c.e9+1		FAM189A2_ENST00000377216.3_5'Flank|FAM189A2_ENST00000455972.1_Splice_Site|FAM189A2_ENST00000303068.7_Splice_Site|FAM189A2_ENST00000469179.1_Splice_Site	NM_004816.3	NP_004807.3	Q15884	F1892_HUMAN	family with sequence similarity 189, member A2							integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(5)|liver(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GAGGAGAGAGGTGATGTCATT	0.577																																																0													90.0	73.0	79.0					9																	72000864		2203	4300	6503	SO:0001630	splice_region_variant	9413			L27479	CCDS6629.1	9q21.11	2009-07-09	2009-07-09	2009-07-09	ENSG00000135063	ENSG00000135063			24820	protein-coding gene	gene with protein product		607710	"""chromosome 9 open reading frame 61"""	C9orf61		7951235	Standard	NM_004816		Approved	X123	uc010mon.1	Q15884	OTTHUMG00000019979	ENST00000257515.8:c.856+1G>T	9.37:g.72000864G>T			Q14CN5|Q5T6C8|Q5T6C9|Q6ZTX4|Q96N10	Splice_Site	SNP	ENST00000257515.8	37	CCDS6629.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.202223	0.58234	.	.	ENSG00000135063	ENST00000455972;ENST00000257515;ENST00000303068;ENST00000377225	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2707	0.87101	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAM189A2	71190684	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	5.184000	0.65070	2.826000	0.97356	0.655000	0.94253	.		0.577	FAM189A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052576.2	NM_004816	Intron	16	39	16	39
CDK16	5127	broad.mit.edu;ucsc.edu	37	X	47082981	47082981	+	Missense_Mutation	SNP	C	C	T	rs180754755		TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chrX:47082981C>T	ENST00000357227.4	+	2	449	c.25C>T	c.(25-27)Cgg>Tgg	p.R9W	CDK16_ENST00000457458.2_Missense_Mutation_p.R15W|CDK16_ENST00000276052.6_Missense_Mutation_p.R83W|CDK16_ENST00000518022.1_Missense_Mutation_p.R9W	NM_006201.4	NP_006192.1	Q00536	CDK16_HUMAN	cyclin-dependent kinase 16	9					exocytosis (GO:0006887)|growth hormone secretion (GO:0030252)|neuron projection development (GO:0031175)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|spermatogenesis (GO:0007283)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)	11						GAAGATCAAACGGCAGCTGTC	0.532													C|||	1	0.000264901	0.0008	0.0	3775	,	,		15976	0.0		0.0	False		,,,				2504	0.0															0													108.0	72.0	84.0					X																	47082981		2203	4300	6503	SO:0001583	missense	5127				CCDS14276.1, CCDS48101.1, CCDS55408.1	Xp11	2011-11-08	2009-12-16	2009-12-16	ENSG00000102225	ENSG00000102225		"""Cyclin-dependent kinases"""	8749	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase"""	311550	"""PCTAIRE protein kinase 1"""	PCTK1		1437147, 19884882	Standard	NM_033018		Approved	PCTAIRE, PCTAIRE1, PCTGAIRE, FLJ16665	uc011mll.2	Q00536	OTTHUMG00000021438	ENST00000357227.4:c.25C>T	X.37:g.47082981C>T	ENSP00000349762:p.Arg9Trp		A8K280|B7Z7C8|J3KN74|J3KQP7	Missense_Mutation	SNP	ENST00000357227.4	37	CCDS14276.1	1	6.027727546714888E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	19.56	3.850706	0.71719	.	.	ENSG00000102225	ENST00000457458;ENST00000522883;ENST00000357227;ENST00000519758;ENST00000520893;ENST00000540877;ENST00000540311;ENST00000517426;ENST00000518391;ENST00000518022;ENST00000276052	T;T;T;T;T;T	0.78126	-0.94;-0.92;-1.15;0.04;-0.92;-0.73	5.04	4.17	0.49024	.	0.087235	0.45126	D	0.000388	D	0.85256	0.5655	M	0.69358	2.11	0.41310	D	0.987107	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.74023	0.976;0.982;0.936;0.959	D	0.85970	0.1476	10	0.87932	D	0	-9.3055	11.4975	0.50417	0.3241:0.6759:0.0:0.0	.	83;9;107;9	B7Z7C8;B7Z461;B7Z8T0;Q00536	.;.;.;CDK16_HUMAN	W	15;9;9;9;9;107;9;9;9;9;83	ENSP00000405798:R15W;ENSP00000349762:R9W;ENSP00000429985:R9W;ENSP00000429044:R9W;ENSP00000429751:R9W;ENSP00000276052:R83W	ENSP00000276052:R83W	R	+	1	2	CDK16	46967925	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.033000	0.41136	0.914000	0.36822	0.431000	0.28591	CGG		0.532	CDK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056406.2	NM_006201		4	26	4	26
SMARCA4	6597	hgsc.bcm.edu	37	19	11170839	11170839	+	Silent	SNP	T	T	C	rs7275	byFrequency	TCGA-FG-8191-01A-11D-2253-08	TCGA-FG-8191-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcc461af-d70d-4fca-ae7f-3f09367b6d51	6a19fe53-192d-492a-98ba-54d24a6f3574	g.chr19:11170839T>C	ENST00000429416.3	+	35	5168	c.4887T>C	c.(4885-4887)gaT>gaC	p.D1629D	SMARCA4_ENST00000590574.1_Silent_p.D1596D|SMARCA4_ENST00000444061.3_Silent_p.D1595D|SMARCA4_ENST00000344626.4_Silent_p.D1629D|SMARCA4_ENST00000450717.3_Silent_p.D1598D|SMARCA4_ENST00000589677.1_Silent_p.D1598D|SMARCA4_ENST00000358026.2_Silent_p.D1661D|SMARCA4_ENST00000541122.2_Silent_p.D1599D|SMARCA4_ENST00000413806.3_Silent_p.D1599D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1629					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGAGTGACGATGACAGTGAGG	0.687			"""F, N, Mis"""		NSCLC								C|||	1251	0.2498	0.3094	0.1715	5008	,	,		14726	0.0724		0.2942	False		,,,				2504	0.362						Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)						C	,,,,,,	1060,2890		143,774,1058	26.0	31.0	29.0		4887,4797,4794,4788,4785,4983,4887	-5.1	0.0	19	dbSNP_52	29	1961,5729		253,1455,2137	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMARCA4	NM_001128844.1,NM_001128845.1,NM_001128846.1,NM_001128847.1,NM_001128848.1,NM_001128849.1,NM_003072.3	,,,,,,	396,2229,3195	CC,CT,TT		25.5007,26.8354,25.9536	,,,,,,	1629/1648,1599/1618,1598/1617,1596/1615,1595/1614,1661/1680,1629/1648	11170839	3021,8619	1975	3845	5820	SO:0001819	synonymous_variant	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4887T>C	19.37:g.11170839T>C			B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																				0.687	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		5	0	5	0
