#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
MIA2	117153	broad.mit.edu	37	14	39716388	39716388	+	Missense_Mutation	SNP	A	A	G			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr14:39716388A>G	ENST00000280082.3	+	4	809	c.610A>G	c.(610-612)Atg>Gtg	p.M204V	MIA2_ENST00000556784.1_Missense_Mutation_p.M203V|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.M204V	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	204					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		TGTTGAAAGTATGGAACAGGA	0.433																																						uc001wux.3																			0				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31						c.(610-612)Atg>Gtg		Homo sapiens melanoma inhibitory activity 2 (MIA2), mRNA.							91.0	91.0	91.0					14																	39716388		2203	4300	6503	SO:0001583	missense	117153					extracellular region		g.chr14:39716388A>G	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.610A>G	14.37:g.39716388A>G	ENSP00000280082:p.Met204Val		Somatic				MIA2_uc010amy.2_Missense_Mutation_p.M135V	p.M204V	NM_054024	NP_473365	WXS	Illumina GAIIx	Phase_I	Q96PC5	MIA2_HUMAN	LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)	3	804	+	Hepatocellular(127;0.213)		204					A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	c.610A>G	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.287599	0.00248	.	.	ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000556784;ENST00000553728	T;T;T	0.39592	1.07;1.08;3.39	5.11	-7.15	0.01521	.	0.886036	0.09343	N	0.815131	T	0.13157	0.0319	N	0.03177	-0.4	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24404	-1.0161	9	.	.	.	-27.3092	4.6197	0.12444	0.5145:0.1859:0.2194:0.0802	.	204;204	Q96PC5;Q96PC5-2	MIA2_HUMAN;.	V	204;203;204	ENSP00000280082:M204V;ENSP00000451934:M203V;ENSP00000452252:M204V	.	M	+	1	0	MIA2;RP11-407N17.3	38786139	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.661000	0.05311	-1.110000	0.02992	-0.132000	0.14878	ATG		0.433	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		3	79	0	0	0	1	0	3	79				
FBXW8	26259	broad.mit.edu	37	12	117402520	117402520	+	Silent	SNP	G	G	A	rs200172747		TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr12:117402520G>A	ENST00000309909.5	+	5	778	c.696G>A	c.(694-696)gtG>gtA	p.V232V	FBXW8_ENST00000455858.2_Silent_p.V166V			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	232					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		CAGGGGATGTGAGAGTGTGGG	0.522																																						uc001twg.1																			0				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22						c.(694-696)gtG>gtA		Homo sapiens F-box and WD repeat domain containing 8 (FBXW8), transcript variant 1, mRNA.							221.0	207.0	212.0					12																	117402520		2203	4300	6503	SO:0001819	synonymous_variant	26259						protein binding	g.chr12:117402520G>A	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.696G>A	12.37:g.117402520G>A			Somatic				FBXW8_uc001twf.1_Silent_p.V166V	p.V232V	NM_153348	NP_699179	WXS	Illumina GAIIx	Phase_I	Q8N3Y1	FBXW8_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.0353)	4	778	+	all_neural(191;0.117)|Medulloblastoma(191;0.163)		232					Q9UK95	Silent	SNP	ENST00000309909.5	37	c.696G>A	CCDS9182.1																																																																																				0.522	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174		75	183	0	0	0	1	0	75	183				
EPHB6	2051	broad.mit.edu	37	7	142565403	142565403	+	Silent	SNP	G	G	C			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr7:142565403G>C	ENST00000392957.2	+	12	2575	c.1788G>C	c.(1786-1788)gtG>gtC	p.V596V	EPHB6_ENST00000411471.2_Silent_p.V319V|EPHB6_ENST00000442129.1_Silent_p.V596V	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	596						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					TCTCCTTGGTGATCGGCTCCA	0.637																																						uc011kst.2																			0				NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87						c.(1786-1788)gtG>gtC		Homo sapiens EPH receptor B6 (EPHB6), mRNA.							60.0	58.0	58.0					7																	142565403		2203	4300	6503	SO:0001819	synonymous_variant	2051					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity	g.chr7:142565403G>C	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1788G>C	7.37:g.142565403G>C			Somatic				EPHB6_uc011ksu.2_Silent_p.V596V|EPHB6_uc003wbs.3_Silent_p.V304V|EPHB6_uc003wbt.3_Silent_p.V70V|EPHB6_uc003wbu.3_Silent_p.V304V|EPHB6_uc003wbv.3_5'UTR	p.V596V	NM_004445	NP_004436	WXS	Illumina GAIIx	Phase_I	O15197	EPHB6_HUMAN			11	2575	+	Melanoma(164;0.059)		596					A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	c.1788G>C	CCDS5873.2																																																																																				0.637	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			10	12	0	0	0	1	0	10	12				
GRIN3A	116443	broad.mit.edu	37	9	104432410	104432410	+	Missense_Mutation	SNP	C	C	T			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr9:104432410C>T	ENST00000361820.3	-	3	2884	c.2284G>A	c.(2284-2286)Gca>Aca	p.A762T		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	762					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	GCCAAGTTTGCCGTGTATGTG	0.418																																						uc004bbp.2																			0				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80						c.(2284-2286)Gca>Aca		Homo sapiens glutamate receptor, ionotropic, N-methyl-D-aspartate 3A (GRIN3A), mRNA.	Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)						87.0	84.0	85.0					9																	104432410		2203	4300	6503	SO:0001583	missense	116443				response to ethanol	N-methyl-D-aspartate selective glutamate receptor complex|cell junction|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|protein phosphatase 2A binding	g.chr9:104432410C>T		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2284G>A	9.37:g.104432410C>T	ENSP00000355155:p.Ala762Thr		Somatic				GRIN3A_uc004bbq.1_Missense_Mutation_p.A762T	p.A762T	NM_133445	NP_597702	WXS	Illumina GAIIx	Phase_I	Q8TCU5	NMD3A_HUMAN			2	2885	-		Acute lymphoblastic leukemia(62;0.0568)	762					B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	c.2284G>A	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.724824	0.89298	.	.	ENSG00000198785	ENST00000361820	T	0.74315	-0.83	5.43	5.43	0.79202	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	D	0.89993	0.6876	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91847	0.5488	10	0.87932	D	0	.	19.6103	0.95602	0.0:1.0:0.0:0.0	.	762	Q8TCU5	NMD3A_HUMAN	T	762	ENSP00000355155:A762T	ENSP00000355155:A762T	A	-	1	0	GRIN3A	103472231	1.000000	0.71417	0.956000	0.39512	0.989000	0.77384	7.776000	0.85560	2.718000	0.92993	0.585000	0.79938	GCA		0.418	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			3	78	0	0	0	1	0	3	78				
CACNA1B	774	broad.mit.edu	37	9	140953611	140953611	+	Silent	SNP	C	C	T	rs575117282		TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr9:140953611C>T	ENST00000371372.1	+	30	4699	c.4554C>T	c.(4552-4554)tgC>tgT	p.C1518C	CACNA1B_ENST00000371355.4_Silent_p.C1519C|CACNA1B_ENST00000371357.1_Silent_p.C1519C|CACNA1B_ENST00000277549.5_Silent_p.C714C|CACNA1B_ENST00000277551.2_Silent_p.C1518C|CACNA1B_ENST00000371363.1_Silent_p.C1518C	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1518					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CCATGGAATGCGTGCTGAAGA	0.507													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22159	0.0		0.0	False		,,,				2504	0.0					uc004cog.3																			0				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80						c.(4552-4554)tgC>tgT		Homo sapiens calcium channel, voltage-dependent, N type, alpha 1B subunit (CACNA1B), transcript variant 1, mRNA.	Amlodipine(DB00381)|Gabapentin(DB00996)						136.0	129.0	131.0					9																	140953611		2147	4245	6392	SO:0001819	synonymous_variant	774				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity	g.chr9:140953611C>T	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.4554C>T	9.37:g.140953611C>T			Somatic				CACNA1B_uc022bqn.1_Silent_p.C1518C|CACNA1B_uc011mfd.2_Silent_p.C1119C|CACNA1B_uc004coi.3_Silent_p.C732C	p.C1518C	NM_000718	NP_000709	WXS	Illumina GAIIx	Phase_I	Q00975	CAC1B_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	29	4699	+	all_cancers(76;0.166)		1518					B1AQK5	Silent	SNP	ENST00000371372.1	37	c.4554C>T	CCDS59522.1																																																																																				0.507	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		13	15	0	0	0	1	0	13	15				
CLIC5	53405	broad.mit.edu	37	6	45917096	45917096	+	Missense_Mutation	SNP	G	G	C			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr6:45917096G>C	ENST00000185206.6	-	3	825	c.673C>G	c.(673-675)Cta>Gta	p.L225V	CLIC5_ENST00000544153.1_Missense_Mutation_p.L66V|CLIC5_ENST00000339561.6_Missense_Mutation_p.L66V	NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	225					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						CCGGGGGCTAGGTTGTGCAGG	0.542																																						uc003oxv.3																			0				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						c.(673-675)Cta>Gta		Homo sapiens chloride intracellular channel 5 (CLIC5), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.							142.0	133.0	136.0					6																	45917096		2203	4300	6503	SO:0001583	missense	53405				female pregnancy	Golgi apparatus|actin cytoskeleton|cell cortex|chloride channel complex|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity	g.chr6:45917096G>C	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"""Ion channels / Chloride channels : Intracellular"""	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.673C>G	6.37:g.45917096G>C	ENSP00000185206:p.Leu225Val		Somatic				CLIC5_uc003oxu.3_Missense_Mutation_p.L66V|CLIC5_uc003oxx.3_Missense_Mutation_p.L66V	p.L225V	NM_001114086	NP_001107558	WXS	Illumina GAIIx	Phase_I	Q9NZA1	CLIC5_HUMAN			2	779	-			225					B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Missense_Mutation	SNP	ENST00000185206.6	37	c.673C>G	CCDS47438.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797117	0.70567	.	.	ENSG00000112782	ENST00000185206;ENST00000339561;ENST00000544153	T;T;T	0.49432	0.78;0.78;0.78	5.73	4.85	0.62838	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.40886	0.1135	L	0.45744	1.44	0.52501	D	0.999951	P;P;P	0.49559	0.925;0.684;0.925	P;P;P	0.55345	0.774;0.694;0.774	T	0.40776	-0.9545	10	0.56958	D	0.05	-22.768	6.9158	0.24359	0.2233:0.0:0.7767:0.0	.	66;225;66	Q8NBY3;Q9NZA1;Q53G01	.;CLIC5_HUMAN;.	V	225;66;66	ENSP00000185206:L225V;ENSP00000344165:L66V;ENSP00000439195:L66V	ENSP00000185206:L225V	L	-	1	2	CLIC5	46025074	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	3.869000	0.56062	2.854000	0.98071	0.655000	0.94253	CTA		0.542	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1			48	80	0	0	0	1	0	48	80				
NOTCH3	4854	broad.mit.edu	37	19	15289709	15289709	+	Silent	SNP	T	T	A			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr19:15289709T>A	ENST00000263388.2	-	23	3837	c.3762A>T	c.(3760-3762)ccA>ccT	p.P1254P		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1254	EGF-like 32. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CATGCTGGCATGGCTGGGACT	0.652																																						uc002nan.3																			0				breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93						c.(3760-3762)ccA>ccT		Homo sapiens notch 3 (NOTCH3), mRNA.							38.0	36.0	37.0					19																	15289709		2201	4299	6500	SO:0001819	synonymous_variant	4854				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi lumen|cytosol|endoplasmic reticulum lumen|extracellular region|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	g.chr19:15289709T>A	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3762A>T	19.37:g.15289709T>A			Somatic				NOTCH3_uc002nao.1_Silent_p.P1202P	p.P1254P	NM_000435	NP_000426	WXS	Illumina GAIIx	Phase_I	Q9UM47	NOTC3_HUMAN	OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)		22	3838	-			1254			EGF-like 32.		Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	c.3762A>T	CCDS12326.1																																																																																				0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		5	12	0	0	0	1	0	5	12				
SYNPO2	171024	broad.mit.edu	37	4	119944646	119944646	+	Missense_Mutation	SNP	T	T	G			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr4:119944646T>G	ENST00000429713.2	+	2	349	c.167T>G	c.(166-168)aTc>aGc	p.I56S	SYNPO2_ENST00000434046.2_Missense_Mutation_p.I56S|SYNPO2_ENST00000448416.2_Missense_Mutation_p.I56S|SYNPO2_ENST00000307142.4_Missense_Mutation_p.I56S	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	56	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GTGGTTTCCATCAATGGCAAC	0.438																																						uc010inb.3																			0		p.I56I(1)		breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						c.(166-168)aTc>aGc		Homo sapiens synaptopodin 2 (SYNPO2), transcript variant 1, mRNA.							140.0	115.0	123.0					4																	119944646		2203	4300	6503	SO:0001583	missense	171024					Z disc|nucleus	14-3-3 protein binding|actin binding|muscle alpha-actinin binding	g.chr4:119944646T>G	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.167T>G	4.37:g.119944646T>G	ENSP00000395143:p.Ile56Ser		Somatic				SYNPO2_uc010ina.3_Missense_Mutation_p.I56S|SYNPO2_uc003icm.4_Missense_Mutation_p.I56S|SYNPO2_uc011cgh.2_Missense_Mutation_p.I56S|SYNPO2_uc010inc.3_5'UTR	p.I56S	NM_133477	NP_597734	WXS	Illumina GAIIx	Phase_I	Q9UMS6	SYNP2_HUMAN			1	363	+			56			PDZ.		B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	c.167T>G	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.4|24.4	4.523739|4.523739	0.85600|0.85600	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000448416;ENST00000429713;ENST00000434046	.|T;T;T;T	.|0.39592	.|1.07;1.07;1.07;1.07	5.66|5.66	5.66|5.66	0.87406|0.87406	.|PDZ/DHR/GLGF (4);	.|0.000000	.|0.64402	.|D	.|0.000005	T|T	0.68238|0.68238	0.2979|0.2979	M|M	0.85710|0.85710	2.77|2.77	0.52099|0.52099	D|D	0.999942|0.999942	.|D;D;D;D	.|0.89917	.|0.999;0.999;1.0;1.0	.|D;D;D;D	.|0.83275	.|0.984;0.996;0.994;0.99	T|T	0.74166|0.74166	-0.3753|-0.3753	5|10	.|0.87932	.|D	.|0	-20.0087|-20.0087	14.4619|14.4619	0.67456|0.67456	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|56;56;56;56	.|B4E258;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	Q|S	7|56	.|ENSP00000306015:I56S;ENSP00000412623:I56S;ENSP00000395143:I56S;ENSP00000390965:I56S	.|ENSP00000306015:I56S	H|I	+|+	3|2	2|0	SYNPO2|SYNPO2	120164094|120164094	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.688000|7.688000	0.84153|0.84153	2.144000|2.144000	0.66660|0.66660	0.528000|0.528000	0.53228|0.53228	CAT|ATC		0.438	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			3	80	0	0	0	1	0	3	80				
KLHL32	114792	broad.mit.edu	37	6	97561919	97561919	+	Silent	SNP	G	G	A			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr6:97561919G>A	ENST00000369261.4	+	7	1251	c.888G>A	c.(886-888)ggG>ggA	p.G296G	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Silent_p.G227G|KLHL32_ENST00000536676.1_Silent_p.G260G	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	296										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		TCATTGGTGGGAAAAAGCGCG	0.517																																						uc010kcm.1																			0				breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38						c.(886-888)ggG>ggA		Homo sapiens kelch-like 32 (Drosophila) (KLHL32), mRNA.							76.0	73.0	74.0					6																	97561919		2203	4300	6503	SO:0001819	synonymous_variant	114792							g.chr6:97561919G>A	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.888G>A	6.37:g.97561919G>A			Somatic				KLHL32_uc003poy.3_Silent_p.G296G|KLHL32_uc003poz.2_Intron|KLHL32_uc011ead.1_Silent_p.G260G|KLHL32_uc011eae.1_Silent_p.G227G|KLHL32_uc003ppa.2_Intron|MIR548H3_uc021zda.1_Intron	p.G296G	NM_052904	NP_443136	WXS	Illumina GAIIx	Phase_I	Q96NJ5	KLH32_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0558)	6	1360	+		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)	296					B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	c.888G>A	CCDS5038.1																																																																																				0.517	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		18	44	0	0	0	1	0	18	44				
TFAMP1	260341	broad.mit.edu	37	7	1654770	1654770	+	IGR	SNP	G	G	C			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr7:1654770G>C								PSMG3-AS1 (25508 upstream) : AC074389.5 (5519 downstream)																							AGGCAAAGCTGAAGACTGTAA	0.333																																						uc003slb.3																			0													Homo sapiens transcription factor A, mitochondrial pseudogene 1 (TFAMP1), non-coding RNA.																																				SO:0001628	intergenic_variant	260341							g.chr7:1654770G>C																													7.37:g.1654770G>C			Somatic								WXS	Illumina GAIIx	Phase_I					0		+									RNA	SNP		37	c.665G>C																																																																																				0	0.333									2	16	0	0	0	1	0	2	16				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		25	61	0	0	0	1	0	25	61				
LCA5	167691	broad.mit.edu	37	6	80228599	80228599	+	Missense_Mutation	SNP	C	C	T			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr6:80228599C>T	ENST00000392959.1	-	3	624	c.13G>A	c.(13-15)Gca>Aca	p.A5T	LCA5_ENST00000369846.4_Missense_Mutation_p.A5T|LCA5_ENST00000467898.3_Missense_Mutation_p.A5T	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	5					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		GGACTTCCTGCTCTTTCCCCC	0.388																																						uc003piy.3																			0				haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32						c.(13-15)Gca>Aca		Homo sapiens Leber congenital amaurosis 5 (LCA5), transcript variant 1, mRNA.							294.0	280.0	284.0					6																	80228599		2203	4300	6503	SO:0001583	missense	167691				protein transport	cilium axoneme|microtubule basal body	protein binding	g.chr6:80228599C>T		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.13G>A	6.37:g.80228599C>T	ENSP00000376686:p.Ala5Thr		Somatic				LCA5_uc003pix.3_Missense_Mutation_p.A5T|LCA5_uc011dyr.2_Missense_Mutation_p.A5T	p.A5T	NM_181714	NP_859065	WXS	Illumina GAIIx	Phase_I	Q86VQ0	LCA5_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0657)	2	625	-		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)	5					E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	c.13G>A	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.232577	0.39498	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.33216	1.42;1.42	5.28	4.38	0.52667	.	0.595355	0.16631	N	0.206071	T	0.10981	0.0268	N	0.22421	0.69	0.33588	D	0.600789	B;P	0.35272	0.16;0.493	B;B	0.34242	0.082;0.178	T	0.08310	-1.0728	10	0.33940	T	0.23	-1.4967	12.9015	0.58128	0.1612:0.8388:0.0:0.0	.	5;5	B4DRL2;Q86VQ0	.;LCA5_HUMAN	T	5	ENSP00000358861:A5T;ENSP00000376686:A5T	ENSP00000358861:A5T	A	-	1	0	LCA5	80285318	0.379000	0.25123	0.957000	0.39632	0.608000	0.37181	0.032000	0.13732	2.736000	0.93811	0.655000	0.94253	GCA		0.388	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		65	174	0	0	0	1	0	65	174				
PRDM9	56979	broad.mit.edu	37	5	23527796	23527796	+	Missense_Mutation	SNP	C	C	T			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr5:23527796C>T	ENST00000296682.3	+	11	2781	c.2599C>T	c.(2599-2601)Cgg>Tgg	p.R867W		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	867					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGAGTGTGGGCGGGGCTTTAG	0.562										HNSCC(3;0.000094)																												uc003jgo.3																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						c.(2599-2601)Cgg>Tgg		Homo sapiens PR domain containing 9 (PRDM9), mRNA.							68.0	76.0	74.0					5																	23527796		2181	4298	6479	SO:0001583	missense	56979				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding	g.chr5:23527796C>T	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2599C>T	5.37:g.23527796C>T	ENSP00000296682:p.Arg867Trp	HNSCC(3;0.000094)	Somatic					p.R867W	NM_020227	NP_064612	WXS	Illumina GAIIx	Phase_I	Q9NQV7	PRDM9_HUMAN			10	2781	+			867					B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	c.2599C>T	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	6.891	0.533934	0.13188	.	.	ENSG00000164256	ENST00000296682	T	0.19806	2.12	2.05	-1.05	0.10036	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26629	0.0651	M	0.90252	3.1	0.09310	N	1	B	0.21688	0.059	B	0.21546	0.035	T	0.40608	-0.9554	9	0.52906	T	0.07	-0.9186	2.6772	0.05084	0.2161:0.3368:0.0:0.4471	.	867	Q9NQV7	PRDM9_HUMAN	W	867	ENSP00000296682:R867W	ENSP00000296682:R867W	R	+	1	2	PRDM9	23563553	0.036000	0.19791	0.052000	0.19188	0.022000	0.10575	1.395000	0.34520	-0.280000	0.09154	0.472000	0.43445	CGG		0.562	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		34	82	0	0	0	1	0	34	82				
ANK3	288	broad.mit.edu	37	10	61835632	61835632	+	Silent	SNP	C	C	T			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr10:61835632C>T	ENST00000280772.2	-	37	5198	c.5007G>A	c.(5005-5007)ccG>ccA	p.P1669P	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1669	Ser-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						AAGATATTAGCGGTGCTGCTG	0.393																																						uc001jky.3																			0				NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						c.(5005-5007)ccG>ccA		Homo sapiens ankyrin 3, node of Ranvier (ankyrin G) (ANK3), transcript variant 1, mRNA.							127.0	121.0	123.0					10																	61835632		2203	4300	6503	SO:0001819	synonymous_variant	288				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding	g.chr10:61835632C>T	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.5007G>A	10.37:g.61835632C>T			Somatic				ANK3_uc001jkw.3_Intron|ANK3_uc009xpa.3_Intron|ANK3_uc001jkx.3_Intron|ANK3_uc010qih.2_Intron|ANK3_uc001jkz.4_Intron|ANK3_uc001jkv.3_Intron|ANK3_uc009xpb.1_Intron	p.P1669P	NM_020987	NP_066267	WXS	Illumina GAIIx	Phase_I	Q12955	ANK3_HUMAN			36	5345	-			1669			Ser-rich.		B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	c.5007G>A	CCDS7258.1																																																																																				0.393	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		27	77	0	0	0	1	0	27	77				
TMEM132A	54972	broad.mit.edu	37	11	60694815	60694815	+	Silent	SNP	C	C	A			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr11:60694815C>A	ENST00000453848.2	+	2	398	c.240C>A	c.(238-240)acC>acA	p.T80T	RP11-881M11.4_ENST00000543907.1_RNA|TMEM132A_ENST00000005286.4_Silent_p.T80T			Q24JP5	T132A_HUMAN	transmembrane protein 132A	80						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GATCTGAGACCTTTCTGCTCC	0.647																																						uc001nqi.3																			0				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						c.(238-240)acC>acA		Homo sapiens transmembrane protein 132A (TMEM132A), transcript variant 1, mRNA.							50.0	55.0	53.0					11																	60694815		2203	4299	6502	SO:0001819	synonymous_variant	54972					Golgi membrane|endoplasmic reticulum membrane|integral to membrane		g.chr11:60694815C>A	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.240C>A	11.37:g.60694815C>A			Somatic				TMEM132A_uc001nqj.3_Silent_p.T80T|TMEM132A_uc001nqk.3_Silent_p.T93T|TMEM132A_uc001nql.1_Silent_p.T93T	p.T80T	NM_017870	NP_060340	WXS	Illumina GAIIx	Phase_I	Q24JP5	T132A_HUMAN			1	433	+			80					Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	37	c.240C>A	CCDS44618.1																																																																																				0.647	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		4	127	0	0	0	1	0	4	127				
SLC7A11	23657	broad.mit.edu	37	4	139163108	139163108	+	Missense_Mutation	SNP	T	T	C			TCGA-IM-A3ED-01A-11D-A202-08	TCGA-IM-A3ED-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b7d3599f-0218-4d1d-aed8-c45c188cd71d	ea16b689-e941-4ea0-ad31-9504e19ed28b	g.chr4:139163108T>C	ENST00000280612.5	-	1	395	c.116A>G	c.(115-117)cAg>cGg	p.Q39R		NM_014331.3	NP_055146.1	Q9UPY5	XCT_HUMAN	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	39					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|brain development (GO:0007420)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|lens fiber cell differentiation (GO:0070306)|leukocyte migration (GO:0050900)|platelet aggregation (GO:0070527)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	cystine:glutamate antiporter activity (GO:0015327)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18	all_hematologic(180;0.166)				Acetylcysteine(DB06151)|L-Cystine(DB00138)|Riluzole(DB00740)|Rosuvastatin(DB01098)|Sulfasalazine(DB00795)|Tauroursodeoxycholic acid(DB08834)	CCTCTTCAGCTGCACTTTCTC	0.527																																						uc021xrw.1																			0				breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18						c.(115-117)cAg>cGg		Homo sapiens solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11 (SLC7A11), mRNA.	L-Cystine(DB00138)|L-Glutamic Acid(DB00142)|Sulfasalazine(DB00795)						145.0	126.0	133.0					4																	139163108		2203	4300	6503	SO:0001583	missense	23657				blood coagulation|cellular nitrogen compound metabolic process|leukocyte migration|response to toxin	integral to membrane|plasma membrane	cystine:glutamate antiporter activity|protein binding	g.chr4:139163108T>C	AB026891	CCDS3742.1	4q28-q32	2013-05-22	2011-07-12		ENSG00000151012	ENSG00000151012		"""Solute carriers"""	11059	protein-coding gene	gene with protein product		607933				10206947, 12763038	Standard	XM_005262875		Approved	xCT	uc021xrw.1	Q9UPY5	OTTHUMG00000133396	ENST00000280612.5:c.116A>G	4.37:g.139163108T>C	ENSP00000280612:p.Gln39Arg		Somatic					p.Q39R	NM_014331	NP_055146	WXS	Illumina GAIIx	Phase_I	Q9UPY5	XCT_HUMAN			0	396	-	all_hematologic(180;0.166)		39					A8K2U4	Missense_Mutation	SNP	ENST00000280612.5	37	c.116A>G	CCDS3742.1	.	.	.	.	.	.	.	.	.	.	T	7.896	0.733404	0.15574	.	.	ENSG00000151012	ENST00000280612	D	0.90385	-2.66	6.03	2.29	0.28610	.	0.226724	0.44688	D	0.000438	T	0.75554	0.3865	N	0.08118	0	0.23720	N	0.997025	B	0.02656	0.0	B	0.04013	0.001	T	0.59359	-0.7469	10	0.15952	T	0.53	.	6.1168	0.20132	0.7431:0.0:0.1319:0.125	.	39	Q9UPY5	XCT_HUMAN	R	39	ENSP00000280612:Q39R	ENSP00000280612:Q39R	Q	-	2	0	SLC7A11	139382558	0.973000	0.33851	0.941000	0.38009	0.624000	0.37722	2.953000	0.49105	0.175000	0.19841	-1.142000	0.01873	CAG		0.527	SLC7A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257251.2			3	91	0	0	0	1	0	3	91				
