#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
SLC8A3	6547	broad.mit.edu	37	14	70634771	70634771	+	Silent	SNP	T	T	A			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr14:70634771T>A	ENST00000381269.2	-	2	1122	c.369A>T	c.(367-369)acA>acT	p.T123T	SLC8A3_ENST00000534137.1_Silent_p.T123T|SLC8A3_ENST00000356921.2_Silent_p.T123T|SLC8A3_ENST00000528359.1_Silent_p.T123T|SLC8A3_ENST00000357887.3_Silent_p.T123T	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	123					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GAATAGTGGTTGTGCTGGTTT	0.488																																						ENST00000381269.2																			0				NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54						c.(367-369)acA>acT		solute carrier family 8 (sodium/calcium exchanger), member 3							112.0	97.0	102.0					14																	70634771		2203	4300	6503	SO:0001819	synonymous_variant	6547				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding	g.chr14:70634771T>A	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.369A>T	14.37:g.70634771T>A						SLC8A3_ENST00000357887.3_Silent_p.T123T|SLC8A3_ENST00000534137.1_Silent_p.T123T|SLC8A3_ENST00000528359.1_Silent_p.T123T|SLC8A3_ENST00000356921.2_Silent_p.T123T	p.T123T	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)	2	1122	-			123					Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	c.369A>T	CCDS35498.1																																																																																				0.488	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			12	43	0	0	0	1	0	12	43				
DGCR2	9993	broad.mit.edu	37	22	19028788	19028788	+	Silent	SNP	G	G	A			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr22:19028788G>A	ENST00000263196.7	-	9	1426	c.1179C>T	c.(1177-1179)ggC>ggT	p.G393G	DGCR2_ENST00000537045.1_Silent_p.G352G|DGCR2_ENST00000545799.1_3'UTR	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	393					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					GGATCCTGCGGCCGAGGTTGA	0.622																																						ENST00000263196.7																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18						c.(1177-1179)ggC>ggT		DiGeorge syndrome critical region gene 2							73.0	72.0	72.0					22																	19028788		2203	4300	6503	SO:0001819	synonymous_variant	9993				cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding	g.chr22:19028788G>A	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1179C>T	22.37:g.19028788G>A						DGCR2_ENST00000545799.1_3'UTR|DGCR2_ENST00000537045.1_Silent_p.G352G	p.G393G	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN			9	1426	-	Colorectal(54;0.0993)		393					A6NIB5|A8K6K5|B5TY34|B7Z935	Silent	SNP	ENST00000263196.7	37	c.1179C>T	CCDS33598.1																																																																																				0.622	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137		25	59	0	0	0	1	0	25	59				
FLOT2	2319	broad.mit.edu	37	17	27209047	27209047	+	Splice_Site	SNP	C	C	A			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr17:27209047C>A	ENST00000394908.4	-	8	804		c.e8-1		FLOT2_ENST00000585169.1_Splice_Site|FLOT2_ENST00000394906.2_Splice_Site|FLOT2_ENST00000577789.1_Splice_Site	NM_004475.2	NP_004466.2	Q14254	FLOT2_HUMAN	flotillin 2						cell adhesion (GO:0007155)|epidermis development (GO:0008544)|establishment of protein localization to plasma membrane (GO:0090002)|negative regulation of amyloid precursor protein catabolic process (GO:1902992)|negative regulation of gene expression (GO:0010629)|protein stabilization (GO:0050821)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|flotillin complex (GO:0016600)|focal adhesion (GO:0005925)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				endometrium(3)|lung(6)|prostate(1)|urinary_tract(1)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			CCTCAGCTGTCTGTGGCAAGA	0.567																																						ENST00000394906.2																			0				endometrium(3)|lung(6)|prostate(1)|urinary_tract(1)	11						c.e10-1		flotillin 2							39.0	40.0	39.0					17																	27209047		2068	4207	6275	SO:0001630	splice_region_variant	2319				cell adhesion|epidermis development	cell surface|endocytic vesicle|endosome|membrane fraction		g.chr17:27209047C>A	M60922	CCDS11245.2	17q11-q12	2008-07-18			ENSG00000132589	ENSG00000132589			3758	protein-coding gene	gene with protein product	"""Flotillin 2 (epidermal surface antigen 1)"", ""membrane component, chromosome 17, surface marker 1 (35kD protein identified by monoclonal antibody ECS-1)"""	131560		M17S1		1769667	Standard	XM_005257950		Approved	ESA, ESA1, ECS-1, ECS1	uc002hdc.3	Q14254	OTTHUMG00000132674	ENST00000394908.4:c.700-1G>T	17.37:g.27209047C>A						FLOT2_ENST00000577789.1_Splice_Site|FLOT2_ENST00000394908.4_Splice_Site|FLOT2_ENST00000585169.1_Splice_Site				Q14254	FLOT2_HUMAN	Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)		10	942	-	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)								Splice_Site	SNP	ENST00000394908.4	37		CCDS11245.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052226	0.75960	.	.	ENSG00000132589	ENST00000394906;ENST00000394908	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4614	0.90739	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FLOT2	24233173	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.783000	0.85696	2.622000	0.88805	0.591000	0.81541	.		0.567	FLOT2-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255935.3	NM_004475	Intron	5	52	1	0	0.00116845	1	0.00116845	5	52				
DPPA3P2	400206	broad.mit.edu	37	14	36840695	36840695	+	RNA	SNP	A	A	G	rs3742593	byFrequency	TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr14:36840695A>G	ENST00000557188.1	+	0	326									developmental pluripotency associated 3 pseudogene 2																		TCCCGGGACGATTCAGGGGCC	0.478													a|||	1371	0.273762	0.1687	0.2983	5008	,	,		17332	0.0972		0.496	False		,,,				2504	0.3517					ENST00000557188.1																			0																																																			0							g.chr14:36840695A>G			14q13.3	2012-07-04			ENSG00000188831	ENSG00000188831			20417	pseudogene	pseudogene							Standard	NG_023379		Approved	STELLAR			OTTHUMG00000170728		14.37:g.36840695A>G														0	326	+									RNA	SNP	ENST00000557188.1	37																																																																																						0.478	DPPA3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000410122.1			5	39	0	0	0	1	0	5	39				
CKAP4	10970	broad.mit.edu	37	12	106633705	106633705	+	Silent	SNP	G	G	A			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr12:106633705G>A	ENST00000378026.4	-	2	1042	c.906C>T	c.(904-906)tcC>tcT	p.S302S	CKAP4_ENST00000552828.1_5'UTR	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	302						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						CCCACTCTCTGGACTTGGCTG	0.537																																						ENST00000378026.4																			0				NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						c.(904-906)tcC>tcT		cytoskeleton-associated protein 4							120.0	122.0	121.0					12																	106633705		2203	4300	6503	SO:0001819	synonymous_variant	10970					ER-Golgi intermediate compartment membrane|integral to membrane|membrane fraction		g.chr12:106633705G>A	X69910	CCDS9103.1	12q23.3	2006-06-23				ENSG00000136026			16991	protein-coding gene	gene with protein product						8314870	Standard	NM_006825		Approved	P63, CLIMP-63, ERGIC-63	uc001tlk.3	Q07065		ENST00000378026.4:c.906C>T	12.37:g.106633705G>A						CKAP4_ENST00000552828.1_5'UTR	p.S302S	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN			2	1042	-			302					Q504S5|Q53ES6	Silent	SNP	ENST00000378026.4	37	c.906C>T	CCDS9103.1																																																																																				0.537	CKAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407196.1			24	136	0	0	0	1	0	24	136				
EFCAB6	64800	broad.mit.edu	37	22	44083357	44083357	+	Missense_Mutation	SNP	C	C	T	rs202185564		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr22:44083357C>T	ENST00000262726.7	-	11	1389	c.1136G>A	c.(1135-1137)aGa>aAa	p.R379K	EFCAB6_ENST00000358439.4_Intron|EFCAB6_ENST00000396231.2_Missense_Mutation_p.R227K	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	379					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATACCTATTTCTTTTTGTCAG	0.308																																						ENST00000262726.7																			0				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						c.(1135-1137)aGa>aAa		EF-hand calcium binding domain 6							41.0	41.0	41.0					22																	44083357		2203	4300	6503	SO:0001583	missense	64800				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding	g.chr22:44083357C>T	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1136G>A	22.37:g.44083357C>T	ENSP00000262726:p.Arg379Lys					EFCAB6_ENST00000358439.4_Intron|EFCAB6_ENST00000396231.2_Missense_Mutation_p.R227K	p.R379K	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN			11	1389	-		Ovarian(80;0.0247)|all_neural(38;0.025)	379					A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	c.1136G>A	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	2.590	-0.295528	0.05532	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.13307	2.6;2.6	4.68	-0.0607	0.13788	.	0.745406	0.12056	N	0.503664	T	0.12050	0.0293	M	0.63428	1.95	0.09310	N	1	B;B	0.21753	0.06;0.041	B;B	0.19666	0.026;0.018	T	0.31530	-0.9940	10	0.29301	T	0.29	-7.7723	3.6739	0.08284	0.0:0.4699:0.1869:0.3432	.	379;379	Q5THR3-6;Q5THR3	.;EFCB6_HUMAN	K	227;379	ENSP00000379533:R227K;ENSP00000262726:R379K	ENSP00000262726:R379K	R	-	2	0	EFCAB6	42414690	0.077000	0.21312	0.006000	0.13384	0.214000	0.24535	0.180000	0.16860	0.208000	0.20626	0.655000	0.94253	AGA		0.308	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		9	33	0	0	0	1	0	9	33				
LRRC17	10234	broad.mit.edu	37	7	102574783	102574783	+	Missense_Mutation	SNP	C	C	G	rs368332401		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr7:102574783C>G	ENST00000339431.4	+	2	718	c.423C>G	c.(421-423)atC>atG	p.I141M	FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000456695.1_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.I141M|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000379306.3_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	141					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						ACAACCAGATCAAAGTCTTGA	0.448																																						ENST00000249377.4																			0				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						c.(421-423)atC>atG		leucine rich repeat containing 17		C	MET/ILE,,MET/ILE,	0,4406		0,0,2203	114.0	109.0	111.0		423,,423,	2.4	1.0	7		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron,missense,intron	LRRC17,FBXL13	NM_001031692.2,NM_001111038.1,NM_005824.2,NM_145032.3	10,,10,	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging,,possibly-damaging,	141/442,,141/314,	102574783	1,13005	2203	4300	6503	SO:0001583	missense	10234				bone marrow development|negative regulation of osteoclast differentiation|ossification	extracellular space		g.chr7:102574783C>G	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.423C>G	7.37:g.102574783C>G	ENSP00000344242:p.Ile141Met					FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000313221.4_Intron|LRRC17_ENST00000339431.4_Missense_Mutation_p.I141M	p.I141M	NM_005824.2	NP_005815.2	Q8N6Y2	LRC17_HUMAN			2	704	+			141					Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	37	c.423C>G	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.310321	0.40895	0.0	1.16E-4	ENSG00000128606	ENST00000339431;ENST00000249377	T;T	0.64618	-0.11;-0.11	5.41	2.42	0.29668	.	0.216848	0.31323	N	0.007859	T	0.59569	0.2203	M	0.84433	2.695	0.49582	D	0.999802	B;B	0.25809	0.099;0.135	B;B	0.25614	0.062;0.037	T	0.61073	-0.7136	10	0.87932	D	0	-11.7694	3.3288	0.07076	0.407:0.3675:0.1336:0.0919	.	141;141	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	M	141	ENSP00000344242:I141M;ENSP00000249377:I141M	ENSP00000249377:I141M	I	+	3	3	LRRC17	102362019	0.996000	0.38824	0.991000	0.47740	0.993000	0.82548	0.472000	0.22116	0.749000	0.32854	0.557000	0.71058	ATC		0.448	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		6	83	0	0	0	1	0	6	83				
BBS12	166379	broad.mit.edu	37	4	123664933	123664933	+	Missense_Mutation	SNP	C	C	G			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr4:123664933C>G	ENST00000314218.3	+	2	2079	c.1886C>G	c.(1885-1887)tCt>tGt	p.S629C	BBS12_ENST00000542236.1_Missense_Mutation_p.S629C	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	629					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						GCCACAGACTCTGGCTCTCCT	0.348									Bardet-Biedl syndrome																													ENST00000542236.1																			0				cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						c.(1885-1887)tCt>tGt		Bardet-Biedl syndrome 12							79.0	76.0	77.0					4																	123664933		2203	4300	6503	SO:0001583	missense	166379	Bardet-Biedl syndrome	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	cellular protein metabolic process	cilium	ATP binding	g.chr4:123664933C>G	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1886C>G	4.37:g.123664933C>G	ENSP00000319062:p.Ser629Cys					BBS12_ENST00000314218.3_Missense_Mutation_p.S629C	p.S629C	NM_001178007.1	NP_001171478.1	Q6ZW61	BBS12_HUMAN			3	2267	+			629					D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	c.1886C>G	CCDS3728.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581096	0.28180	.	.	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.69685	-0.42;-0.42	5.81	4.92	0.64577	.	0.440682	0.22942	N	0.053772	T	0.60650	0.2285	L	0.50919	1.6	0.09310	N	1	B	0.34399	0.452	B	0.36766	0.232	T	0.55566	-0.8121	10	0.35671	T	0.21	-13.6	11.4072	0.49904	0.1199:0.711:0.1692:0.0	.	629	Q6ZW61	BBS12_HUMAN	C	629	ENSP00000319062:S629C;ENSP00000438273:S629C	ENSP00000319062:S629C	S	+	2	0	BBS12	123884383	1.000000	0.71417	0.329000	0.25429	0.790000	0.44656	2.572000	0.45999	2.746000	0.94184	0.591000	0.81541	TCT		0.348	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		17	61	0	0	0	1	0	17	61				
IMPG1	3617	broad.mit.edu	37	6	76751735	76751735	+	Missense_Mutation	SNP	C	C	T	rs147225489		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr6:76751735C>T	ENST00000369950.3	-	2	365	c.176G>A	c.(175-177)cGa>cAa	p.R59Q	IMPG1_ENST00000369963.3_Intron	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				ATCGAATATTCGTCTCATAGT	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		18192	0.0		0.001	False		,,,				2504	0.0				Pancreas(37;839 1141 2599 26037)	ENST00000369950.3																			0				breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						c.(175-177)cGa>cAa		interphotoreceptor matrix proteoglycan 1		C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	191.0	178.0	182.0		176	2.0	0.4	6	dbSNP_134	182	0,8600		0,0,4300	no	missense	IMPG1	NM_001563.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	59/798	76751735	1,13005	2203	4300	6503	SO:0001583	missense	3617				visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity	g.chr6:76751735C>T	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.176G>A	6.37:g.76751735C>T	ENSP00000358966:p.Arg59Gln					IMPG1_ENST00000369963.3_Intron	p.R59Q	NM_001563.2	NP_001554.2	Q17R60	IMPG1_HUMAN			2	365	-		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)	59						Missense_Mutation	SNP	ENST00000369950.3	37	c.176G>A	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	C	9.654	1.142296	0.21205	2.27E-4	0.0	ENSG00000112706	ENST00000369950	T	0.23950	1.88	6.07	1.97	0.26223	.	0.327775	0.25130	N	0.032906	T	0.06050	0.0157	L	0.43152	1.355	0.34239	D	0.677363	P	0.34934	0.476	B	0.19946	0.027	T	0.30995	-0.9959	9	.	.	.	.	7.3362	0.26611	0.1173:0.6825:0.0:0.2002	.	59	Q17R60	IMPG1_HUMAN	Q	59	ENSP00000358966:R59Q	.	R	-	2	0	IMPG1	76808455	0.097000	0.21791	0.351000	0.25721	0.200000	0.23975	0.370000	0.20433	0.064000	0.16427	0.655000	0.94253	CGA		0.358	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		40	81	0	0	0	1	0	40	81				
SPEN	23013	broad.mit.edu	37	1	16262471	16262471	+	Missense_Mutation	SNP	A	A	C			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr1:16262471A>C	ENST00000375759.3	+	11	9940	c.9736A>C	c.(9736-9738)Acc>Ccc	p.T3246P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3246	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ccccacccccacccctgcccc	0.662																																						ENST00000375759.3																			0				NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149						c.(9736-9738)Acc>Ccc		spen family transcriptional repressor																																				SO:0001583	missense	23013				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding	g.chr1:16262471A>C		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.9736A>C	1.37:g.16262471A>C	ENSP00000364912:p.Thr3246Pro						p.T3246P	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	11	9940	+		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)	3246			Pro-rich.		Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	c.9736A>C	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.376361	0.00207	.	.	ENSG00000065526	ENST00000375759	T	0.09255	3.0	1.72	-0.922	0.10468	.	.	.	.	.	T	0.04588	0.0125	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42172	-0.9467	9	0.30078	T	0.28	.	5.1828	0.15169	0.5273:0.0:0.4727:0.0	.	3246	Q96T58	MINT_HUMAN	P	3246	ENSP00000364912:T3246P	ENSP00000364912:T3246P	T	+	1	0	SPEN	16135058	0.018000	0.18449	0.000000	0.03702	0.001000	0.01503	0.804000	0.27098	-0.457000	0.07033	-1.751000	0.00678	ACC		0.662	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		3	17	0	0	0	1	0	3	17				
FLG	2312	broad.mit.edu	37	1	152285621	152285621	+	Missense_Mutation	SNP	T	T	A	rs145627745	byFrequency	TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr1:152285621T>A	ENST00000368799.1	-	3	1776	c.1741A>T	c.(1741-1743)Acc>Tcc	p.T581S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	581	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGTGCCTGGTGCCGTCTCCT	0.567									Ichthyosis				-|||	15	0.00299521	0.0	0.0014	5008	,	,		18116	0.0		0.0089	False		,,,				2504	0.0051					ENST00000368799.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(1741-1743)Acc>Tcc		filaggrin		A	SER/THR	13,4393		0,13,2190	392.0	368.0	376.0		1741	-4.3	0.0	1	dbSNP_134	376	101,8499		2,97,4201	no	missense	FLG	NM_002016.1	58	2,110,6391	AA,AT,TT		1.1744,0.2951,0.8765	benign	581/4062	152285621	114,12892	2203	4300	6503	SO:0001583	missense	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152285621T>A	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1741A>T	1.37:g.152285621T>A	ENSP00000357789:p.Thr581Ser					FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	p.T581S	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	1776	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		581			Ser-rich.		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	c.1741A>T	CCDS30860.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	-	1.132	-0.652029	0.03506	0.002951	0.011744	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01548	4.78	2.15	-4.3	0.03710	.	.	.	.	.	T	0.00109	0.0003	N	0.00265	-1.74	0.09310	N	1	B	0.23316	0.083	B	0.28139	0.086	T	0.37361	-0.9709	9	0.06365	T	0.9	.	0.4631	0.00519	0.1939:0.3015:0.2321:0.2724	.	581	P20930	FILA_HUMAN	S	581;113	ENSP00000357789:T581S	ENSP00000357789:T581S	T	-	1	0	FLG	150552245	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.125000	0.00079	-3.882000	0.00095	-1.828000	0.00595	ACC		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		21	448	0	0	0	1	0	21	448				
CRYM	1428	broad.mit.edu	37	16	21272640	21272640	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr16:21272640A>T	ENST00000219599.3	-	9	1080	c.815T>A	c.(814-816)cTg>cAg	p.L272Q	CRYM_ENST00000396023.2_Missense_Mutation_p.L272Q|CRYM_ENST00000415987.2_Missense_Mutation_p.L230Q|CRYM_ENST00000543948.1_Missense_Mutation_p.L272Q	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN	crystallin, mu	272					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sensory perception of sound (GO:0007605)|thyroid hormone metabolic process (GO:0042403)|thyroid hormone transport (GO:0070327)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|thiomorpholine-carboxylate dehydrogenase activity (GO:0047127)|thyroid hormone binding (GO:0070324)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(3)	4				GBM - Glioblastoma multiforme(48;0.0573)		CACTTCTCCCAGCTCAGCAAA	0.507																																						ENST00000219599.3																			0				large_intestine(1)|lung(3)	4						c.(814-816)cTg>cAg		crystallin, mu	Levothyroxine(DB00451)						123.0	101.0	108.0					16																	21272640		2199	4300	6499	SO:0001583	missense	1428				negative regulation of transcription from RNA polymerase II promoter|sensory perception of sound|thyroid hormone transport	cytoplasm|nucleus|plasma membrane	NADP binding|protein homodimerization activity|thyroid hormone binding|transcription corepressor activity	g.chr16:21272640A>T		CCDS10597.1	16p12.2	2013-02-14			ENSG00000103316	ENSG00000103316	1.5.1.25		2418	protein-coding gene	gene with protein product	"""thiomorpholine-carboxylate dehydrogenase"""	123740				1478656, 21332720	Standard	NM_001014444		Approved	DFNA40	uc002dim.3	Q14894	OTTHUMG00000090707	ENST00000219599.3:c.815T>A	16.37:g.21272640A>T	ENSP00000219599:p.Leu272Gln					CRYM_ENST00000415987.2_Missense_Mutation_p.L230Q|CRYM_ENST00000396023.2_Missense_Mutation_p.L272Q|CRYM_ENST00000543948.1_Missense_Mutation_p.L272Q	p.L272Q	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN		GBM - Glioblastoma multiforme(48;0.0573)	9	1080	-			272					D5MNX0|Q5HYB7	Missense_Mutation	SNP	ENST00000219599.3	37	c.815T>A	CCDS10597.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.501180	0.85176	.	.	ENSG00000103316	ENST00000543948;ENST00000219599;ENST00000396023;ENST00000415987	D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.66	5.49	5.49	0.81192	NAD(P)-binding domain (1);	0.069610	0.64402	D	0.000014	D	0.93517	0.7931	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.95163	0.8283	10	0.87932	D	0	-17.801	13.3133	0.60393	1.0:0.0:0.0:0.0	.	272	Q14894	CRYM_HUMAN	Q	272;272;272;230	ENSP00000440227:L272Q;ENSP00000219599:L272Q;ENSP00000379341:L272Q;ENSP00000390928:L230Q	ENSP00000219599:L272Q	L	-	2	0	CRYM	21180141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.327000	0.90012	2.090000	0.63153	0.533000	0.62120	CTG		0.507	CRYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207398.1			10	35	0	0	0	1	0	10	35				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		5	60	0	0	0	1	0	5	60				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		24	79	0	0	0	1	0	24	79				
RGPD8	727851	broad.mit.edu	37	2	113147636	113147636	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr2:113147636delA	ENST00000302558.3	-	20	3077	c.2886delT	c.(2884-2886)tttfs	p.F962fs	RGPD8_ENST00000409750.1_Frame_Shift_Del_p.F822fs	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	962					protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						TTGTTTGGCCAAAAATCACAC	0.408																																						ENST00000302558.3																			0				endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						c.(2884-2886)ttfs		RANBP2-like and GRIP domain containing 8							80.0	72.0	74.0					2																	113147636		686	1568	2254	SO:0001589	frameshift_variant	727851							g.chr2:113147636delA	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.2886delT	2.37:g.113147636delA	ENSP00000306637:p.Phe962fs					RGPD8_ENST00000409750.1_Frame_Shift_Del_p.F822fs	p.F962fs	NM_001164463.1	NP_001157935.1					20	3077	-								Q5CZA8	Frame_Shift_Del	DEL	ENST00000302558.3	37	c.2886delT	CCDS46394.1																																																																																				0.408	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279		7	249						7	249	---	---	---	---
UBP1	7342	broad.mit.edu	37	3	33437658	33437661	+	Frame_Shift_Del	DEL	GGGT	GGGT	-			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr3:33437658_33437661delGGGT	ENST00000283629.3	-	13	1912_1915	c.1383_1386delACCC	c.(1381-1386)gcacccfs	p.AP461fs	UBP1_ENST00000283628.5_Frame_Shift_Del_p.AP461fs|UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Frame_Shift_Del_p.AP425fs	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	461					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P462S(1)		breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						ACCTACCATAGGGTGCCCCACTGC	0.534																																						ENST00000283629.3																			1	Substitution - Missense(1)	p.P462S(1)	lung(1)	breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						c.(1381-1386)gcfs		upstream binding protein 1 (LBP-1a)																																				SO:0001589	frameshift_variant	7342				negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity	g.chr3:33437658_33437661delGGGT	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.1383_1386delACCC	3.37:g.33437658_33437661delGGGT	ENSP00000283629:p.Ala461fs					UBP1_ENST00000283628.5_Frame_Shift_Del_p.AP461fs|UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Frame_Shift_Del_p.AP425fs	p.AP461fs	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN			13	1912_1915	-			461					Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Frame_Shift_Del	DEL	ENST00000283629.3	37	c.1383_1386delACCC	CCDS2659.1																																																																																				0.534	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		7	147						7	147	---	---	---	---
LOC101927841	101927841	broad.mit.edu	37	7	22896087	22896089	+	RNA	DEL	AAA	AAA	-	rs58988088|rs568268634|rs202186704	byFrequency	TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr7:22896087_22896089delAAA	ENST00000415611.3	+	0	103				SNORD93_ENST00000408813.1_RNA																							ACCACTCATTAAAAAACAAAATT	0.345														498	0.0994409	0.1157	0.0951	5008	,	,		19930	0.1379		0.0388	False		,,,				2504	0.1033					ENST00000415611.2																			0																																																			0							g.chr7:22896087_22896089delAAA																													7.37:g.22896090_22896092delAAA														0	25	+									RNA	DEL	ENST00000415611.3	37																																																																																						0.345	AC005682.5-001	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000326767.3			2	4						2	4	---	---	---	---
LOC101928283	101928283	broad.mit.edu	37	7	124940517	124940517	+	lincRNA	DEL	G	G	-			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr7:124940517delG	ENST00000424515.2	+	0	648																											ttttttttttGCAATTTTGTA	0.264																																						ENST00000424515.2																			0																																																			0							g.chr7:124940517delG																													7.37:g.124940517delG														0	648	+									RNA	DEL	ENST00000424515.2	37																																																																																						0.264	RP11-3B12.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000347734.2			3	5						3	5	---	---	---	---
RP11-493L12.5	0	broad.mit.edu	37	12	47761313	47761314	+	lincRNA	INS	-	-	T	rs397801707|rs201148896|rs11419253	byFrequency	TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr12:47761313_47761314insT	ENST00000550019.1	+	0	262																											ttcgctctctattttttttttt	0.406													|||unknown(HR)	3540	0.706869	0.5461	0.6888	5008	,	,		19745	0.8621		0.7624	False		,,,				2504	0.7198					ENST00000550019.1																			0																																																			0							g.chr12:47761313_47761314insT																													12.37:g.47761324_47761324dupT														0	262	+									RNA	INS	ENST00000550019.1	37																																																																																						0.406	RP11-493L12.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000405335.1			3	5						3	5	---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64660102	64660102	+	IGR	DEL	T	T	-			TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr12:64660102delT	ENST00000543942.2	-	0	3242				RPS11P6_ENST00000535684.1_RNA|C12orf56_ENST00000536975.1_5'Flank	NM_001170633.1	NP_001164104.1	Q8IXR9	CL056_HUMAN	chromosome 12 open reading frame 56											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)	15			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		TCTTAGAACCTTTTTTTCTGG	0.393																																						ENST00000535684.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr12:64660102delT		CCDS44935.1, CCDS61182.1	12q14.2	2012-08-15			ENSG00000185306	ENSG00000185306			26967	protein-coding gene	gene with protein product							Standard	NM_001099676		Approved		uc021qzu.1	Q8IXR9	OTTHUMG00000168782		12.37:g.64660102delT														0	319	+									RNA	DEL	ENST00000543942.2	37																																																																																						0.393	C12orf56-008	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000401058.2	NM_001099676		2	4						2	4	---	---	---	---
TRAV9-2	28677	broad.mit.edu	37	14	22409539	22409539	+	RNA	DEL	C	C	-	rs2178778|rs367992314|rs374912343|rs371270332	byFrequency	TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr14:22409539delC	ENST00000390441.2	+	0	102									T cell receptor alpha variable 9-2																		ctctctctctctTTTTTTTTT	0.428													|||unknown(STR2?)	2067	0.41274	0.3903	0.4697	5008	,	,		16901	0.3373		0.4573	False		,,,				2504	0.4346					ENST00000390441.2																			0																				20.0	18.0	19.0					14																	22409539		1790	4037	5827			0							g.chr14:22409539delC	AE000659		14q11.2	2012-02-07			ENSG00000211793	ENSG00000211793		"""T cell receptors / TRA locus"""	12154	other	T cell receptor gene						8188290	Standard	NG_001332		Approved				OTTHUMG00000170637		14.37:g.22409539delC														0	102	+									RNA	DEL	ENST00000390441.2	37																																																																																						0.428	TRAV9-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000409885.1	NG_001332		2	4						2	4	---	---	---	---
COQ9	57017	broad.mit.edu	37	16	57486732	57486734	+	In_Frame_Del	DEL	GAG	GAG	-	rs149029279		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr16:57486732_57486734delGAG	ENST00000262507.6	+	3	331_333	c.262_264delGAG	c.(262-264)gagdel	p.E91del	COQ9_ENST00000567933.1_In_Frame_Del_p.E91del|COQ9_ENST00000567072.1_In_Frame_Del_p.E91del|COQ9_ENST00000567384.1_3'UTR	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	91					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CCAGGGCGGCGAGGAGGAGGAGG	0.576																																						ENST00000262507.6																			0				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						c.(262-264)del		coenzyme Q9																																				SO:0001651	inframe_deletion	57017				ubiquinone biosynthetic process	mitochondrion		g.chr16:57486732_57486734delGAG	BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"""chromosome 16 open reading frame 49"", ""coenzyme Q9 homolog (yeast)"", ""coenzyme Q9 homolog (S. cerevisiae)"""	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.262_264delGAG	16.37:g.57486741_57486743delGAG	ENSP00000262507:p.Glu91del					COQ9_ENST00000567072.1_In_Frame_Del_p.E91del|COQ9_ENST00000567933.1_In_Frame_Del_p.E91del|COQ9_ENST00000567384.1_3'UTR	p.E91del	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN			3	331_333	+			91					A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	In_Frame_Del	DEL	ENST00000262507.6	37	c.262_264delGAG	CCDS32459.1																																																																																				0.576	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432598.3	NM_020312		8	162						8	162	---	---	---	---
OSBP2	23762	broad.mit.edu	37	22	31090938	31090939	+	Frame_Shift_Ins	INS	-	-	G	rs143022866		TCGA-DJ-A3VF-01A-11D-A23M-08	TCGA-DJ-A3VF-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5477ece-95a6-4fdf-a9df-e81444e69336	d269d2ff-62b4-48c6-8020-9473ae00cbb2	g.chr22:31090938_31090939insG	ENST00000332585.6	+	1	146_147	c.42_43insG	c.(43-45)ggcfs	p.G15fs	OSBP2_ENST00000382310.3_Frame_Shift_Ins_p.G15fs|OSBP2_ENST00000403222.3_Intron|OSBP2_ENST00000446658.2_Frame_Shift_Ins_p.G15fs|OSBP2_ENST00000407373.1_Intron	NM_001282739.1|NM_001282740.1|NM_001282741.1|NM_001282742.1|NM_030758.3	NP_001269668.1|NP_001269669.1|NP_001269670.1|NP_001269671.1|NP_110385.1	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2	15					lipid transport (GO:0006869)	membrane (GO:0016020)	cholesterol binding (GO:0015485)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						GCGGCTGTGGCGGCCGCTCCCG	0.792																																						ENST00000332585.6																			0				breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						c.(40-45)gggccgfs		oxysterol binding protein 2																																				SO:0001589	frameshift_variant	23762				lipid transport	membrane	lipid binding	g.chr22:31090938_31090939insG		CCDS43002.1, CCDS63448.1, CCDS63449.1, CCDS63450.1, CCDS63451.1	22q12.2	2013-01-10			ENSG00000184792	ENSG00000184792		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	8504	protein-coding gene	gene with protein product		606729		OSBPL1		10591208, 11278871, 11802775	Standard	NM_001282738		Approved	KIAA1664, ORP-4, ORP4	uc003aiy.1	Q969R2	OTTHUMG00000151153	ENST00000332585.6:c.44dupG	22.37:g.31090940_31090940dupG	ENSP00000332576:p.Gly15fs					OSBP2_ENST00000403222.3_Intron|OSBP2_ENST00000382310.3_Frame_Shift_Ins_p.P15fs|OSBP2_ENST00000407373.1_Intron|OSBP2_ENST00000446658.2_Frame_Shift_Ins_p.P15fs	p.P15fs	NM_030758.3	NP_110385.1	Q969R2	OSBP2_HUMAN			1	146_147	+			15					B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Frame_Shift_Ins	INS	ENST00000332585.6	37	c.42_43insG	CCDS43002.1																																																																																				0.792	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758		2	4						2	4	---	---	---	---
