#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_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	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
ZNF573	126231	broad.mit.edu	37	19	38230588	38230588	+	Missense_Mutation	SNP	T	T	A			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr19:38230588T>A	ENST00000590414.2	-	4	824	c.803A>T	c.(802-804)cAt>cTt	p.H268L	ZNF573_ENST00000357309.3_Missense_Mutation_p.H180L|ZNF573_ENST00000339503.4_Missense_Mutation_p.H210L|ZNF573_ENST00000536220.1_Missense_Mutation_p.H180L|ZNF573_ENST00000392138.1_Missense_Mutation_p.H181L			Q86YE8	ZN573_HUMAN	zinc finger protein 573	268					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			TTCGCCAGTATGAACTCTCTG	0.433																																						uc002ohe.3																			0				NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						c.(802-804)cAt>cTt		Homo sapiens zinc finger protein 573 (ZNF573), transcript variant 3, mRNA.							116.0	111.0	113.0					19																	38230588		2203	4300	6503	SO:0001583	missense	126231				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:38230588T>A	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"""Zinc fingers, C2H2-type"", ""-"""	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.803A>T	19.37:g.38230588T>A	ENSP00000465020:p.His268Leu					ZNF573_uc010efs.2_Missense_Mutation_p.H181L|ZNF573_uc002ohd.3_Missense_Mutation_p.H266L|ZNF573_uc002ohf.3_Missense_Mutation_p.H210L|ZNF573_uc002ohg.3_Missense_Mutation_p.H180L|ZNF573_uc021utv.1_Missense_Mutation_p.H180L	p.H268L	NM_001172690	NP_001166161	Q86YE8	ZN573_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)		4	872	-			248					B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Missense_Mutation	SNP	ENST00000590414.2	37	c.803A>T	CCDS59381.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.699348	0.48307	.	.	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	2.33	2.33	0.28932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85141	0.5629	H	0.96633	3.855	0.30386	N	0.78146	D;D;D;D	0.76494	0.998;0.998;0.999;0.998	D;P;D;P	0.67382	0.951;0.904;0.942;0.904	T	0.81523	-0.0894	9	0.87932	D	0	.	9.0479	0.36358	0.0:0.0:0.0:1.0	.	181;210;248;180	Q86YE8-4;Q86YE8-3;Q86YE8;Q86YE8-2	.;.;ZN573_HUMAN;.	L	181;180;180;210;180	ENSP00000375983:H181L;ENSP00000440464:H180L;ENSP00000349861:H180L;ENSP00000340171:H210L	ENSP00000340171:H210L	H	-	2	0	ZNF573	42922428	1.000000	0.71417	0.999000	0.59377	0.898000	0.52572	4.839000	0.62810	0.935000	0.37341	0.477000	0.44152	CAT		0.433	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		37	68	0	0	0	1	0	37	68				
PDZRN4	29951	broad.mit.edu	37	12	41966816	41966816	+	Silent	SNP	C	C	T			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr12:41966816C>T	ENST00000402685.2	+	10	2243	c.2235C>T	c.(2233-2235)tgC>tgT	p.C745C	PDZRN4_ENST00000298919.7_Silent_p.C485C|PDZRN4_ENST00000539469.2_Silent_p.C487C	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	745							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CTGAGAGCTGCAGAAGTACTC	0.483																																						uc010skn.2																			0				breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77						c.(2233-2235)tgC>tgT		Homo sapiens PDZ domain containing ring finger 4 (PDZRN4), transcript variant 1, mRNA.							106.0	104.0	105.0					12																	41966816		2203	4300	6503	SO:0001819	synonymous_variant	29951						ubiquitin-protein ligase activity|zinc ion binding	g.chr12:41966816C>T	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2235C>T	12.37:g.41966816C>T						PDZRN4_uc001rmq.4_Silent_p.C487C|PDZRN4_uc009zjz.3_Silent_p.C485C|PDZRN4_uc001rmr.3_Silent_p.C372C	p.C745C	NM_001164595	NP_001158067	Q6ZMN7	PZRN4_HUMAN			9	2243	+	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)	745					Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	c.2235C>T	CCDS53777.1																																																																																				0.483	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		39	60	0	0	0	1	0	39	60				
BEND2	139105	broad.mit.edu	37	X	18234789	18234789	+	Missense_Mutation	SNP	T	T	A			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chrX:18234789T>A	ENST00000380033.4	-	2	222	c.90A>T	c.(88-90)gaA>gaT	p.E30D	BEND2_ENST00000380030.3_Missense_Mutation_p.E30D	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	30										NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						TTTCAGAAACTTCCACCATCT	0.358																																						uc004cyj.4																			0				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						c.(88-90)gaA>gaT		Homo sapiens BEN domain containing 2 (BEND2), transcript variant 1, mRNA.							191.0	146.0	161.0					X																	18234789		2203	4300	6503	SO:0001583	missense	139105							g.chrX:18234789T>A	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"""BEN domain containing"""	28509	protein-coding gene	gene with protein product			"""chromosome X open reading frame 20"""	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.90A>T	X.37:g.18234789T>A	ENSP00000369372:p.Glu30Asp					BEND2_uc010nfb.2_Missense_Mutation_p.E30D	p.E30D	NM_153346	NP_699177	Q8NDZ0	BEND2_HUMAN			1	244	-			30					E9PFY2|Q4V9S2|Q5JXE5	Missense_Mutation	SNP	ENST00000380033.4	37	c.90A>T	CCDS14184.1	.	.	.	.	.	.	.	.	.	.	t	11.43	1.636762	0.29068	.	.	ENSG00000177324	ENST00000380033;ENST00000380030	T;T	0.24723	1.87;1.84	3.17	-2.6	0.06190	.	346.429000	0.00166	N	0.000000	T	0.13927	0.0337	N	0.19112	0.55	0.09310	N	1	B;B	0.34290	0.447;0.447	B;B	0.23018	0.043;0.043	T	0.16897	-1.0387	10	0.87932	D	0	-2.3967	4.0961	0.09991	0.0:0.3366:0.4091:0.2543	.	30;30	E9PFY2;Q8NDZ0	.;BEND2_HUMAN	D	30	ENSP00000369372:E30D;ENSP00000369369:E30D	ENSP00000369369:E30D	E	-	3	2	BEND2	18144710	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.710000	0.05024	-0.640000	0.05495	0.414000	0.27820	GAA		0.358	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346		6	51	0	0	0	1	0	6	51				
ALG13	79868	broad.mit.edu	37	X	110951452	110951452	+	Missense_Mutation	SNP	C	C	T			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chrX:110951452C>T	ENST00000394780.3	+	4	593	c.581C>T	c.(580-582)cCt>cTt	p.P194L	ALG13-AS1_ENST00000430794.1_RNA|ALG13_ENST00000251943.4_Missense_Mutation_p.P90L	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	194	Deubiquitinase activity.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						GCTTTTTTTCCTCTCCCTCTT	0.473																																						uc011msy.2																			0				endometrium(2)|lung(10)|skin(1)	13						c.(580-582)cCt>cTt		Homo sapiens asparagine-linked glycosylation 13 homolog (S. cerevisiae) (ALG13), transcript variant 1, mRNA.							125.0	105.0	111.0					X																	110951452		1568	3582	5150	SO:0001583	missense	79868				dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity|carbohydrate binding	g.chrX:110951452C>T	AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"""Tudor domain containing"", ""OTU domain containing"""	30881	protein-coding gene	gene with protein product	"""tudor domain containing 13"", ""N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"""	300776	"""glycosyltransferase 28 domain containing 1"", ""chromosome X open reading frame 45"", ""asparagine-linked glycosylation 13 homolog (S. cerevisiae)"""	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.581C>T	X.37:g.110951452C>T	ENSP00000378260:p.Pro194Leu					ALG13_uc011msw.2_Missense_Mutation_p.P116L|ALG13_uc011msx.2_Missense_Mutation_p.P90L|ALG13_uc011msz.2_Missense_Mutation_p.P116L|ALG13_uc011mta.2_Missense_Mutation_p.P90L|ALG13_uc011mtb.2_Missense_Mutation_p.P90L	p.P194L	NM_001099922	NP_001093392	Q9NP73	ALG13_HUMAN			3	682	+			194					B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Missense_Mutation	SNP	ENST00000394780.3	37	c.581C>T	CCDS55477.1	.	.	.	.	.	.	.	.	.	.	C	7.200	0.593195	0.13875	.	.	ENSG00000101901	ENST00000251943;ENST00000486353;ENST00000394780;ENST00000495283	T;T;T;T	0.76968	1.57;-1.06;0.6;1.57	5.03	1.88	0.25563	.	.	.	.	.	T	0.51719	0.1691	N	0.08118	0	0.09310	N	1	B;B;B	0.15473	0.013;0.008;0.013	B;B;B	0.21917	0.037;0.016;0.022	T	0.38265	-0.9669	9	0.07030	T	0.85	.	4.8818	0.13683	0.1992:0.595:0.0:0.2058	.	116;194;90	Q9NP73-3;Q9NP73;Q9NP73-4	.;ALG13_HUMAN;.	L	90;194;194;90	ENSP00000251943:P90L;ENSP00000426892:P194L;ENSP00000378260:P194L;ENSP00000427093:P90L	ENSP00000251943:P90L	P	+	2	0	ALG13	110838108	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.314000	0.19432	0.063000	0.16370	-1.178000	0.01721	CCT		0.473	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466		6	70	0	0	0	1	0	6	70				
ALPK2	115701	broad.mit.edu	37	18	56246284	56246284	+	Missense_Mutation	SNP	A	A	G			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr18:56246284A>G	ENST00000361673.3	-	4	1937	c.1724T>C	c.(1723-1725)cTa>cCa	p.L575P	ALPK2_ENST00000587399.1_5'UTR	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	575						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						ACTCTGGGTTAGTGGGGGCTC	0.498											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002lhj.4																			0				NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						c.(1723-1725)cTa>cCa		Homo sapiens alpha-kinase 2 (ALPK2), mRNA.							98.0	88.0	91.0					18																	56246284		2203	4300	6503	SO:0001583	missense	115701						ATP binding|protein serine/threonine kinase activity	g.chr18:56246284A>G	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.1724T>C	18.37:g.56246284A>G	ENSP00000354991:p.Leu575Pro		OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1014		p.L575P	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN			3	1938	-			575					Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	c.1724T>C	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	A	15.31	2.796533	0.50208	.	.	ENSG00000198796	ENST00000361673	T	0.55234	0.53	5.76	0.506	0.16961	.	2.381610	0.02710	N	0.112745	T	0.48822	0.1521	L	0.55990	1.75	0.19575	N	0.999969	B	0.22851	0.076	B	0.20577	0.03	T	0.34976	-0.9807	10	0.66056	D	0.02	0.1959	5.6533	0.17629	0.5936:0.2701:0.1363:0.0	.	575	Q86TB3	ALPK2_HUMAN	P	575	ENSP00000354991:L575P	ENSP00000354991:L575P	L	-	2	0	ALPK2	54397264	0.002000	0.14202	0.000000	0.03702	0.043000	0.13939	0.253000	0.18296	-0.124000	0.11724	0.533000	0.62120	CTA		0.498	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		30	63	0	0	0	1	0	30	63				
CLK1	1195	broad.mit.edu	37	2	201718131	201718131	+	Silent	SNP	A	A	G			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr2:201718131A>G	ENST00000321356.4	-	13	1488	c.1353T>C	c.(1351-1353)ttT>ttC	p.F451F	CLK1_ENST00000409769.2_Silent_p.F274F|CLK1_ENST00000434813.2_Silent_p.F493F	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	451	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GAATGAGGTCAAAGAGACGCT	0.363																																						uc010zhi.1																			0				NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						c.(1477-1479)ttT>ttC		Homo sapiens CDC-like kinase 1 (CLK1), transcript variant 2, mRNA.							87.0	85.0	86.0					2																	201718131		2203	4300	6503	SO:0001819	synonymous_variant	1195				cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity	g.chr2:201718131A>G	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"""CDC-like kinases"""	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.1353T>C	2.37:g.201718131A>G						CLK1_uc002uwe.2_Silent_p.F451F|CLK1_uc002uwf.2_Silent_p.F225F|CLK1_uc002uwg.2_Silent_p.F300F	p.F493F	NM_001162407	NP_004062	P49759	CLK1_HUMAN			12	1814	-			451					B4DFW7|Q0P694|Q8N5V8	Silent	SNP	ENST00000321356.4	37	c.1479T>C	CCDS2331.1																																																																																				0.363	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			14	28	0	0	0	1	0	14	28				
SLIT1	6585	broad.mit.edu	37	10	98806446	98806446	+	Silent	SNP	G	G	A	rs527636768		TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr10:98806446G>A	ENST00000266058.4	-	18	2063	c.1818C>T	c.(1816-1818)agC>agT	p.S606S	SLIT1_ENST00000371070.4_Silent_p.S606S|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	606					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GGAACATGCCGCTCCGGATGG	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18592	0.0		0.0	False		,,,				2504	0.0					uc001kmw.2																			0				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78						c.(1816-1818)agC>agT		Homo sapiens slit homolog 1 (Drosophila) (SLIT1), mRNA.							52.0	43.0	46.0					10																	98806446		2203	4300	6503	SO:0001819	synonymous_variant	6585				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	Roundabout binding|calcium ion binding	g.chr10:98806446G>A	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1818C>T	10.37:g.98806446G>A						SLIT1_uc009xvh.1_Silent_p.S616S	p.S606S	NM_003061	NP_003052	O75093	SLIT1_HUMAN		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)	17	2070	-		Colorectal(252;0.162)	606					Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	c.1818C>T	CCDS7453.1																																																																																				0.617	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		14	23	0	0	0	1	0	14	23				
ITPA	3704	broad.mit.edu	37	20	3204049	3204049	+	Missense_Mutation	SNP	T	T	G			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr20:3204049T>G	ENST00000380113.3	+	8	718	c.526T>G	c.(526-528)Tcc>Gcc	p.S176A	ITPA_ENST00000483354.1_3'UTR|ITPA_ENST00000399838.3_Missense_Mutation_p.S135A|ITPA_ENST00000455664.2_Missense_Mutation_p.S159A	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)											autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						GAACGCTGTCTCCCATCGCTT	0.617																																						uc002wid.3																			0				autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						c.(526-528)Tcc>Gcc		Homo sapiens inosine triphosphatase (nucleoside triphosphate pyrophosphatase) (ITPA), transcript variant 1, mRNA.							65.0	49.0	54.0					20																	3204049		2203	4300	6503	SO:0001583	missense	3704				nucleotide metabolic process	cytoplasm	metal ion binding|nucleoside-triphosphate diphosphatase activity|nucleotide binding	g.chr20:3204049T>G	AF026816	CCDS13051.1, CCDS46576.1, CCDS58762.1	20p	2002-02-01			ENSG00000125877	ENSG00000125877	3.6.1.19		6176	protein-coding gene	gene with protein product		147520		C20orf37		11278832	Standard	NM_033453		Approved	HLC14-06-P, dJ794I6.3	uc002wid.4	Q9BY32	OTTHUMG00000031738	ENST00000380113.3:c.526T>G	20.37:g.3204049T>G	ENSP00000369456:p.Ser176Ala					ITPA_uc002wie.3_Missense_Mutation_p.S159A|ITPA_uc002wif.3_Non-coding_Transcript	p.S176A	NM_033453	NP_258412	Q9BY32	ITPA_HUMAN			7	668	+			176						Missense_Mutation	SNP	ENST00000380113.3	37	c.526T>G	CCDS13051.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.052321	0.75960	.	.	ENSG00000125877	ENST00000380113;ENST00000455664;ENST00000399838	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.91656	0.7363	H	0.99937	4.99	0.49213	D	0.999763	D;D	0.89917	0.999;1.0	D;D	0.97110	1.0;0.999	D	0.94624	0.7816	9	0.87932	D	0	.	12.574	0.56354	0.0:0.0:0.0:1.0	.	159;176	B2BCH7;Q9BY32	.;ITPA_HUMAN	A	176;159;135	.	ENSP00000369456:S176A	S	+	1	0	ITPA	3152049	1.000000	0.71417	0.999000	0.59377	0.535000	0.34838	5.851000	0.69481	2.225000	0.72522	0.460000	0.39030	TCC		0.617	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2			7	28	0	0	0	1	0	7	28				
RSF1	51773	broad.mit.edu	37	11	77412844	77412844	+	Missense_Mutation	SNP	T	T	C			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr11:77412844T>C	ENST00000308488.6	-	6	1732	c.1430A>G	c.(1429-1431)gAc>gGc	p.D477G	RSF1_ENST00000360355.2_Missense_Mutation_p.D446G|RSF1_ENST00000480887.1_Missense_Mutation_p.D225G			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	477					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			GATATTTCTGTCCTTAGAGGG	0.403																																						uc001oyn.3																			0				breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43						c.(1429-1431)gAc>gGc		Homo sapiens remodeling and spacing factor 1 (RSF1), mRNA.							122.0	120.0	121.0					11																	77412844		2200	4292	6492	SO:0001583	missense	51773				CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding	g.chr11:77412844T>C	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.1430A>G	11.37:g.77412844T>C	ENSP00000311513:p.Asp477Gly					RSF1_uc001oym.3_Missense_Mutation_p.D225G	p.D477G	NM_016578	NP_057662	Q96T23	RSF1_HUMAN	Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)		5	1550	-	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		477					Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	c.1430A>G	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.232874	0.39498	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.86627	-2.12;-2.14;-2.12;-2.15;1.28	5.54	3.23	0.37069	.	0.339854	0.25469	N	0.030443	T	0.79695	0.4490	L	0.32530	0.975	0.39706	D	0.971252	B	0.12630	0.006	B	0.09377	0.004	T	0.73043	-0.4107	10	0.66056	D	0.02	-3.853	9.66	0.39950	0.0:0.1338:0.0:0.8662	.	477	Q96T23	RSF1_HUMAN	G	477;225;446;278;476	ENSP00000311513:D477G;ENSP00000434509:D225G;ENSP00000353511:D446G;ENSP00000432022:D278G;ENSP00000436408:D476G	ENSP00000311513:D477G	D	-	2	0	RSF1	77090492	0.998000	0.40836	0.516000	0.27786	0.969000	0.65631	2.552000	0.45828	0.411000	0.25702	0.533000	0.62120	GAC		0.403	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		23	51	0	0	0	1	0	23	51				
GFI1B	8328	broad.mit.edu	37	9	135865148	135865148	+	Missense_Mutation	SNP	G	G	A	rs367947845		TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr9:135865148G>A	ENST00000339463.3	+	10	1487	c.668G>A	c.(667-669)cGc>cAc	p.R223H	GFI1B_ENST00000372124.1_Missense_Mutation_p.R177H|GFI1B_ENST00000372123.1_Missense_Mutation_p.R177H|GFI1B_ENST00000450530.1_Missense_Mutation_p.R223H|GFI1B_ENST00000372122.1_Missense_Mutation_p.R223H|GFI1B_ENST00000534944.1_Missense_Mutation_p.R177H			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	223	Interaction with ARIH2.|Mediates interaction with GATA1.				cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)	p.R223F(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		TTCGAGTGCCGCATGTGCGGC	0.677																																						uc004ccg.3																			1	Substitution - Missense(1)	p.R223F(2)	lung(1)	central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21						c.(667-669)cGc>cAc		Homo sapiens growth factor independent 1B transcription repressor (GFI1B), transcript variant 1, mRNA.		G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	49.0	43.0	45.0		530,668	1.4	1.0	9		45	0,8600		0,0,4300	no	missense,missense	GFI1B	NM_001135031.1,NM_004188.4	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	177/285,223/331	135865148	1,13005	2203	4300	6503	SO:0001583	missense	8328				cell proliferation|chromatin modification|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|zinc ion binding	g.chr9:135865148G>A	AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"""Zinc fingers, C2H2-type"""	4238	protein-coding gene	gene with protein product		604383	"""growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"""			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.668G>A	9.37:g.135865148G>A	ENSP00000344782:p.Arg223His					GFI1B_uc010mzy.3_Missense_Mutation_p.R177H	p.R223H	NM_004188	NP_004179	Q5VTD9	GFI1B_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)	5	1023	+			223			Interaction with ARIH2.|Mediates interaction with GATA1.		O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	c.668G>A	CCDS6957.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849738	0.51270	2.27E-4	0.0	ENSG00000165702	ENST00000372124;ENST00000339463;ENST00000450530;ENST00000534944;ENST00000372123;ENST00000372122	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	4.8	1.39	0.22231	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.065346	0.64402	D	0.000017	T	0.25232	0.0613	N	0.12443	0.215	0.27970	N	0.93643	B;B	0.16166	0.016;0.009	B;B	0.17098	0.01;0.017	T	0.15752	-1.0426	10	0.72032	D	0.01	-25.6719	5.495	0.16797	0.5423:0.0:0.4577:0.0	.	177;223	Q5VTD9-2;Q5VTD9	.;GFI1B_HUMAN	H	177;223;223;177;177;223	ENSP00000361197:R177H;ENSP00000344782:R223H;ENSP00000409546:R223H;ENSP00000446134:R177H;ENSP00000361196:R177H;ENSP00000361195:R223H	ENSP00000344782:R223H	R	+	2	0	GFI1B	134854969	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.572000	0.45999	0.547000	0.28938	0.591000	0.81541	CGC		0.677	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		3	29	0	0	0	1	0	3	29				
ITGAV	3685	broad.mit.edu	37	2	187541588	187541588	+	Missense_Mutation	SNP	C	C	A			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr2:187541588C>A	ENST00000261023.3	+	29	3251	c.2977C>A	c.(2977-2979)Cct>Act	p.P993T	ITGAV_ENST00000374907.3_Missense_Mutation_p.P957T|ITGAV_ENST00000433736.2_Missense_Mutation_p.P947T|AC017101.10_ENST00000453665.1_RNA	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	993					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CATGCCTGTGCCTGTGTGGGT	0.423																																					Melanoma(58;108 1995 6081)	uc002upq.3																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47						c.(2977-2979)Cct>Act		Homo sapiens integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51) (ITGAV), transcript variant 1, mRNA.							136.0	128.0	131.0					2																	187541588		2203	4300	6503	SO:0001583	missense	3685				ERK1 and ERK2 cascade|angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding	g.chr2:187541588C>A		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"""CD molecules"", ""Integrins"""	6150	protein-coding gene	gene with protein product		193210	"""antigen identified by monoclonal antibody L230"", ""vitronectin receptor"", ""integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"""	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2977C>A	2.37:g.187541588C>A	ENSP00000261023:p.Pro993Thr					ITGAV_uc010frs.3_Missense_Mutation_p.P957T|ITGAV_uc010zfv.2_Missense_Mutation_p.P947T	p.P993T	NM_002210	NP_002201	P06756	ITAV_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	28	3253	+			993					A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	37	c.2977C>A	CCDS2292.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.988509	0.74589	.	.	ENSG00000138448	ENST00000261023;ENST00000374907;ENST00000433736	D;D;D	0.98901	-5.22;-5.22;-5.22	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.99137	0.9702	M	0.83483	2.645	0.47123	D	0.999329	D;D;D	0.76494	0.986;0.999;0.986	P;D;P	0.74674	0.843;0.984;0.843	D	0.99719	1.1009	10	0.87932	D	0	.	18.5007	0.90879	0.0:1.0:0.0:0.0	.	947;957;993	E7EWZ6;P06756-2;P06756	.;.;ITAV_HUMAN	T	993;957;947	ENSP00000261023:P993T;ENSP00000364042:P957T;ENSP00000404291:P947T	ENSP00000261023:P993T	P	+	1	0	ITGAV	187249833	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	4.291000	0.59025	2.423000	0.82170	0.650000	0.86243	CCT		0.423	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		25	62	0	0	0	1	0	25	62				
SYTL5	94122	broad.mit.edu	37	X	37931394	37931394	+	Missense_Mutation	SNP	T	T	A			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chrX:37931394T>A	ENST00000357972.5	+	4	970	c.424T>A	c.(424-426)Tcc>Acc	p.S142T	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000456733.2_Missense_Mutation_p.S142T|SYTL5_ENST00000297875.2_Missense_Mutation_p.S142T			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	142					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						TGTCCGACAGTCCATTTTAAG	0.373																																						uc004ddx.3																			0				central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						c.(424-426)Tcc>Acc		Homo sapiens synaptotagmin-like 5 (SYTL5), transcript variant 3, mRNA.							152.0	128.0	136.0					X																	37931394		2202	4300	6502	SO:0001583	missense	94122				intracellular protein transport	membrane	Rab GTPase binding|metal ion binding	g.chrX:37931394T>A		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.424T>A	X.37:g.37931394T>A	ENSP00000350657:p.Ser142Thr					SYTL5_uc004ddu.3_Missense_Mutation_p.S142T|SYTL5_uc004ddv.3_Missense_Mutation_p.S142T	p.S142T	NM_001163334	NP_001156806	Q8TDW5	SYTL5_HUMAN			2	780	+			142					A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	37	c.424T>A	CCDS14244.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.045442	0.75846	.	.	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.26067	1.76;1.76;2.1	5.33	5.33	0.75918	.	0.113104	0.64402	D	0.000007	T	0.54046	0.1834	M	0.86178	2.8	0.32074	N	0.594001	D;D	0.89917	0.966;1.0	B;D	0.76071	0.395;0.987	T	0.67860	-0.5561	10	0.49607	T	0.09	-9.136	13.4248	0.61020	0.0:0.0:0.0:1.0	.	142;142	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	T	142	ENSP00000297875:S142T;ENSP00000350657:S142T;ENSP00000395220:S142T	ENSP00000297875:S142T	S	+	1	0	SYTL5	37816338	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.114000	0.64648	1.882000	0.54519	0.417000	0.27973	TCC		0.373	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		8	71	0	0	0	1	0	8	71				
PGK2	5232	broad.mit.edu	37	6	49754598	49754598	+	Silent	SNP	G	G	A	rs549102825		TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr6:49754598G>A	ENST00000304801.3	-	1	455	c.303C>T	c.(301-303)ggC>ggT	p.G101G		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	101					glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47	Lung NSC(77;0.0402)					CCACTTCTGCGCCTACACAGT	0.522													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19522	0.0		0.0	False		,,,				2504	0.0					uc003ozu.3																			0				autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47						c.(301-303)ggC>ggT		Homo sapiens phosphoglycerate kinase 2 (PGK2), mRNA.							123.0	115.0	117.0					6																	49754598		2203	4300	6503	SO:0001819	synonymous_variant	5232				glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity	g.chr6:49754598G>A	K03019	CCDS4930.1	6p12.3	2012-09-20		2002-04-19	ENSG00000170950	ENSG00000170950			8898	protein-coding gene	gene with protein product		172270				3839763, 3453121	Standard	NM_138733		Approved	PGKPS, PGK-2	uc003ozu.3	P07205	OTTHUMG00000014824	ENST00000304801.3:c.303C>T	6.37:g.49754598G>A							p.G101G	NM_138733	NP_620061	P07205	PGK2_HUMAN			0	456	-	Lung NSC(77;0.0402)		101					B2R6Y8|Q9H107	Silent	SNP	ENST00000304801.3	37	c.303C>T	CCDS4930.1																																																																																				0.522	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			14	100	0	0	0	1	0	14	100				
BRAF	673	broad.mit.edu	37	7	140453135	140453136	+	Missense_Mutation	DNP	CA	CA	TT	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr7:140453135_140453136CA>TT	ENST00000288602.6	-	15	1859_1860	c.1799_1800TG>AA	c.(1798-1800)gTG>gAA	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.V600V(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)	ATCGAGATTTCACTGTAGCTAG	0.371	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)	15809	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)|Substitution - coding silent(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.V600V(2)|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.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(337)|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>gAA		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)																																			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.chr7:140453135_140453136CA>TT	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.1799_1800delinsTT	7.37:g.140453135_140453136delinsTT	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860_1861	-	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	DNP	ENST00000288602.6	37	c.1799_1800TG>AA	CCDS5863.1																																																																																				0.371	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		13	39	0	0	0	1	0	13	39				
SLC12A6	9990	broad.mit.edu	37	15	34549844	34549844	+	Splice_Site	SNP	C	C	A			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr15:34549844C>A	ENST00000354181.3	-	6	1181	c.689G>T	c.(688-690)tGt>tTt	p.C230F	SLC12A6_ENST00000558667.1_Splice_Site_p.C230F|SLC12A6_ENST00000560164.1_Intron|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000558589.1_Splice_Site_p.C221F|SLC12A6_ENST00000397707.2_Splice_Site_p.C215F|SLC12A6_ENST00000397702.2_Splice_Site_p.C171F|SLC12A6_ENST00000458406.2_Splice_Site_p.C171F|SLC12A6_ENST00000560611.1_Splice_Site_p.C230F|SLC12A6_ENST00000451844.2_Intron|SLC12A6_ENST00000290209.5_Splice_Site_p.C179F			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	230	Poly-Cys.				angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	AGTACTTACACAGCAGCAGCA	0.438																																						uc001zhw.3																			0				central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45						c.e5+1		Homo sapiens solute carrier family 12 (potassium/chloride transporters), member 6 (SLC12A6), transcript variant 1, mRNA.	Potassium Chloride(DB00761)						75.0	66.0	69.0					15																	34549844		2201	4298	6499	SO:0001630	splice_region_variant	9990				angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity	g.chr15:34549844C>A	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.690+1G>T	15.37:g.34549844C>A						SLC12A6_uc001zhv.3_Splice_Site_p.C179_splice|SLC12A6_uc001zhz.3_Splice_Site|SLC12A6_uc001zhx.3_Splice_Site_p.C215_splice|SLC12A6_uc001zhy.3_Splice_Site|SLC12A6_uc001zia.3_Splice_Site_p.C171_splice|SLC12A6_uc001zib.3_Splice_Site_p.C221_splice|SLC12A6_uc001zic.3_Splice_Site_p.C230_splice|SLC12A6_uc010bau.3_Splice_Site_p.C230_splice|SLC12A6_uc001zid.3_Splice_Site_p.C171_splice|SLC12A6_uc001zhu.3_Intron	p.C230_splice	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	5	854	-		all_lung(180;2.78e-08)	230			Poly-Cys.		A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Splice_Site	SNP	ENST00000354181.3	37	c.690_splice	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.931477	0.92389	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406	D;D;D;D	0.98684	-5.07;-5.07;-5.07;-5.07	5.55	5.55	0.83447	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99242	0.9736	M	0.89095	3.005	0.80722	D	1	D;D;D	0.69078	0.99;0.997;0.978	P;D;D	0.70227	0.906;0.968;0.936	D	0.99406	1.0929	10	0.87932	D	0	.	18.4345	0.90640	0.0:1.0:0.0:0.0	.	215;230;179	Q9UHW9-3;Q9UHW9;A0AV76	.;S12A6_HUMAN;.	F	179;215;221;171;171	ENSP00000290209:C179F;ENSP00000380819:C215F;ENSP00000380814:C171F;ENSP00000387725:C171F	ENSP00000290209:C179F	C	-	2	0	SLC12A6	32337136	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.651000	0.83577	2.885000	0.99019	0.655000	0.94253	TGT		0.438	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	Missense_Mutation	7	17	0	0	0	1	0	7	17				
VSTM1	284415	broad.mit.edu	37	19	54545172	54545172	+	Missense_Mutation	SNP	G	G	A			TCGA-E8-A437-01A-12D-A23U-08	TCGA-E8-A437-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	790acd37-23ee-49d1-bf24-05d6ac48d678	5dfb3d6d-6d77-40bd-bd60-4d86741432ac	g.chr19:54545172G>A	ENST00000338372.2	-	7	726	c.551C>T	c.(550-552)gCc>gTc	p.A184V	VSTM1_ENST00000366170.2_Missense_Mutation_p.A96V|VSTM1_ENST00000425006.2_3'UTR|VSTM1_ENST00000376626.1_Missense_Mutation_p.A153V	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	184					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		TCCCTTACCGGCAGCCTCCTG	0.478																																						uc002qcw.4																			0				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						c.(550-552)gCc>gTc		Homo sapiens V-set and transmembrane domain containing 1 (VSTM1), mRNA.							59.0	60.0	60.0					19																	54545172		2203	4300	6503	SO:0001583	missense	284415					integral to membrane		g.chr19:54545172G>A	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.551C>T	19.37:g.54545172G>A	ENSP00000343366:p.Ala184Val					VSTM1_uc021vbe.1_Non-coding_Transcript|VSTM1_uc021vbf.1_Missense_Mutation_p.A96V|VSTM1_uc002qcx.4_Missense_Mutation_p.A153V|VSTM1_uc010erb.3_Non-coding_Transcript|VSTM1_uc021vbg.1_Missense_Mutation_p.A64V	p.A184V	NM_198481	NP_940883	Q6UX27	VSTM1_HUMAN		GBM - Glioblastoma multiforme(134;0.165)	6	727	-	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)		184					B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	37	c.551C>T	CCDS12872.1	.	.	.	.	.	.	.	.	.	.	G	7.669	0.686596	0.14973	.	.	ENSG00000189068	ENST00000419106;ENST00000338372;ENST00000376626;ENST00000366170	T;T;T;T	0.48522	2.65;6.78;6.45;0.81	2.63	0.382	0.16234	.	2.851890	0.01693	U	0.026742	T	0.23210	0.0561	N	0.19112	0.55	0.20489	N	0.999892	B;P	0.35575	0.267;0.51	B;B	0.19666	0.026;0.026	T	0.16837	-1.0389	10	0.02654	T	1	.	3.9453	0.09346	0.1454:0.2489:0.6057:0.0	.	153;184	D2DJS4;Q6UX27	.;VSTM1_HUMAN	V	74;184;153;96	ENSP00000409412:A74V;ENSP00000343366:A184V;ENSP00000365813:A153V;ENSP00000444153:A96V	ENSP00000343366:A184V	A	-	2	0	VSTM1	59236984	0.004000	0.15560	0.005000	0.12908	0.004000	0.04260	0.342000	0.19926	0.196000	0.20367	0.638000	0.83543	GCC		0.478	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481		3	45	0	0	0	1	0	3	45				
