#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
PIK3CD	5293	broad.mit.edu	37	1	9783218	9783218	+	Missense_Mutation	SNP	G	G	A	rs573872848		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:9783218G>A	ENST00000377346.4	+	20	2657	c.2462G>A	c.(2461-2463)cGc>cAc	p.R821H	PIK3CD_ENST00000361110.2_Missense_Mutation_p.R845H|PIK3CD_ENST00000536656.1_Missense_Mutation_p.R845H	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	821	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.R821H(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	ACCGGGGACCGCACAGGCCTC	0.602													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18134	0.0		0.0	False		,,,				2504	0.0					uc001aqe.4																			1	Substitution - Missense(1)	p.R821H(1)	endometrium(1)	central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						c.(2533-2535)cGc>cAc		Homo sapiens phosphoinositide-3-kinase, catalytic, delta polypeptide (PIK3CD), mRNA.							142.0	141.0	141.0					1																	9783218		2203	4300	6503	SO:0001583	missense	5293				phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding	g.chr1:9783218G>A		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2462G>A	1.37:g.9783218G>A	ENSP00000366563:p.Arg821His					PIK3CD_uc001aqb.4_Missense_Mutation_p.R821H|PIK3CD_uc010oaf.2_Missense_Mutation_p.R820H|PIK3CD_uc021ogb.1_Missense_Mutation_p.R605H	p.R845H	NM_005026	NP_005017	O00329	PK3CD_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	18	2742	+	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)	821			PI3K/PI4K.		A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	37	c.2534G>A	CCDS104.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.207994	0.39003	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	T;T;T	0.80653	-1.4;-1.4;-1.4	4.75	0.731	0.18277	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.070648	0.56097	D	0.000021	T	0.68860	0.3047	L	0.35414	1.06	0.80722	D	1	B;B;B	0.19935	0.04;0.04;0.004	B;B;B	0.25884	0.064;0.014;0.008	T	0.57481	-0.7804	10	0.46703	T	0.11	-14.8148	9.0597	0.36427	0.4652:0.0:0.5348:0.0	.	820;845;821	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	H	845;821;845;845	ENSP00000446444:R845H;ENSP00000366563:R821H;ENSP00000354410:R845H	ENSP00000353766:R845H	R	+	2	0	PIK3CD	9705805	1.000000	0.71417	0.023000	0.16930	0.932000	0.56968	1.800000	0.38833	-0.131000	0.11578	0.563000	0.77884	CGC		0.602	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		5	398	0	0	0	1	0	5	398				
LY9	4063	broad.mit.edu	37	1	160784239	160784239	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:160784239G>A	ENST00000263285.6	+	4	790	c.760G>A	c.(760-762)Ggg>Agg	p.G254R	LY9_ENST00000368037.5_Missense_Mutation_p.G254R|LY9_ENST00000471816.1_3'UTR|LY9_ENST00000368041.2_Missense_Mutation_p.G214R|LY9_ENST00000368040.1_5'UTR|LY9_ENST00000341032.4_Missense_Mutation_p.G254R|LY9_ENST00000392203.4_Missense_Mutation_p.G254R			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	254	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AGGAACAACGGGGGAGACTGT	0.582																																						uc001fwu.3																			0				autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						c.(760-762)Ggg>Agg		Homo sapiens lymphocyte antigen 9 (LY9), transcript variant 1, mRNA.							61.0	64.0	63.0					1																	160784239		2203	4300	6503	SO:0001583	missense	4063				cell adhesion|immunoglobulin mediated immune response	integral to membrane		g.chr1:160784239G>A	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.760G>A	1.37:g.160784239G>A	ENSP00000263285:p.Gly254Arg					LY9_uc010pjs.1_Missense_Mutation_p.G254R|LY9_uc001fwv.3_Missense_Mutation_p.G254R|LY9_uc001fww.3_Missense_Mutation_p.G254R|LY9_uc001fwy.1_Missense_Mutation_p.G156R|LY9_uc001fwz.3_5'UTR	p.G254R	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00737)		3	810	+	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		254			Ig-like V-type 2.		A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	37	c.760G>A	CCDS30916.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.323300	0.24080	.	.	ENSG00000122224	ENST00000368041;ENST00000341032;ENST00000263285;ENST00000542780;ENST00000392203;ENST00000368037;ENST00000368036	T;T	0.36699	1.24;1.31	3.76	1.84	0.25277	Immunoglobulin subtype (1);	2.127130	0.02585	N	0.099349	T	0.44350	0.1289	M	0.75447	2.3	0.19300	N	0.999977	D;D;P;D;D;D	0.89917	1.0;1.0;0.94;1.0;1.0;1.0	D;D;B;D;D;D	0.97110	0.999;0.999;0.437;0.999;1.0;0.999	T	0.03483	-1.1032	10	0.59425	D	0.04	-8.5653	6.4283	0.21782	0.2429:0.0:0.7571:0.0	.	254;214;214;254;254;254	B4E0J5;Q5VYH7;Q5VYH9;E7EME5;Q9HBG7-2;Q9HBG7	.;.;.;.;.;LY9_HUMAN	R	254;254;254;254;214;214;156	ENSP00000342921:G254R;ENSP00000263285:G254R	ENSP00000263285:G254R	G	+	1	0	LY9	159050863	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	0.718000	0.25866	0.327000	0.23409	0.563000	0.77884	GGG		0.582	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		50	92	0	0	0	1	0	50	92				
POM121	9883	broad.mit.edu	37	7	72413486	72413486	+	Missense_Mutation	SNP	C	C	T	rs372474703		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr7:72413486C>T	ENST00000434423.2	+	11	2954	c.2954C>T	c.(2953-2955)cCg>cTg	p.P985L	POM121_ENST00000446813.1_Missense_Mutation_p.P720L|POM121_ENST00000395270.1_Missense_Mutation_p.P720L|POM121_ENST00000358357.3_Missense_Mutation_p.P720L|POM121_ENST00000257622.4_Missense_Mutation_p.P720L			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	985	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				GCCGCCAAGCCGGCCCTTGCC	0.657																																						uc003twk.2																			0				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(2953-2955)cCg>cTg		Homo sapiens POM121 membrane glycoprotein (POM121), mRNA.		C	LEU/PRO	2,4404		0,2,2201	41.0	54.0	50.0		2159	1.4	0.0	7		50	0,8598		0,0,4299	no	missense	POM121	NM_172020.2	98	0,2,6500	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging	720/985	72413486	2,13002	2203	4299	6502	SO:0001583	missense	9883				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore		g.chr7:72413486C>T	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2954C>T	7.37:g.72413486C>T	ENSP00000405562:p.Pro985Leu					POM121_uc003twj.3_Missense_Mutation_p.P720L|POM121_uc010lam.1_Missense_Mutation_p.P720L	p.P985L	NM_172020	NP_742017	Q96HA1	P121A_HUMAN			10	2954	+		Lung NSC(55;0.163)	985			Pore side (Potential).		A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37	c.2954C>T		.	.	.	.	.	.	.	.	.	.	C	4.198	0.035470	0.08148	4.54E-4	0.0	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.09538	2.97;3.04;2.97;3.04;3.22	2.33	1.41	0.22369	.	0.421011	0.17633	N	0.167314	T	0.13200	0.0320	M	0.64676	1.99	0.09310	N	0.999998	D;P	0.55605	0.972;0.95	B;P	0.46885	0.425;0.53	T	0.11060	-1.0603	10	0.36615	T	0.2	.	6.8353	0.23933	0.0:0.8457:0.0:0.1543	.	720;985	A8MXF9;Q96HA1	.;P121A_HUMAN	L	720;720;720;720;985	ENSP00000393020:P720L;ENSP00000257622:P720L;ENSP00000378687:P720L;ENSP00000351124:P720L;ENSP00000405562:P985L	ENSP00000257622:P720L	P	+	2	0	POM121	72051422	0.736000	0.28164	0.017000	0.16124	0.027000	0.11550	2.797000	0.47877	1.309000	0.44985	0.173000	0.16961	CCG		0.657	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			8	171	0	0	0	1	0	8	171				
CYP24A1	1591	broad.mit.edu	37	20	52775530	52775530	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr20:52775530G>A	ENST00000216862.3	-	8	1516	c.1123C>T	c.(1123-1125)Ccg>Tcg	p.P375S	CYP24A1_ENST00000460643.1_5'Flank|CYP24A1_ENST00000395955.3_Missense_Mutation_p.P375S|CYP24A1_ENST00000395954.3_Missense_Mutation_p.P233S	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	375					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	TTTAAATACGGCATATTCCTC	0.388																																						uc002xwv.2																			0				breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						c.(1123-1125)Ccg>Tcg		Homo sapiens cytochrome P450, family 24, subfamily A, polypeptide 1 (CYP24A1), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	Calcidiol(DB00146)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)						128.0	134.0	132.0					20																	52775530		2203	4300	6503	SO:0001583	missense	1591				hormone biosynthetic process|osteoblast differentiation|vitamin D catabolic process|vitamin D receptor signaling pathway|xenobiotic metabolic process	mitochondrial inner membrane	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity|electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen	g.chr20:52775530G>A	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"""Cytochrome P450s"""	2602	protein-coding gene	gene with protein product		126065	"""cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"""	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.1123C>T	20.37:g.52775530G>A	ENSP00000216862:p.Pro375Ser					CYP24A1_uc002xwu.1_Missense_Mutation_p.P233S|CYP24A1_uc002xww.2_Missense_Mutation_p.P375S	p.P375S	NM_000782	NP_000773	Q07973	CP24A_HUMAN	STAD - Stomach adenocarcinoma(23;0.206)		7	1521	-	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		375					Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	c.1123C>T	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665841	0.67700	.	.	ENSG00000019186	ENST00000216862;ENST00000395955;ENST00000395954	T;T;T	0.74842	-0.88;-0.88;-0.88	5.43	4.48	0.54585	.	0.051522	0.85682	N	0.000000	D	0.84844	0.5562	M	0.74389	2.26	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.977;0.999;0.999	D	0.86075	0.1540	10	0.62326	D	0.03	-14.531	13.1815	0.59657	0.077:0.0:0.923:0.0	.	375;375;233	Q32ML3;Q07973;Q5I2W7	.;CP24A_HUMAN;.	S	375;375;233	ENSP00000216862:P375S;ENSP00000379285:P375S;ENSP00000379284:P233S	ENSP00000216862:P375S	P	-	1	0	CYP24A1	52208937	1.000000	0.71417	0.995000	0.50966	0.606000	0.37113	7.519000	0.81809	1.274000	0.44362	0.650000	0.86243	CCG		0.388	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			4	206	0	0	0	1	0	4	206				
PHLDB2	90102	broad.mit.edu	37	3	111693318	111693318	+	Missense_Mutation	SNP	T	T	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr3:111693318T>A	ENST00000431670.2	+	18	4081	c.3670T>A	c.(3670-3672)Tat>Aat	p.Y1224N	PHLDB2_ENST00000481953.1_Missense_Mutation_p.Y1181N|PHLDB2_ENST00000412622.1_Missense_Mutation_p.Y1181N|PHLDB2_ENST00000393925.3_Missense_Mutation_p.Y1224N|PHLDB2_ENST00000393923.3_Missense_Mutation_p.Y1208N|PHLDB2_ENST00000495180.1_Missense_Mutation_p.Y715N	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	1224	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TGACAGAATCTATTATATGGT	0.388																																						uc010hqa.3																			0				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						c.(3670-3672)Tat>Aat		Homo sapiens pleckstrin homology-like domain, family B, member 2 (PHLDB2), transcript variant 1, mRNA.							103.0	105.0	105.0					3																	111693318		2203	4300	6503	SO:0001583	missense	90102					cytoplasm|intermediate filament cytoskeleton|plasma membrane		g.chr3:111693318T>A		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.3670T>A	3.37:g.111693318T>A	ENSP00000405405:p.Tyr1224Asn					PHLDB2_uc003dyc.3_Missense_Mutation_p.Y1208N|PHLDB2_uc003dyd.3_Missense_Mutation_p.Y1181N|PHLDB2_uc003dyg.3_Missense_Mutation_p.Y1224N|PHLDB2_uc003dyh.3_Missense_Mutation_p.Y1181N|PHLDB2_uc003dyi.3_Missense_Mutation_p.Y715N|PHLDB2_uc003dyj.3_Missense_Mutation_p.Y279N	p.Y1224N	NM_001134438	NP_001127911	Q86SQ0	PHLB2_HUMAN			17	4081	+			1224			PH.		A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	37	c.3670T>A	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.478339	0.44044	.	.	ENSG00000144824	ENST00000393923;ENST00000431670;ENST00000412622;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17;-1.17	6.17	5.0	0.66597	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.183165	0.49916	D	0.000129	D	0.90463	0.7013	M	0.93939	3.475	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;1.0;1.0	D	0.92053	0.5650	10	0.87932	D	0	.	12.8294	0.57738	0.0:0.0:0.1366:0.8634	.	336;715;1224;1181;1208	Q658P8;E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;.;PHLB2_HUMAN;.;.	N	1208;1224;1181;1224;1181;715	ENSP00000377500:Y1208N;ENSP00000405405:Y1224N;ENSP00000405292:Y1181N;ENSP00000377502:Y1224N;ENSP00000418319:Y1181N;ENSP00000420303:Y715N	ENSP00000377500:Y1208N	Y	+	1	0	PHLDB2	113176008	1.000000	0.71417	0.998000	0.56505	0.006000	0.05464	8.040000	0.89188	1.132000	0.42129	-0.316000	0.08728	TAT		0.388	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		47	112	0	0	0	1	0	47	112				
CGN	57530	broad.mit.edu	37	1	151491695	151491695	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:151491695C>T	ENST00000271636.7	+	2	833	c.700C>T	c.(700-702)Cac>Tac	p.H234Y		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	228	Head.|Interacts with ZO-2.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCCACCAACCACTGGACCTC	0.587																																						uc009wmw.3																			0				NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45						c.(700-702)Cac>Tac		Homo sapiens cingulin (CGN), mRNA.							89.0	93.0	92.0					1																	151491695		2203	4300	6503	SO:0001583	missense	57530					myosin complex|tight junction	actin binding|motor activity	g.chr1:151491695C>T	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.700C>T	1.37:g.151491695C>T	ENSP00000271636:p.His234Tyr						p.H234Y	NM_020770	NP_065821	Q9P2M7	CING_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.181)		1	844	+	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		228			Head.|Interacts with ZO-2.		A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	c.700C>T	CCDS999.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.890447	0.33348	.	.	ENSG00000143375	ENST00000427934;ENST00000271636	T;T	0.63744	0.92;-0.06	4.96	3.04	0.35103	.	0.561259	0.20537	N	0.090392	T	0.29716	0.0742	L	0.51422	1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09079	-1.0691	9	.	.	.	-4.1539	5.1662	0.15086	0.1432:0.6148:0.1588:0.0832	.	228	Q9P2M7	CING_HUMAN	Y	234	ENSP00000410836:H234Y;ENSP00000271636:H234Y	.	H	+	1	0	CGN	149758319	0.082000	0.21442	0.010000	0.14722	0.012000	0.07955	0.846000	0.27682	1.416000	0.47057	0.561000	0.74099	CAC		0.587	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		89	176	0	0	0	1	0	89	176				
GLG1	2734	broad.mit.edu	37	16	74530417	74530417	+	Silent	SNP	C	C	T			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr16:74530417C>T	ENST00000422840.2	-	5	899	c.900G>A	c.(898-900)gaG>gaA	p.E300E	GLG1_ENST00000205061.5_Silent_p.E300E|GLG1_ENST00000447066.2_Silent_p.E289E	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	300					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CCGATGACAGCTCAGCCACCC	0.448																																						uc002fcx.3																			0				breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						c.(898-900)gaG>gaA		Homo sapiens golgi glycoprotein 1 (GLG1), transcript variant 1, mRNA.							91.0	95.0	94.0					16																	74530417		2198	4300	6498	SO:0001819	synonymous_variant	2734					Golgi membrane|integral to membrane	receptor binding	g.chr16:74530417C>T		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.900G>A	16.37:g.74530417C>T						GLG1_uc002fcw.4_Silent_p.E289E|GLG1_uc002fcy.4_Silent_p.E300E|GLG1_uc002fcz.4_Intron	p.E300E	NM_012201	NP_036333	Q92896	GSLG1_HUMAN			4	950	-			300					B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	37	c.900G>A	CCDS45527.1																																																																																				0.448	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		6	123	0	0	0	1	0	6	123				
PRDX1	5052	broad.mit.edu	37	1	45984618	45984618	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:45984618T>C	ENST00000262746.1	-	2	437	c.98A>G	c.(97-99)gAc>gGc	p.D33G	PRDX1_ENST00000319248.8_Missense_Mutation_p.D33G|PRDX1_ENST00000372079.1_Intron|PRDX1_ENST00000483583.1_5'UTR	NM_002574.3|NM_181696.2	NP_002565.1|NP_859047.1	Q06830	PRDX1_HUMAN	peroxiredoxin 1	33	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell proliferation (GO:0008283)|erythrocyte homeostasis (GO:0034101)|hydrogen peroxide catabolic process (GO:0042744)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of NF-kappaB import into nucleus (GO:0042345)|regulation of stress-activated MAPK cascade (GO:0032872)|removal of superoxide radicals (GO:0019430)|retina homeostasis (GO:0001895)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)	heme binding (GO:0020037)|peroxidase activity (GO:0004601)|poly(A) RNA binding (GO:0044822)|thioredoxin peroxidase activity (GO:0008379)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	12	Acute lymphoblastic leukemia(166;0.155)					ACCTTTGTAGTCAGACAGGCT	0.413																																						uc001coc.3																			0		p.S32fs*41(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	12						c.(97-99)gAc>gGc		Homo sapiens peroxiredoxin 1 (PRDX1), transcript variant 2, mRNA.							82.0	81.0	81.0					1																	45984618		2203	4300	6503	SO:0001583	missense	5052				cell proliferation|cell redox homeostasis|hydrogen peroxide catabolic process|skeletal system development	melanosome|mitochondrion|nucleus	protein binding|thioredoxin peroxidase activity	g.chr1:45984618T>C	BC021683	CCDS522.1	1p34.1	2008-02-05			ENSG00000117450	ENSG00000117450			9352	protein-coding gene	gene with protein product		176763		PAGA		8496166	Standard	NM_181697		Approved	NKEFA	uc021omw.1	Q06830	OTTHUMG00000007738	ENST00000262746.1:c.98A>G	1.37:g.45984618T>C	ENSP00000262746:p.Asp33Gly					PRDX1_uc001cob.3_Missense_Mutation_p.D33G|PRDX1_uc001coa.3_Missense_Mutation_p.D33G|PRDX1_uc021omw.1_Missense_Mutation_p.D33G	p.D33G	NM_181696	NP_859048	Q06830	PRDX1_HUMAN			1	413	-	Acute lymphoblastic leukemia(166;0.155)		33			Thioredoxin.		B5BU26|D3DPZ8|P35703|Q2V576|Q5T154|Q5T155	Missense_Mutation	SNP	ENST00000262746.1	37	c.98A>G	CCDS522.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.183679	0.57800	.	.	ENSG00000117450	ENST00000262746;ENST00000319248;ENST00000447184;ENST00000424390	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.67	5.67	0.87782	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);	0.217265	0.53938	D	0.000053	T	0.67887	0.2941	H	0.95328	3.655	0.58432	D	0.999999	P	0.39862	0.692	P	0.48141	0.568	T	0.77225	-0.2666	10	0.87932	D	0	-10.2806	16.2002	0.82067	0.0:0.0:0.0:1.0	rs11544939	33	Q06830	PRDX1_HUMAN	G	33	ENSP00000262746:D33G;ENSP00000361152:D33G;ENSP00000407034:D33G;ENSP00000389047:D33G	ENSP00000262746:D33G	D	-	2	0	PRDX1	45757205	1.000000	0.71417	1.000000	0.80357	0.345000	0.29048	4.678000	0.61641	2.285000	0.76669	0.528000	0.53228	GAC		0.413	PRDX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020845.1	NM_181697		6	89	0	0	0	1	0	6	89				
CACNA1E	777	broad.mit.edu	37	1	181767534	181767534	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:181767534T>C	ENST00000367573.2	+	48	6506	c.6506T>C	c.(6505-6507)cTc>cCc	p.L2169P	CACNA1E_ENST00000367567.4_Missense_Mutation_p.L1733P|CACNA1E_ENST00000357570.5_Missense_Mutation_p.L2120P|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L2150P|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L2107P|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L2058P|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L2126P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2169					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCCCGGCCCCTCCTTTCCTAC	0.637																																						uc009wxt.3																			0				NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						c.(6505-6507)cTc>cCc		Homo sapiens calcium channel, voltage-dependent, R type, alpha 1E subunit (CACNA1E), transcript variant 1, mRNA.							71.0	83.0	79.0					1																	181767534		1985	4162	6147	SO:0001583	missense	777				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity	g.chr1:181767534T>C	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6506T>C	1.37:g.181767534T>C	ENSP00000356545:p.Leu2169Pro					CACNA1E_uc001gow.3_Missense_Mutation_p.L2126P|CACNA1E_uc009wxs.3_Missense_Mutation_p.L2107P	p.L2169P	NM_001205293	NP_001192222	Q15878	CAC1E_HUMAN			47	6701	+			2169					B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	c.6506T>C	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.236000	0.39498	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96300	-3.9;-3.9;-3.9;-3.9;-3.97;-3.9;-3.9	5.55	5.55	0.83447	.	0.542919	0.20103	N	0.099188	D	0.95749	0.8617	L	0.29908	0.895	0.80722	D	1	B;D	0.60160	0.045;0.987	B;P	0.58391	0.023;0.838	D	0.95078	0.8210	10	0.35671	T	0.21	.	15.432	0.75108	0.0:0.0:0.0:1.0	.	2107;2126	Q15878-2;Q15878-3	.;.	P	2126;2107;2120;2058;1733;2150;2169	ENSP00000356542:L2126P;ENSP00000434814:L2107P;ENSP00000350183:L2120P;ENSP00000351101:L2058P;ENSP00000356539:L1733P;ENSP00000353222:L2150P;ENSP00000356545:L2169P	ENSP00000350183:L2120P	L	+	2	0	CACNA1E	180034157	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.432000	0.59922	2.117000	0.64856	0.456000	0.33151	CTC		0.637	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		4	202	0	0	0	1	0	4	202				
COL1A2	1278	broad.mit.edu	37	7	94058709	94058709	+	Silent	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr7:94058709G>A	ENST00000297268.6	+	51	4392	c.3921G>A	c.(3919-3921)agG>agA	p.R1307R		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1307	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GCAACAGCAGGTTCACTTACA	0.453										HNSCC(75;0.22)																												uc003ung.1																		COL1A2/PLAG1(3)	0				NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115						c.(3919-3921)agG>agA		Homo sapiens collagen, type I, alpha 2 (COL1A2), mRNA.	Collagenase(DB00048)						116.0	99.0	104.0					7																	94058709		2203	4300	6503	SO:0001819	synonymous_variant	1278				Rho protein signal transduction|axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging	g.chr7:94058709G>A	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3921G>A	7.37:g.94058709G>A		HNSCC(75;0.22)				COL1A2_uc011kib.1_Silent_p.R159R	p.R1307R	NM_000089	NP_000080	P08123	CO1A2_HUMAN	STAD - Stomach adenocarcinoma(171;0.0031)		50	4392	+	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		1307			Fibrillar collagen NC1.		P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	c.3921G>A	CCDS34682.1																																																																																				0.453	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		28	51	0	0	0	1	0	28	51				
CYSLTR2	57105	broad.mit.edu	37	13	49281729	49281729	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr13:49281729G>A	ENST00000282018.3	+	1	779	c.776G>A	c.(775-777)tGt>tAt	p.C259Y		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	259					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	TTCTTCTTGTGTTTCCTGCCC	0.498																																						uc010acw.1																			0				endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20						c.(775-777)tGt>tAt		Homo sapiens cysteinyl leukotriene receptor 2 (CYSLTR2), mRNA.	Nedocromil(DB00716)						140.0	125.0	130.0					13																	49281729		2203	4300	6503	SO:0001583	missense	57105				immune response	integral to membrane|plasma membrane		g.chr13:49281729G>A	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"""GPCR / Class A : Leukotriene receptors"""	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.776G>A	13.37:g.49281729G>A	ENSP00000282018:p.Cys259Tyr					CYSLTR2_uc010acx.1_Missense_Mutation_p.C259Y|CYSLTR2_uc010acy.1_Missense_Mutation_p.C259Y|CYSLTR2_uc010acz.1_Missense_Mutation_p.C259Y|CYSLTR2_uc010ada.1_Missense_Mutation_p.C259Y|CYSLTR2_uc010adb.1_Missense_Mutation_p.C259Y|CYSLTR2_uc010adc.1_Missense_Mutation_p.C259Y|CYSLTR2_uc010add.1_Missense_Mutation_p.C259Y|CYSLTR2_uc001vck.2_Missense_Mutation_p.C259Y|CYSLTR2_uc021rjl.1_Missense_Mutation_p.C259Y	p.C259Y	NM_020377	NP_065110	Q9NS75	CLTR2_HUMAN		GBM - Glioblastoma multiforme(99;1.19e-09)	1	1066	+		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)	259					Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	37	c.776G>A	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.438036	0.83885	.	.	ENSG00000152207	ENST00000282018	T	0.54279	0.58	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.82958	0.5150	H	0.97540	4.025	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	D	0.88082	0.2807	10	0.56958	D	0.05	.	18.7244	0.91708	0.0:0.0:1.0:0.0	.	259	Q9NS75	CLTR2_HUMAN	Y	259	ENSP00000282018:C259Y	ENSP00000282018:C259Y	C	+	2	0	CYSLTR2	48179730	1.000000	0.71417	0.998000	0.56505	0.900000	0.52787	9.823000	0.99369	2.678000	0.91216	0.655000	0.94253	TGT		0.498	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			50	63	0	0	0	1	0	50	63				
SFI1	9814	broad.mit.edu	37	22	31927093	31927093	+	Missense_Mutation	SNP	A	A	G			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr22:31927093A>G	ENST00000400288.2	+	4	421	c.316A>G	c.(316-318)Aga>Gga	p.R106G	SFI1_ENST00000443326.1_Intron|SFI1_ENST00000540643.1_Intron|SFI1_ENST00000432498.1_Missense_Mutation_p.R106G|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	106					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GACTTTTGGAAGAGTATTTCC	0.318																																						uc003ale.3																			0				NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						c.(316-318)Aga>Gga		Homo sapiens Sfi1 homolog, spindle assembly associated (yeast) (SFI1), transcript variant 1, mRNA.							112.0	106.0	108.0					22																	31927093		1829	4081	5910	SO:0001583	missense	9814				G2/M transition of mitotic cell cycle	centriole|cytosol		g.chr22:31927093A>G	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.316A>G	22.37:g.31927093A>G	ENSP00000383145:p.Arg106Gly					SFI1_uc003ald.1_Intron|SFI1_uc003alf.3_Missense_Mutation_p.R106G|SFI1_uc003alg.3_Intron|SFI1_uc011alp.2_Intron|SFI1_uc011alq.2_Intron|SFI1_uc003alh.3_Intron	p.R106G	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN			3	709	+			106					A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	c.316A>G	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.988624	0.74589	.	.	ENSG00000198089	ENST00000432498;ENST00000400288;ENST00000450787	T;T;T	0.30981	2.71;2.73;1.51	4.26	4.26	0.50523	.	0.074424	0.51477	D	0.000092	T	0.32315	0.0825	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;0.989	D;D	0.87578	0.998;0.985	T	0.31641	-0.9936	10	0.72032	D	0.01	.	9.9562	0.41668	1.0:0.0:0.0:0.0	.	106;106	A8K8P3-2;A8K8P3	.;SFI1_HUMAN	G	106;106;57	ENSP00000402679:R106G;ENSP00000383145:R106G;ENSP00000389364:R57G	ENSP00000383145:R106G	R	+	1	2	SFI1	30257093	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.310000	0.43708	1.926000	0.55796	0.363000	0.22086	AGA		0.318	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		6	87	0	0	0	1	0	6	87				
GPR97	222487	broad.mit.edu	37	16	57718006	57718006	+	Silent	SNP	C	C	T	rs368898879		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr16:57718006C>T	ENST00000333493.4	+	9	1205	c.1044C>T	c.(1042-1044)ttC>ttT	p.F348F	GPR97_ENST00000327655.6_Silent_p.F138F|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000450388.3_Silent_p.F228F	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	348					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCCACTACTTCCTGCTCTGTG	0.587																																						uc002emh.3																			0				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						c.(1042-1044)ttC>ttT		Homo sapiens G protein-coupled receptor 97 (GPR97), mRNA.		C		0,4396		0,0,2198	105.0	101.0	102.0		1044	1.0	1.0	16		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR97	NM_170776.4		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		348/550	57718006	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	222487				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr16:57718006C>T	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1044C>T	16.37:g.57718006C>T						GPR97_uc010vhv.2_Silent_p.F228F|GPR97_uc010cdd.3_Intron|GPR97_uc010cde.3_Intron	p.F348F	NM_170776	NP_740746	Q86Y34	GPR97_HUMAN			8	1147	+			348					Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	c.1044C>T	CCDS10786.1																																																																																				0.587	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		49	118	0	0	0	1	0	49	118				
ALPI	248	broad.mit.edu	37	2	233321115	233321115	+	Missense_Mutation	SNP	G	G	T			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr2:233321115G>T	ENST00000295463.3	+	2	201	c.124G>T	c.(124-126)Gcc>Tcc	p.A42S		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	42					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CCTGGATGCTGCCAAGAAGCT	0.632																																						uc002vst.4																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24						c.(124-126)Gcc>Tcc		Homo sapiens alkaline phosphatase, intestinal (ALPI), mRNA.							69.0	69.0	69.0					2																	233321115		2203	4300	6503	SO:0001583	missense	248				phosphorylation	anchored to membrane|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding|protein binding	g.chr2:233321115G>T	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.124G>T	2.37:g.233321115G>T	ENSP00000295463:p.Ala42Ser					ALPI_uc002vsu.4_5'UTR	p.A42S	NM_001631	NP_001622	P09923	PPBI_HUMAN		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)	1	201	+		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)	42					B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	37	c.124G>T	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	g	10.35	1.325840	0.24080	.	.	ENSG00000163295	ENST00000295463	D	0.96200	-3.94	5.49	4.61	0.57282	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96119	0.8735	M	0.83953	2.67	0.29821	N	0.830818	B	0.30824	0.296	B	0.44108	0.441	D	0.94236	0.7481	10	0.51188	T	0.08	.	9.3877	0.38354	0.0766:0.0:0.7805:0.1429	.	42	P09923	PPBI_HUMAN	S	42	ENSP00000295463:A42S	ENSP00000295463:A42S	A	+	1	0	ALPI	233029359	0.625000	0.27111	0.688000	0.30117	0.017000	0.09413	1.440000	0.35024	1.464000	0.47987	0.655000	0.94253	GCC		0.632	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		4	154	0	0	0	1	0	4	154				
SLC25A32	81034	broad.mit.edu	37	8	104427255	104427255	+	5'UTR	SNP	G	G	C			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr8:104427255G>C	ENST00000297578.4	-	0	77				SLC25A32_ENST00000543107.1_5'UTR|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|DCAF13_ENST00000297579.5_Missense_Mutation_p.V13L	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	GTCGCCCCTTGTGAGCGCAAC	0.697																																						uc003yln.3																			0				NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						c.(37-39)Gtg>Ctg		Homo sapiens DDB1 and CUL4 associated factor 13 (DCAF13), mRNA.							19.0	16.0	17.0					8																	104427255		2194	4292	6486	SO:0001623	5_prime_UTR_variant	25879				rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex		g.chr8:104427255G>C	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.-90C>G	8.37:g.104427255G>C						SLC25A32_uc003yll.3_5'UTR|SLC25A32_uc011lhr.2_5'UTR|DCAF13_uc003ylm.1_5'UTR	p.V13L	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN			0	314	+			0					Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	c.37G>C	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.904625	0.33628	.	.	ENSG00000164934	ENST00000297579	T	0.75589	-0.95	3.86	-7.73	0.01245	.	3.277830	0.01342	U	0.011608	T	0.62380	0.2423	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.55903	-0.8067	7	0.87932	D	0	5.6314	1.7396	0.02949	0.2588:0.0855:0.3414:0.3144	.	.	.	.	L	13	ENSP00000297579:V13L	ENSP00000297579:V13L	V	+	1	0	DCAF13	104496431	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.713000	0.00816	-2.935000	0.00299	-2.520000	0.00184	GTG		0.697	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		16	19	0	0	0	1	0	16	19				
VPS53	55275	broad.mit.edu	37	17	617889	617889	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr17:617889G>A	ENST00000571805.1	-	1	197	c.61C>T	c.(61-63)Ccc>Tcc	p.P21S	VPS53_ENST00000291074.5_Missense_Mutation_p.P21S|VPS53_ENST00000437048.2_Missense_Mutation_p.P21S|VPS53_ENST00000401468.3_Missense_Mutation_p.P21S|VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000574029.1_Missense_Mutation_p.P21S			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	21					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		TGCACCTCGGGCGTGAGCTGC	0.711																																						uc010cjo.2																			0				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19						c.(61-63)Ccc>Tcc		Homo sapiens vacuolar protein sorting 53 homolog (S. cerevisiae) (VPS53), transcript variant 1, mRNA.							61.0	63.0	62.0					17																	617889		2203	4300	6503	SO:0001583	missense	55275				protein transport	Golgi apparatus|endosome membrane		g.chr17:617889G>A		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.61C>T	17.37:g.617889G>A	ENSP00000459312:p.Pro21Ser					VPS53_uc002frl.2_Non-coding_Transcript|VPS53_uc002frm.2_Missense_Mutation_p.P21S|VPS53_uc002frn.2_Missense_Mutation_p.P21S|VPS53_uc002fro.2_5'UTR|VPS53_uc010cjp.1_Missense_Mutation_p.P21S	p.P21S	NM_001128159	NP_001121631	Q5VIR6	VPS53_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)	0	208	-			21					A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37	c.61C>T		.	.	.	.	.	.	.	.	.	.	G	34	5.381303	0.95945	.	.	ENSG00000141252	ENST00000437048;ENST00000291074;ENST00000401468;ENST00000389040	T;T;T;T	0.47528	1.56;1.44;0.84;1.53	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.64404	1.975	0.80722	D	1	D;D;D;D	0.76494	0.993;0.997;0.998;0.999	D;D;D;D	0.72338	0.968;0.963;0.962;0.977	T	0.67692	-0.5605	10	0.59425	D	0.04	-15.7492	16.5629	0.84570	0.0:0.0:1.0:0.0	.	21;21;21;21	E7EVT8;Q5VIR6-4;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	S	21	ENSP00000401435:P21S;ENSP00000291074:P21S;ENSP00000384294:P21S;ENSP00000373692:P21S	ENSP00000291074:P21S	P	-	1	0	VPS53	564639	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.002000	0.88514	2.506000	0.84524	0.591000	0.81541	CCC		0.711	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		16	212	0	0	0	1	0	16	212				
FOXP3	50943	broad.mit.edu	37	X	49114015	49114015	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chrX:49114015G>A	ENST00000376207.4	-	4	510	c.323C>T	c.(322-324)aCg>aTg	p.T108M	FOXP3_ENST00000376199.2_Missense_Mutation_p.T73M|FOXP3_ENST00000455775.2_Missense_Mutation_p.T108M|FOXP3_ENST00000376197.1_Missense_Mutation_p.T58M|FOXP3_ENST00000518685.1_Missense_Mutation_p.T73M|FOXP3_ENST00000557224.1_Missense_Mutation_p.T73M	NM_014009.3	NP_054728.2	Q9BZS1	FOXP3_HUMAN	forkhead box P3	108					B cell homeostasis (GO:0001782)|CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|chromatin remodeling (GO:0006338)|cytokine production (GO:0001816)|myeloid cell homeostasis (GO:0002262)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chronic inflammatory response (GO:0002677)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of immune response (GO:0050777)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of histone acetylation (GO:0035066)|positive regulation of immature T cell proliferation in thymus (GO:0033092)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of peripheral T cell tolerance induction (GO:0002851)|positive regulation of T cell anergy (GO:0002669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of isotype switching to IgG isotypes (GO:0048302)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell activation (GO:0042110)|T cell homeostasis (GO:0043029)|T cell mediated immunity (GO:0002456)|T cell receptor signaling pathway (GO:0050852)|tolerance induction to self antigen (GO:0002513)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|NFAT protein binding (GO:0051525)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)	10	Ovarian(276;0.236)					GGCATCCACCGTTGAGAGCTG	0.677													G|||	2	0.000529801	0.0	0.0014	3775	,	,		12462	0.0		0.0	False		,,,				2504	0.001				GBM(182;1432 2112 16160 23073 31774)	uc011mnb.2																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)	10	GRCh37	CM066087	FOXP3	M		c.(322-324)aCg>aTg		Homo sapiens forkhead box P3 (FOXP3), transcript variant 1, mRNA.							34.0	31.0	32.0					X																	49114015		2199	4298	6497	SO:0001583	missense	50943				B cell homeostasis|T cell homeostasis|T cell receptor signaling pathway|cerebellum development|chromatin remodeling|embryo development|myeloid cell homeostasis|negative regulation of CREB transcription factor activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell cytokine production|negative regulation of activated T cell proliferation|negative regulation of chronic inflammatory response|negative regulation of cytokine secretion|negative regulation of histone acetylation|negative regulation of histone deacetylation|negative regulation of interferon-gamma biosynthetic process|negative regulation of interferon-gamma production|negative regulation of interleukin-10 production|negative regulation of interleukin-2 biosynthetic process|negative regulation of interleukin-2 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of interleukin-6 production|negative regulation of isotype switching to IgE isotypes|negative regulation of tumor necrosis factor production|pattern specification process|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation|positive regulation of T cell anergy|positive regulation of histone acetylation|positive regulation of immature T cell proliferation in thymus|positive regulation of peripheral T cell tolerance induction|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transforming growth factor-beta1 production|post-embryonic development|regulation of isotype switching to IgG isotypes|response to virus|tolerance induction to self antigen	cytoplasm|nucleus|transcription factor complex	DNA bending activity|NF-kappaB binding|NFAT protein binding|chromatin binding|double-stranded DNA binding|histone acetyltransferase binding|histone deacetylase binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription corepressor activity|zinc ion binding	g.chrX:49114015G>A		CCDS14323.1, CCDS48109.1	Xp11.23	2014-09-17		2002-09-20	ENSG00000049768	ENSG00000049768		"""Forkhead boxes"""	6106	protein-coding gene	gene with protein product		300292	"""immune dysregulation, polyendocrinopathy, enteropathy, X-linked"""	IPEX		10677306, 11138001	Standard	NM_014009		Approved	JM2, XPID, AIID, PIDX, DIETER, SCURFIN	uc004dnf.4	Q9BZS1	OTTHUMG00000024135	ENST00000376207.4:c.323C>T	X.37:g.49114015G>A	ENSP00000365380:p.Thr108Met					FOXP3_uc011mnc.2_Missense_Mutation_p.T108M|FOXP3_uc004dnf.4_Missense_Mutation_p.T108M|FOXP3_uc004dne.4_Missense_Mutation_p.T73M|FOXP3_uc022bwa.1_Missense_Mutation_p.T58M	p.T108M	NM_014009	NP_054728	Q9BZS1	FOXP3_HUMAN			2	345	-	Ovarian(276;0.236)		108					A5HJT1|B7ZLG0|B9UN80|O60827|Q14DD8|Q4ZH51	Missense_Mutation	SNP	ENST00000376207.4	37	c.323C>T	CCDS14323.1	.	.	.	.	.	.	.	.	.	.	G	8.651	0.898233	0.17686	.	.	ENSG00000049768	ENST00000376207;ENST00000376199;ENST00000557224;ENST00000518685;ENST00000376197;ENST00000455775	D;D;D;D;D;D	0.98550	-3.72;-4.01;-4.98;-4.01;-4.99;-4.18	5.33	3.4	0.38934	.	0.500579	0.18737	N	0.132552	D	0.92348	0.7572	N	0.19112	0.55	0.09310	N	1	B;B;P;B;B	0.38167	0.037;0.111;0.621;0.037;0.063	B;B;B;B;B	0.21360	0.009;0.023;0.034;0.009;0.032	D	0.88156	0.2854	10	0.87932	D	0	.	4.7924	0.13256	0.1097:0.0:0.6143:0.2759	.	108;108;73;108;73	B9UN80;B7ZLG1;Q9BZS1-3;Q9BZS1;Q9BZS1-2	.;.;.;FOXP3_HUMAN;.	M	108;73;73;73;58;108	ENSP00000365380:T108M;ENSP00000365372:T73M;ENSP00000451208:T73M;ENSP00000428952:T73M;ENSP00000365369:T58M;ENSP00000396415:T108M	ENSP00000365369:T58M	T	-	2	0	FOXP3	49000959	0.018000	0.18449	0.128000	0.21923	0.724000	0.41520	2.123000	0.41996	0.971000	0.38288	0.506000	0.49869	ACG		0.677	FOXP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060814.1	NM_014009		3	29	0	0	0	1	0	3	29				
CHMP7	91782	broad.mit.edu	37	8	23115930	23115930	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr8:23115930G>A	ENST00000397677.1	+	7	1576	c.928G>A	c.(928-930)Gac>Aac	p.D310N	CHMP7_ENST00000313219.7_Missense_Mutation_p.D310N|CHMP7_ENST00000520102.1_3'UTR	NM_152272.3	NP_689485.1	Q8WUX9	CHMP7_HUMAN	charged multivesicular body protein 7	310					endosomal transport (GO:0016197)|late endosome to vacuole transport (GO:0045324)|membrane organization (GO:0061024)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|ESCRT III complex (GO:0000815)	protein transporter activity (GO:0008565)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		AGGCATCCTGGACCGGATCTA	0.572																																						uc003xdc.2																			0				breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11						c.(928-930)Gac>Aac		Homo sapiens charged multivesicular body protein 7 (CHMP7), mRNA.							245.0	209.0	221.0					8																	23115930		2203	4300	6503	SO:0001583	missense	91782				cellular membrane organization|late endosome to vacuole transport	ESCRT III complex|cytosol	protein transporter activity	g.chr8:23115930G>A	BC019110	CCDS6040.1	8p21.2	2011-09-21	2011-09-21		ENSG00000147457	ENSG00000147457		"""Charged multivesicular body proteins"""	28439	protein-coding gene	gene with protein product		611130	"""CHMP family, member 7"""			16856878	Standard	NM_152272		Approved	MGC29816	uc003xdc.2	Q8WUX9	OTTHUMG00000131785	ENST00000397677.1:c.928G>A	8.37:g.23115930G>A	ENSP00000380794:p.Asp310Asn					CHMP7_uc011kzs.1_Non-coding_Transcript|CHMP7_uc003xdd.2_Missense_Mutation_p.D200N|CHMP7_uc003xde.2_Missense_Mutation_p.D168N	p.D310N	NM_152272	NP_689485	Q8WUX9	CHMP7_HUMAN		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)	6	1576	+		Prostate(55;0.0513)	310					B2RDT3|B4DKJ6|D3DSS1|Q8NDM1|Q9BT50	Missense_Mutation	SNP	ENST00000397677.1	37	c.928G>A	CCDS6040.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.539401	0.85917	.	.	ENSG00000147457	ENST00000397677;ENST00000313219	T;T	0.71341	-0.56;-0.56	5.91	5.91	0.95273	.	0.080649	0.85682	D	0.000000	T	0.76521	0.3999	M	0.62723	1.935	0.58432	D	0.999991	D;B	0.56968	0.978;0.008	P;B	0.54590	0.756;0.038	T	0.70680	-0.4805	10	0.13470	T	0.59	-13.2932	16.9982	0.86373	0.0:0.0:1.0:0.0	.	200;310	B3KRZ9;Q8WUX9	.;CHMP7_HUMAN	N	310	ENSP00000380794:D310N;ENSP00000324491:D310N	ENSP00000324491:D310N	D	+	1	0	CHMP7	23171875	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.860000	0.92272	2.801000	0.96364	0.655000	0.94253	GAC		0.572	CHMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254717.1	NM_152272		11	531	0	0	0	1	0	11	531				
HK2	3099	broad.mit.edu	37	2	75081444	75081444	+	Missense_Mutation	SNP	C	C	T	rs567201785		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr2:75081444C>T	ENST00000290573.2	+	2	688	c.88C>T	c.(88-90)Cgc>Tgc	p.R30C	HK2_ENST00000409174.1_Missense_Mutation_p.R2C	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	30	Hexokinase type-1 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.R30C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CTACCACATGCGCCTCTCTGA	0.488																																						uc002snd.3																			1	Substitution - Missense(1)	p.R30C(2)	endometrium(1)	breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						c.(88-90)Cgc>Tgc		Homo sapiens hexokinase 2 (HK2), mRNA.							242.0	252.0	248.0					2																	75081444		2203	4300	6503	SO:0001583	missense	3099				apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity	g.chr2:75081444C>T		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.88C>T	2.37:g.75081444C>T	ENSP00000290573:p.Arg30Cys						p.R30C	NM_000189	NP_000180	P52789	HXK2_HUMAN			1	2014	+			30			Regulatory.		D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	c.88C>T	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772471	0.90108	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98550	-4.99;-4.99	5.13	5.13	0.70059	Hexokinase, N-terminal (1);	0.191170	0.47852	D	0.000216	D	0.98579	0.9525	M	0.80616	2.505	0.80722	D	1	D	0.67145	0.996	P	0.59171	0.853	D	0.98640	1.0675	10	0.48119	T	0.1	-13.6651	16.123	0.81375	0.0:1.0:0.0:0.0	.	30	P52789	HXK2_HUMAN	C	30;30;2	ENSP00000290573:R30C;ENSP00000387140:R2C	ENSP00000290573:R30C	R	+	1	0	HK2	74934952	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.320000	0.79064	2.665000	0.90641	0.561000	0.74099	CGC		0.488	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		5	570	0	0	0	1	0	5	570				
ACACB	32	broad.mit.edu	37	12	109614053	109614053	+	Silent	SNP	G	G	T			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr12:109614053G>T	ENST00000338432.7	+	9	1541	c.1422G>T	c.(1420-1422)ccG>ccT	p.P474P	ACACB_ENST00000377848.3_Silent_p.P474P|ACACB_ENST00000377854.5_Silent_p.P474P|ACACB_ENST00000543080.1_3'UTR			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	474	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	AGGACTTCCCGATCCTTTTCA	0.478																																						uc001tob.3																			0				NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95						c.(1420-1422)ccG>ccT		Homo sapiens acetyl-CoA carboxylase beta (ACACB), mRNA.	Biotin(DB00121)						183.0	188.0	186.0					12																	109614053		2203	4300	6503	SO:0001819	synonymous_variant	32				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	Golgi apparatus|cytosol|endomembrane system|membrane	ATP binding|acetyl-CoA carboxylase activity|biotin carboxylase activity|metal ion binding|protein binding	g.chr12:109614053G>T	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1422G>T	12.37:g.109614053G>T						ACACB_uc001toc.3_Silent_p.P474P	p.P474P	NM_001093	NP_001084	O00763	ACACB_HUMAN			8	1541	+			474			ATP-grasp.|Biotin carboxylation.		A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	c.1422G>T	CCDS31898.1																																																																																				0.478	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		169	227	0	0	0	1	0	169	227				
NCAPD3	23310	broad.mit.edu	37	11	134080347	134080347	+	Splice_Site	SNP	G	G	A	rs142896286	byFrequency	TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr11:134080347G>A	ENST00000534548.2	-	4	448	c.384C>T	c.(382-384)ggC>ggT	p.G128G		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	128					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TGGCTACACTGCCTATTCATG	0.358													G|||	2	0.000399361	0.0	0.0	5008	,	,		19361	0.0		0.002	False		,,,				2504	0.0					uc001qhd.1																			0				NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						c.e4-1		Homo sapiens non-SMC condensin II complex, subunit D3 (NCAPD3), mRNA.		G		0,4402		0,0,2201	99.0	96.0	97.0		384	-2.8	1.0	11	dbSNP_134	97	6,8588	5.0+/-18.6	0,6,4291	yes	coding-synonymous-near-splice	NCAPD3	NM_015261.2		0,6,6492	AA,AG,GG		0.0698,0.0,0.0462		128/1499	134080347	6,12990	2201	4297	6498	SO:0001630	splice_region_variant	23310				cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding	g.chr11:134080347G>A	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.383-1C>T	11.37:g.134080347G>A						NCAPD3_uc010scm.1_Splice_Site|NCAPD3_uc009zda.1_Splice_Site	p.G128_splice	NM_015261	NP_056076	P42695	CNDD3_HUMAN		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)	4	989	-	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)	128					A6NFS2|Q4KMQ9	Splice_Site	SNP	ENST00000534548.2	37	c.383_splice	CCDS31723.1																																																																																				0.358	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Silent	50	63	0	0	0	1	0	50	63				
PDLIM3	27295	broad.mit.edu	37	4	186429465	186429465	+	Missense_Mutation	SNP	G	G	A	rs1141102		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr4:186429465G>A	ENST00000284770.5	-	5	723	c.650C>T	c.(649-651)aCa>aTa	p.T217I	PDLIM3_ENST00000284771.6_Intron|PDLIM3_ENST00000284767.5_3'UTR	NM_014476.5	NP_055291.2	Q53GG5	PDLI3_HUMAN	PDZ and LIM domain 3	217				T -> I (in Ref. 1; AAC16670). {ECO:0000305}.	actin filament organization (GO:0007015)|heart development (GO:0007507)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of muscle (GO:0008307)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17		all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171)		CATCAAAGGTGTTTCCCCTAG	0.393																																						uc003ixw.4																			0		p.E216K(1)		breast(2)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						c.(649-651)aCa>aTa		Homo sapiens PDZ and LIM domain 3 (PDLIM3), transcript variant 1, mRNA.							135.0	125.0	128.0					4																	186429465		2203	4300	6503	SO:0001583	missense	27295					sarcomere	zinc ion binding	g.chr4:186429465G>A	AF002280	CCDS3844.1, CCDS47172.1, CCDS75218.1, CCDS75219.1	4q35	2014-09-17			ENSG00000154553	ENSG00000154553			20767	protein-coding gene	gene with protein product		605889				10063829, 8828038	Standard	NM_014476		Approved	ALP	uc003ixw.4	Q53GG5	OTTHUMG00000160412	ENST00000284770.5:c.650C>T	4.37:g.186429465G>A	ENSP00000284770:p.Thr217Ile					PDLIM3_uc003ixx.4_Intron|PDLIM3_uc010isi.3_Intron	p.T217I	NM_014476	NP_055291	Q53GG5	PDLI3_HUMAN		OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171)	4	774	-		all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243)	217	T -> I (in Ref. 1; AAC16670).				B2R866|O43590|O60439|O60440|Q8N6Y6|Q9BVP4	Missense_Mutation	SNP	ENST00000284770.5	37	c.650C>T	CCDS3844.1	.	.	.	.	.	.	.	.	.	.	G	9.943	1.218131	0.22373	.	.	ENSG00000154553	ENST00000284770	T	0.35605	1.3	5.95	5.1	0.69264	.	0.607305	0.19354	N	0.116338	T	0.31389	0.0795	L	0.44542	1.39	0.58432	D	0.999999	B	0.15473	0.013	B	0.19391	0.025	T	0.07028	-1.0794	10	0.37606	T	0.19	-0.0933	10.581	0.45255	0.0:0.129:0.6038:0.2672	rs1141102;rs3205111;rs17400979	217	Q53GG5	PDLI3_HUMAN	I	217	ENSP00000284770:T217I	ENSP00000284770:T217I	T	-	2	0	PDLIM3	186666459	0.690000	0.27699	0.369000	0.25952	0.647000	0.38526	1.529000	0.35996	1.495000	0.48549	0.563000	0.77884	ACA		0.393	PDLIM3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360499.2	NM_014476		7	220	0	0	0	1	0	7	220				
OR4C46	119749	broad.mit.edu	37	11	51515327	51515327	+	Missense_Mutation	SNP	A	A	G			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr11:51515327A>G	ENST00000328188.1	+	1	46	c.46A>G	c.(46-48)Aca>Gca	p.T16A		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						GCTGGGGCTTACAGAGAATCC	0.343																																						uc010ric.2																			0				endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						c.(46-48)Aca>Gca		Homo sapiens olfactory receptor, family 4, subfamily C, member 46 (OR4C46), mRNA.							148.0	142.0	144.0					11																	51515327		2201	4296	6497	SO:0001583	missense	119749				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:51515327A>G		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.46A>G	11.37:g.51515327A>G	ENSP00000329056:p.Thr16Ala						p.T16A	NM_001004703	NP_001004703	A6NHA9	O4C46_HUMAN			0	46	+			16						Missense_Mutation	SNP	ENST00000328188.1	37	c.46A>G	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	12.69	2.014663	0.35511	.	.	ENSG00000185926	ENST00000328188	T	0.00421	7.46	2.63	-0.182	0.13287	.	0.000000	0.35495	U	0.003161	T	0.00524	0.0017	M	0.76170	2.325	0.09310	N	1	P	0.46706	0.883	P	0.52267	0.694	T	0.49978	-0.8881	10	0.66056	D	0.02	.	1.9323	0.03330	0.5666:0.0:0.1656:0.2678	.	16	A6NHA9	O4C46_HUMAN	A	16	ENSP00000329056:T16A	ENSP00000329056:T16A	T	+	1	0	OR4C46	51371903	0.000000	0.05858	0.010000	0.14722	0.041000	0.13682	0.083000	0.14871	0.270000	0.21984	0.113000	0.15668	ACA		0.343	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		5	188	0	0	0	1	0	5	188				
ATP1A2	477	broad.mit.edu	37	1	160094203	160094203	+	Missense_Mutation	SNP	T	T	A			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:160094203T>A	ENST00000361216.3	+	6	702	c.613T>A	c.(613-615)Tct>Act	p.S205T	ATP1A2_ENST00000392233.3_Missense_Mutation_p.S205T	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	205					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCGGATCATCTCTTCTCATGG	0.562																																						uc001fvc.3																			0				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69						c.(613-615)Tct>Act		Homo sapiens ATPase, Na+/K+ transporting, alpha 2 polypeptide (ATP1A2), mRNA.							96.0	75.0	82.0					1																	160094203		2203	4300	6503	SO:0001583	missense	477				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity	g.chr1:160094203T>A	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.613T>A	1.37:g.160094203T>A	ENSP00000354490:p.Ser205Thr					ATP1A2_uc001fvb.2_Missense_Mutation_p.S205T|ATP1A2_uc010piz.1_Missense_Mutation_p.S50T	p.S205T	NM_000702	NP_000693	P50993	AT1A2_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)		5	745	+	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		205					D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	c.613T>A	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.091287	0.55968	.	.	ENSG00000018625	ENST00000538123;ENST00000361216;ENST00000392233	D;D	0.91237	-2.81;-2.81	5.27	5.27	0.74061	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.172944	0.52532	D	0.000067	T	0.77025	0.4070	N	0.21194	0.64	0.41343	D	0.987315	B;B	0.22414	0.069;0.021	B;B	0.29524	0.103;0.086	T	0.76429	-0.2962	10	0.46703	T	0.11	.	9.5694	0.39418	0.1568:0.0:0.0:0.8432	.	50;205	B4DHD7;P50993	.;AT1A2_HUMAN	T	50;205;205	ENSP00000354490:S205T;ENSP00000376066:S205T	ENSP00000354490:S205T	S	+	1	0	ATP1A2	158360827	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.023000	0.64084	1.997000	0.58415	0.533000	0.62120	TCT		0.562	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		13	20	0	0	0	1	0	13	20				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		63	76	0	0	0	1	0	63	76				
RP1	6101	broad.mit.edu	37	8	55541490	55541490	+	Missense_Mutation	SNP	C	C	A	rs375430744		TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr8:55541490C>A	ENST00000220676.1	+	4	5196	c.5048C>A	c.(5047-5049)tCt>tAt	p.S1683Y		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1683					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTTGGCTCTTCTGAACAGGTA	0.413																																					Colon(91;1014 1389 7634 14542 40420)	uc003xsd.1																			0				NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169						c.(5047-5049)tCt>tAt		Homo sapiens retinitis pigmentosa 1 (autosomal dominant) (RP1), mRNA.							157.0	160.0	159.0					8																	55541490		2203	4300	6503	SO:0001583	missense	6101				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding	g.chr8:55541490C>A	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5048C>A	8.37:g.55541490C>A	ENSP00000220676:p.Ser1683Tyr					RP1_uc011ldy.1_Intron	p.S1683Y	NM_006269	NP_006260	P56715	RP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		3	5196	+		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	1683						Missense_Mutation	SNP	ENST00000220676.1	37	c.5048C>A	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.037834	0.35989	.	.	ENSG00000104237	ENST00000220676	T	0.24538	1.85	5.67	2.73	0.32206	.	0.000000	0.48767	D	0.000177	T	0.23094	0.0558	M	0.61703	1.905	0.09310	N	1	B	0.18741	0.03	B	0.17098	0.017	T	0.29640	-1.0005	10	0.87932	D	0	.	4.5313	0.12006	0.3034:0.5257:0.0:0.1709	.	1683	P56715	RP1_HUMAN	Y	1683	ENSP00000220676:S1683Y	ENSP00000220676:S1683Y	S	+	2	0	RP1	55704043	0.000000	0.05858	0.229000	0.23960	0.981000	0.71138	-0.181000	0.09740	0.254000	0.21573	0.655000	0.94253	TCT		0.413	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		20	219	0	0	0	1	0	20	219				
GON4L	54856	broad.mit.edu	37	1	155734928	155734928	+	Missense_Mutation	SNP	C	C	G			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr1:155734928C>G	ENST00000368331.1	-	21	4384	c.4336G>C	c.(4336-4338)Gtt>Ctt	p.V1446L	GON4L_ENST00000271883.5_Missense_Mutation_p.V1446L|GON4L_ENST00000361040.5_Missense_Mutation_p.V1446L|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Missense_Mutation_p.V1446L	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1446					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCTGGCCCAACTGGAGTCCCC	0.502																																						uc001flz.2																			0				NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45						c.(4336-4338)Gtt>Ctt		Homo sapiens gon-4-like (C. elegans) (GON4L), transcript variant 1, mRNA.							118.0	124.0	122.0					1																	155734928		2203	4300	6503	SO:0001583	missense	54856				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding	g.chr1:155734928C>G	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"""gon-4 homolog (C.elegans)"""	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.4336G>C	1.37:g.155734928C>G	ENSP00000357315:p.Val1446Leu					GON4L_uc021paz.1_Intron|GON4L_uc009wrg.1_Non-coding_Transcript|GON4L_uc001fly.1_Missense_Mutation_p.V1446L|GON4L_uc009wrh.1_Missense_Mutation_p.V1446L|GON4L_uc001fma.1_Missense_Mutation_p.V1446L|GON4L_uc001fmb.4_Missense_Mutation_p.V642L|GON4L_uc001fmc.3_Missense_Mutation_p.V1446L|GON4L_uc001fmd.4_Missense_Mutation_p.V1446L|GON4L_uc009wri.3_Missense_Mutation_p.V1032L	p.V1446L	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN			20	4433	-	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)		1446					B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37	c.4336G>C		.	.	.	.	.	.	.	.	.	.	C	7.683	0.689485	0.14973	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000361040	T;T;T;T	0.12361	2.9;2.9;2.9;2.69	5.24	3.34	0.38264	.	0.158827	0.43747	D	0.000539	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.41413	-0.9510	10	0.54805	T	0.06	.	8.3315	0.32189	0.1543:0.7669:0.0:0.0789	.	1446;642;1446;1446	Q3T8J9-2;Q1ED43;Q3T8J9;Q3T8J9-3	.;.;GON4L_HUMAN;.	L	1446	ENSP00000396117:V1446L;ENSP00000357315:V1446L;ENSP00000271883:V1446L;ENSP00000354322:V1446L	ENSP00000271883:V1446L	V	-	1	0	GON4L	154001552	0.950000	0.32346	0.005000	0.12908	0.005000	0.04900	5.418000	0.66429	0.780000	0.33566	-0.141000	0.14075	GTT		0.502	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		22	232	0	0	0	1	0	22	232				
HACL1	26061	broad.mit.edu	37	3	15616558	15616558	+	Missense_Mutation	SNP	A	A	G			TCGA-ET-A2N4-01A-12D-A19J-08	TCGA-ET-A2N4-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4e2107cb-8c52-4f2a-8c41-1a305c14044c	c9f32c4e-5746-4269-9e5b-e8816cf87b93	g.chr3:15616558A>G	ENST00000321169.5	-	10	1202	c.835T>C	c.(835-837)Ttt>Ctt	p.F279L	HACL1_ENST00000456194.2_Missense_Mutation_p.F252L|HACL1_ENST00000451445.2_Missense_Mutation_p.F197L|HACL1_ENST00000457447.2_Missense_Mutation_p.F253L|HACL1_ENST00000435217.2_Intron	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	279					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CTGGCACCAAATAACACAATT	0.318																																						uc003caf.3																			0				NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						c.(835-837)Ttt>Ctt		Homo sapiens 2-hydroxyacyl-CoA lyase 1 (HACL1), mRNA.							75.0	74.0	74.0					3																	15616558		2203	4300	6503	SO:0001583	missense	26061				fatty acid alpha-oxidation	peroxisomal matrix	carbon-carbon lyase activity|identical protein binding|magnesium ion binding|thiamine pyrophosphate binding	g.chr3:15616558A>G	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"""2-hydroxyphytanoyl-CoA lyase"""	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.835T>C	3.37:g.15616558A>G	ENSP00000323811:p.Phe279Leu					HACL1_uc011avr.1_Non-coding_Transcript|HACL1_uc010hep.3_Intron|HACL1_uc011avs.2_Missense_Mutation_p.F252L|HACL1_uc011avt.2_Missense_Mutation_p.F253L|HACL1_uc003cag.3_Intron|HACL1_uc011avu.2_Missense_Mutation_p.F197L	p.F279L	NM_012260	NP_036392	Q9UJ83	HACL1_HUMAN			9	995	-			279					B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Missense_Mutation	SNP	ENST00000321169.5	37	c.835T>C	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	A	6.887	0.533062	0.13188	.	.	ENSG00000131373	ENST00000321169;ENST00000451445;ENST00000456194;ENST00000457447	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.5	-3.26	0.05064	Thiamine pyrophosphate enzyme, central domain (1);	0.411949	0.29280	N	0.012604	T	0.05364	0.0142	N	0.00131	-2.04	0.30146	N	0.803535	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.39231	-0.9624	10	0.07175	T	0.84	.	15.0661	0.71996	0.2097:0.0:0.7903:0.0	.	197;253;252;279	B4DXI5;E9PEN4;B4DWI1;Q9UJ83	.;.;.;HACL1_HUMAN	L	279;197;252;253	ENSP00000323811:F279L;ENSP00000403656:F197L;ENSP00000390699:F252L;ENSP00000404883:F253L	ENSP00000323811:F279L	F	-	1	0	HACL1	15591562	0.999000	0.42202	0.969000	0.41365	0.988000	0.76386	0.756000	0.26419	-0.501000	0.06605	-0.385000	0.06624	TTT		0.318	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260		12	78	0	0	0	1	0	12	78				
