#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
RAB3GAP2	25782	broad.mit.edu	37	1	220387224	220387224	+	Missense_Mutation	SNP	C	C	T	rs371630366		TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr1:220387224C>T	ENST00000358951.2	-	3	394	c.278G>A	c.(277-279)cGa>cAa	p.R93Q		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	93					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TTTTTGCTCTCGAGCTATCAC	0.363																																						ENST00000358951.2																			0				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39						c.(277-279)cGa>cAa		RAB3 GTPase activating protein subunit 2 (non-catalytic)		C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	110.0	106.0	108.0		278	5.7	1.0	1		108	0,8600		0,0,4300	no	missense	RAB3GAP2	NM_012414.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	93/1394	220387224	1,13005	2203	4300	6503	SO:0001583	missense	25782				intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity	g.chr1:220387224C>T	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.278G>A	1.37:g.220387224C>T	ENSP00000351832:p.Arg93Gln						p.R93Q	NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN		GBM - Glioblastoma multiforme(131;0.0443)	3	394	-			93					A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	c.278G>A	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098643	0.56183	2.27E-4	0.0	ENSG00000118873	ENST00000358951	T	0.30981	1.51	5.66	5.66	0.87406	.	0.156225	0.56097	D	0.000021	T	0.18045	0.0433	L	0.29908	0.895	0.47123	D	0.999321	P;P	0.40476	0.718;0.6	B;B	0.29785	0.107;0.085	T	0.03060	-1.1077	10	0.29301	T	0.29	.	10.6179	0.45462	0.0:0.8548:0.0:0.1452	.	93;93	Q9H2M9-2;Q9H2M9	.;RBGPR_HUMAN	Q	93	ENSP00000351832:R93Q	ENSP00000351832:R93Q	R	-	2	0	RAB3GAP2	218453847	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.177000	0.50871	2.829000	0.97493	0.591000	0.81541	CGA		0.363	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		23	58	0	0	0	0.667858	0	23	58				
SLC7A9	11136	broad.mit.edu	37	19	33355655	33355655	+	Missense_Mutation	SNP	T	T	G			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr19:33355655T>G	ENST00000023064.4	-	3	306	c.115A>C	c.(115-117)Atc>Ctc	p.I39L	RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000590341.1_Missense_Mutation_p.I39L|SLC7A9_ENST00000587772.1_Missense_Mutation_p.I39L	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	39					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	GTGCCCACGATGATGGAGATG	0.622																																					GBM(181;1335 2108 9644 44178 46689)	ENST00000023064.4																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32						c.(115-117)Atc>Ctc		solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	L-Cystine(DB00138)						170.0	158.0	162.0					19																	33355655		2203	4300	6503	SO:0001583	missense	11136				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	integral to plasma membrane	L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding	g.chr19:33355655T>G	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.115A>C	19.37:g.33355655T>G	ENSP00000023064:p.Ile39Leu					SLC7A9_ENST00000587772.1_Missense_Mutation_p.I39L|SLC7A9_ENST00000590341.1_Missense_Mutation_p.I39L	p.I39L	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN			3	306	-	Esophageal squamous(110;0.137)		39					B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	37	c.115A>C	CCDS12425.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.935490	0.92458	.	.	ENSG00000021488	ENST00000023064	D	0.90261	-2.64	4.87	4.87	0.63330	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.91623	0.7353	M	0.64567	1.98	0.80722	D	1	P	0.39022	0.655	P	0.47015	0.534	D	0.92215	0.5779	10	0.59425	D	0.04	.	14.7704	0.69671	0.0:0.0:0.0:1.0	.	39	P82251	BAT1_HUMAN	L	39	ENSP00000023064:I39L	ENSP00000023064:I39L	I	-	1	0	SLC7A9	38047495	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	8.015000	0.88690	1.956000	0.56807	0.379000	0.24179	ATC		0.622	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			75	60	0	0	0	0.870114	0	75	60				
NCOR1P1	149934	broad.mit.edu	37	20	26084295	26084295	+	RNA	SNP	C	C	T	rs76611503		TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr20:26084295C>T	ENST00000478176.1	-	0	162					NR_003678.1		Q9H4R4	CT191_HUMAN	nuclear receptor corepressor 1 pseudogene 1									p.G41R(1)									TGTTTGCCTCCAAATGCTGGA	0.373																																						ENST00000478176.1																			1	Substitution - Missense(1)	p.G41R(1)	kidney(1)																	42.0	30.0	34.0					20																	26084295		692	1590	2282			0							g.chr20:26084295C>T	AL391119		20p11.1	2011-09-16	2011-09-16	2011-09-16	ENSG00000240108	ENSG00000240108			16724	pseudogene	pseudogene			"""chromosome 20 open reading frame 191"""	C20orf191			Standard	NR_003678		Approved	bB329D4.2	uc002wvj.5	Q9H4R4	OTTHUMG00000032145		20.37:g.26084295C>T								NR_003678.1						0	162	-								A2RUA0	RNA	SNP	ENST00000478176.1	37																																																																																						0.373	NCOR1P1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000078478.2			4	86	0	0	0	0.150653	0	4	86				
CIC	23152	broad.mit.edu	37	19	42799060	42799060	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr19:42799060G>A	ENST00000575354.2	+	20	4584	c.4544G>A	c.(4543-4545)cGc>cAc	p.R1515H	CIC_ENST00000572681.2_Missense_Mutation_p.R2421H|CIC_ENST00000160740.3_Missense_Mutation_p.R1513H	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R1515L(1)|p.R1515H(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CGTGAGGTGCGCCAGAAGATC	0.632			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		2	Substitution - Missense(2)	p.R1515L(1)|p.R1515H(1)	central_nervous_system(2)	autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(7261-7263)cGc>cAc		capicua transcriptional repressor							45.0	45.0	45.0					19																	42799060		2203	4300	6503	SO:0001583	missense	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42799060G>A	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4544G>A	19.37:g.42799060G>A	ENSP00000458663:p.Arg1515His					CIC_ENST00000160740.3_Missense_Mutation_p.R1513H|CIC_ENST00000575354.2_Missense_Mutation_p.R1515H	p.R2421H			Q96RK0	CIC_HUMAN			21	7330	+		Prostate(69;0.00682)	1515					Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	c.7262G>A	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573446	0.86542	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.65037	0.2653	L	0.29908	0.895	0.48395	D	0.999647	D	0.76494	0.999	D	0.74674	0.984	T	0.68911	-0.5284	8	0.87932	D	0	-10.1007	15.0527	0.71888	0.0:0.0:1.0:0.0	.	1515	Q96RK0	CIC_HUMAN	H	1515	.	ENSP00000160740:R1515H	R	+	2	0	CIC	47490900	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.215000	0.89762	2.513000	0.84729	0.491000	0.48974	CGC		0.632	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			4	46	0	0	0	0.150653	0	4	46				
VANGL2	57216	broad.mit.edu	37	1	160389291	160389291	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr1:160389291A>G	ENST00000368061.2	+	4	1166	c.692A>G	c.(691-693)tAc>tGc	p.Y231C	VANGL2_ENST00000483408.1_3'UTR	NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	231					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)				biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTCGTGCACTACCTGGCCGTG	0.647																																						ENST00000368061.2																			0				biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37						c.(691-693)tAc>tGc		VANGL planar cell polarity protein 2							76.0	77.0	77.0					1																	160389291		2203	4300	6503	SO:0001583	missense	57216				apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane		g.chr1:160389291A>G	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.692A>G	1.37:g.160389291A>G	ENSP00000357040:p.Tyr231Cys					VANGL2_ENST00000483408.1_3'UTR	p.Y231C	NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.111)		4	1166	+	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		231					D3DVE9|Q5T212	Missense_Mutation	SNP	ENST00000368061.2	37	c.692A>G	CCDS30915.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286396	0.80803	.	.	ENSG00000162738	ENST00000368061	D	0.87571	-2.27	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.93497	0.7925	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94808	0.7976	10	0.87932	D	0	-19.7537	14.0338	0.64632	1.0:0.0:0.0:0.0	.	231	Q9ULK5	VANG2_HUMAN	C	231	ENSP00000357040:Y231C	ENSP00000357040:Y231C	Y	+	2	0	VANGL2	158655915	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.013000	0.76373	2.037000	0.60232	0.460000	0.39030	TAC		0.647	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1	NM_020335		3	77	0	0	0	0.115264	0	3	77				
GTSF1	121355	broad.mit.edu	37	12	54857017	54857017	+	Missense_Mutation	SNP	C	C	A			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr12:54857017C>A	ENST00000552397.1	-	4	1078	c.182G>T	c.(181-183)cGa>cTa	p.R61L	RP11-753H16.5_ENST00000552785.1_RNA|GTSF1_ENST00000552395.1_5'UTR|RP11-753H16.3_ENST00000550474.1_RNA|GTSF1_ENST00000305879.5_Missense_Mutation_p.R61L			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1	61						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				AATTTCAGCTCGAGGAACCTG	0.413																																						ENST00000552397.1																			0				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						c.(181-183)cGa>cTa		gametocyte specific factor 1							119.0	108.0	112.0					12																	54857017		2203	4300	6503	SO:0001583	missense	121355						metal ion binding	g.chr12:54857017C>A	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"""family with sequence similarity 112, member B"""	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.182G>T	12.37:g.54857017C>A	ENSP00000446485:p.Arg61Leu					RP11-753H16.5_ENST00000552785.1_RNA|GTSF1_ENST00000552395.1_5'UTR|GTSF1_ENST00000305879.5_Missense_Mutation_p.R61L|RP11-753H16.3_ENST00000550474.1_RNA	p.R61L			Q8WW33	GTSF1_HUMAN			4	1078	-		Myeloproliferative disorder(1001;0.00452)	61					B3KQ60|Q0VGM4|Q8N778	Missense_Mutation	SNP	ENST00000552397.1	37	c.182G>T	CCDS8881.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938496	0.52972	.	.	ENSG00000170627	ENST00000552397;ENST00000305879	T;T	0.42131	0.98;0.98	6.02	5.13	0.70059	TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain (1);	0.174674	0.51477	D	0.000087	T	0.34019	0.0883	L	0.36672	1.1	0.39437	D	0.967178	P	0.39696	0.683	B	0.38755	0.281	T	0.14337	-1.0476	10	0.42905	T	0.14	-14.4727	12.3044	0.54893	0.0:0.9196:0.0:0.0804	.	61	Q8WW33	GTSF1_HUMAN	L	61	ENSP00000446485:R61L;ENSP00000304185:R61L	ENSP00000304185:R61L	R	-	2	0	GTSF1	53143284	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.575000	0.36493	2.865000	0.98341	0.655000	0.94253	CGA		0.413	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594		4	98	1	0	0.184627	0.184627	0.237378	4	98				
SUZ12P1	440423	broad.mit.edu	37	17	29061941	29061941	+	RNA	SNP	T	T	C	rs112064181		TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr17:29061941T>C	ENST00000582557.1	+	0	861																											TAGATTTCTTTGAACTCGGAA	0.303																																						ENST00000582557.1																			0																																																			0							g.chr17:29061941T>C																													17.37:g.29061941T>C														0	861	+									RNA	SNP	ENST00000582557.1	37																																																																																						0.303	SUZ12P-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000444260.1			4	143	0	0	0	0.150653	0	4	143				
NBPF10	100132406	broad.mit.edu	37	1	145359109	145359109	+	Missense_Mutation	SNP	T	T	A	rs3967942	byFrequency	TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr1:145359109T>A	ENST00000342960.5	+	72	9084	c.9049T>A	c.(9049-9051)Tgt>Agt	p.C3017S	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	575						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.C3017S(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TCTTGAACTGTGTGACTCATG	0.483													.|||	520	0.103834	0.1944	0.1297	5008	,	,		8025	0.0357		0.0726	False		,,,				2504	0.0654					ENST00000342960.5																			1	Substitution - Missense(1)	p.C3017S(1)	endometrium(1)	NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(9049-9051)Tgt>Agt		neuroblastoma breakpoint family, member 10																																				SO:0001583	missense	100132406							g.chr1:145359109T>A	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.9049T>A	1.37:g.145359109T>A	ENSP00000345684:p.Cys3017Ser					NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron	p.C3017S	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	72	9084	+	all_hematologic(923;0.032)		3017					Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	c.9049T>A	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.481396	0.00163	.	.	ENSG00000163386	ENST00000342960	T	0.05513	3.43	.	.	.	.	.	.	.	.	T	0.00412	0.0013	N	0.01640	-0.785	0.09310	N	1	.	.	.	.	.	.	T	0.44205	-0.9343	5	0.02654	T	1	.	.	.	.	rs3967942	.	.	.	S	3017	ENSP00000345684:C3017S	ENSP00000345684:C3017S	C	+	1	0	NBPF10	144070466	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.392000	0.07314	-0.792000	0.04480	0.128000	0.15822	TGT		0.483	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703		3	41	0	0	0	0.115264	0	3	41				
SVIL	6840	broad.mit.edu	37	10	29770516	29770516	+	Missense_Mutation	SNP	G	G	T			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr10:29770516G>T	ENST00000355867.4	-	28	5849	c.5097C>A	c.(5095-5097)caC>caA	p.H1699Q	PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.H1273Q|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.H613Q|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000538146.1_Missense_Mutation_p.H491Q|SVIL_ENST00000375398.2_Missense_Mutation_p.H1699Q	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1699					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GGAATACCTTGTGCTGGGCAA	0.463																																						ENST00000375398.2																			0				breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112						c.(5095-5097)caC>caA		supervillin							183.0	203.0	196.0					10																	29770516		2203	4300	6503	SO:0001583	missense	6840				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding	g.chr10:29770516G>T	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5097C>A	10.37:g.29770516G>T	ENSP00000348128:p.His1699Gln					SVIL_ENST00000375400.3_Missense_Mutation_p.H1273Q|SVIL_ENST00000535393.1_Missense_Mutation_p.H613Q|SVIL_ENST00000460007.1_5'UTR|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000355867.4_Missense_Mutation_p.H1699Q|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000538146.1_Missense_Mutation_p.H491Q|PTCHD3P1_ENST00000446807.1_RNA	p.H1699Q			O95425	SVIL_HUMAN			30	5546	-		Breast(68;0.103)	1699					D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	c.5097C>A	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	0.022	-1.415521	0.01136	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4	3.94	0.78	0.18556	.	0.537320	0.21522	N	0.073183	T	0.02929	0.0087	N	0.00308	-1.67	0.28197	N	0.927526	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.43196	-0.9406	10	0.06099	T	0.92	-8.8179	7.1275	0.25479	0.0:0.5585:0.3431:0.0984	.	613;491;1273;1699	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	Q	1273;1699;1699;613;653;491	ENSP00000364549:H1273Q;ENSP00000364547:H1699Q;ENSP00000348128:H1699Q;ENSP00000445472:H613Q;ENSP00000440343:H491Q	ENSP00000348128:H1699Q	H	-	3	2	SVIL	29810522	0.998000	0.40836	0.994000	0.49952	0.524000	0.34500	0.875000	0.28079	0.053000	0.16036	-0.311000	0.09066	CAC		0.463	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			189	365	1	0	1.35662e-99	0.870114	1.92782e-99	189	365				
AREL1	9870	broad.mit.edu	37	14	75139816	75139816	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr14:75139816C>G	ENST00000356357.4	-	10	1779	c.1264G>C	c.(1264-1266)Gca>Cca	p.A422P	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	422					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAAGTGGCTGCTAGAATGTTC	0.512																																						ENST00000356357.4																			0											c.(1264-1266)Gca>Cca		apoptosis resistant E3 ubiquitin protein ligase 1							90.0	91.0	91.0					14																	75139816		1954	4148	6102	SO:0001583	missense	9870							g.chr14:75139816C>G	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"""KIAA0317"""	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.1264G>C	14.37:g.75139816C>G	ENSP00000348714:p.Ala422Pro					AREL1_ENST00000557401.1_5'UTR	p.A422P	NM_001039479.1	NP_001034568.1					10	1779	-								B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	37	c.1264G>C	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	C	35	5.440456	0.96168	.	.	ENSG00000119682	ENST00000356357;ENST00000543377;ENST00000556202	T;T	0.55760	0.5;0.5	6.17	6.17	0.99709	.	0.092161	0.85682	D	0.000000	T	0.73055	0.3538	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.996;0.972	T	0.67945	-0.5539	10	0.40728	T	0.16	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	422;422	O15033-2;O15033	.;K0317_HUMAN	P	422;261;261	ENSP00000348714:A422P;ENSP00000452101:A261P	ENSP00000348714:A422P	A	-	1	0	KIAA0317	74209569	1.000000	0.71417	0.856000	0.33681	0.902000	0.53008	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	GCA		0.512	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		6	72	0	0	0	0.681144	0	6	72				
ARPC1B	10095	broad.mit.edu	37	7	98987611	98987611	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr7:98987611C>T	ENST00000451682.1	+	7	785	c.476C>T	c.(475-477)gCc>gTc	p.A159V	PDAP1_ENST00000496335.1_5'Flank|ARPC1B_ENST00000252725.5_Missense_Mutation_p.A159V			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	159					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CTGCTGGCTGCCGGCTCCTGT	0.632																																						ENST00000451682.1																			0				central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11						c.(475-477)gCc>gTc		actin related protein 2/3 complex, subunit 1B, 41kDa							100.0	96.0	97.0					7																	98987611		2203	4300	6503	SO:0001583	missense	10095				cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton	g.chr7:98987611C>T	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"""Actin related protein 2/3 complex subunits"", ""WD repeat domain containing"""	704	protein-coding gene	gene with protein product	"""ARP2/3 protein complex subunit p41"", ""actin related protein 2/3 complex, subunit 1A (41 kD)"""	604223	"""actin related protein 2/3 complex, subunit 1B (41 kD)"""			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.476C>T	7.37:g.98987611C>T	ENSP00000389631:p.Ala159Val					ARPC1B_ENST00000252725.5_Missense_Mutation_p.A159V	p.A159V			O15143	ARC1B_HUMAN	STAD - Stomach adenocarcinoma(171;0.215)		7	785	+	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		159					Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	37	c.476C>T	CCDS5661.1	.	.	.	.	.	.	.	.	.	.	C	36	5.707271	0.96821	.	.	ENSG00000130429	ENST00000252725;ENST00000451682	T;T	0.59906	0.23;0.23	5.69	5.69	0.88448	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.66567	0.2802	L	0.33137	0.985	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.64042	0.921;0.921	T	0.64466	-0.6401	10	0.41790	T	0.15	-19.4454	19.4229	0.94729	0.0:1.0:0.0:0.0	.	159;159	A4D275;O15143	.;ARC1B_HUMAN	V	159	ENSP00000252725:A159V;ENSP00000389631:A159V	ENSP00000252725:A159V	A	+	2	0	ARPC1B	98825547	1.000000	0.71417	0.346000	0.25655	0.963000	0.63663	7.714000	0.84703	2.694000	0.91930	0.561000	0.74099	GCC		0.632	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		4	168	0	0	0	0.184627	0	4	168				
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382565.1_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		5	97	0	0	0	0.307466	0	5	97				
CIC	23152	broad.mit.edu	37	19	42791743	42791743	+	Missense_Mutation	SNP	T	T	G			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr19:42791743T>G	ENST00000575354.2	+	5	669	c.629T>G	c.(628-630)tTc>tGc	p.F210C	CIC_ENST00000572681.2_Missense_Mutation_p.F1119C|CIC_ENST00000160740.3_Missense_Mutation_p.F210C	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TTCATGATCTTCAGCAAGCGG	0.627			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		0				autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(3355-3357)tTc>tGc		capicua transcriptional repressor							65.0	67.0	66.0					19																	42791743		2203	4300	6503	SO:0001583	missense	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42791743T>G	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.629T>G	19.37:g.42791743T>G	ENSP00000458663:p.Phe210Cys					CIC_ENST00000160740.3_Missense_Mutation_p.F210C|CIC_ENST00000575354.2_Missense_Mutation_p.F210C	p.F1119C			Q96RK0	CIC_HUMAN			6	3424	+		Prostate(69;0.00682)	210			Pro-rich.		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	c.3356T>G	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.711614	0.48517	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.39	4.39	0.52855	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	D	0.88194	0.6371	H	0.98738	4.315	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.91613	0.5304	8	0.87932	D	0	-10.7648	11.626	0.51145	0.0:0.0:0.0:1.0	.	210	Q96RK0	CIC_HUMAN	C	210	.	ENSP00000160740:F210C	F	+	2	0	CIC	47483583	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.778000	0.68940	1.853000	0.53794	0.454000	0.30748	TTC		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			39	38	0	0	0	0.859065	0	39	38				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382565.1_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000403642.1_Silent_p.S281S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	95	0	0	0	0.307466	0	4	95				
GIMAP6	474344	broad.mit.edu	37	7	150325310	150325310	+	Missense_Mutation	SNP	C	C	T	rs138521615	byFrequency	TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr7:150325310C>T	ENST00000328902.5	-	3	592	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	GIMAP6_ENST00000493969.1_Missense_Mutation_p.R51H	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	126	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCAGGAGCACGGCGTGGGGC	0.622																																						ENST00000328902.5																			0				endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29						c.(376-378)Gtg>Atg		GTPase, IMAP family member 6		C	MET/VAL	0,4406		0,0,2203	53.0	56.0	55.0		376	3.1	0.9	7	dbSNP_134	55	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	21	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging	126/293	150325310	4,13002	2203	4300	6503	SO:0001583	missense	474344						GTP binding	g.chr7:150325310C>T	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.376G>A	7.37:g.150325310C>T	ENSP00000330374:p.Val126Met					GIMAP6_ENST00000493969.1_Missense_Mutation_p.R51H	p.V126M	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	3	592	-			126					C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	c.376G>A	CCDS34778.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	8.179|8.179	0.793385|0.793385	0.16327|0.16327	0.0|0.0	4.65E-4|4.65E-4	ENSG00000133561|ENSG00000133561	ENST00000493969|ENST00000328902;ENST00000392862	.|T	.|0.08458	.|3.09	4.07|4.07	3.14|3.14	0.36123|0.36123	.|AIG1 (1);	.|0.140369	.|0.48767	.|D	.|0.000164	T|T	0.22244|0.22244	0.0536|0.0536	M|M	0.73217|0.73217	2.22|2.22	0.27428|0.27428	N|N	0.954093|0.954093	.|D;D	.|0.76494	.|0.997;0.999	.|D;D	.|0.68943	.|0.96;0.961	T|T	0.00819|0.00819	-1.1553|-1.1553	6|10	0.87932|0.59425	D|D	0|0.04	.|.	8.7634|8.7634	0.34689|0.34689	0.0:0.7444:0.2556:0.0|0.0:0.7444:0.2556:0.0	.|.	.|126;46	.|Q6P9H5;Q6P9H5-2	.|GIMA6_HUMAN;.	H|M	51|126;187	.|ENSP00000330374:V126M	ENSP00000418304:R51H|ENSP00000330374:V126M	R|V	-|-	2|1	0|0	GIMAP6|GIMAP6	149956243|149956243	0.004000|0.004000	0.15560|0.15560	0.935000|0.935000	0.37517|0.37517	0.118000|0.118000	0.20060|0.20060	-0.061000|-0.061000	0.11693|0.11693	2.123000|2.123000	0.65237|0.65237	0.561000|0.561000	0.74099|0.74099	CGT|GTG		0.622	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		40	81	0	0	0	0.847076	0	40	81				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			46	72	0	0	0	0.870114	0	46	72				
PARN	5073	broad.mit.edu	37	16	14680201	14680201	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DB-5278-01A-01D-1468-08	TCGA-DB-5278-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6847e993-1414-4e6f-a2af-39ebe218dd7c	80b03480-5d28-481e-a447-59140d82f1f8	g.chr16:14680201delT	ENST00000437198.2	-	14	1077	c.936delA	c.(934-936)aaafs	p.K312fs	PARN_ENST00000539279.1_Frame_Shift_Del_p.K137fs|PARN_ENST00000420015.2_Frame_Shift_Del_p.K266fs|PARN_ENST00000341484.7_Frame_Shift_Del_p.K251fs	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	312					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						TTGTCATCTCTTTAAACTCAC	0.373																																						ENST00000437198.2																			0				cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						c.(934-936)aafs		poly(A)-specific ribonuclease							94.0	92.0	93.0					16																	14680201		1825	4077	5902	SO:0001589	frameshift_variant	5073				female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding	g.chr16:14680201delT	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"""deadenylation nuclease"""	604212	"""poly(A)-specific ribonuclease (deadenylation nuclease)"""			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.936delA	16.37:g.14680201delT	ENSP00000387911:p.Lys312fs					PARN_ENST00000539279.1_Frame_Shift_Del_p.K137fs|PARN_ENST00000420015.2_Frame_Shift_Del_p.K266fs|PARN_ENST00000341484.7_Frame_Shift_Del_p.K251fs	p.K312fs	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN			14	1077	-			312					B2RCB3|B4DDG8|B4DWR4|B4E1H6	Frame_Shift_Del	DEL	ENST00000437198.2	37	c.936delA	CCDS45419.1																																																																																				0.373	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582		2	4						2	4	---	---	---	---
