#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
TNFRSF8	943	broad.mit.edu	37	1	12172031	12172031	+	Silent	SNP	C	C	T	rs536842664		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:12172031C>T	ENST00000263932.2	+	7	975	c.753C>T	c.(751-753)gaC>gaT	p.D251D	TNFRSF8_ENST00000417814.2_Silent_p.D140D	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	251					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	ACTACCTGGACGAGGCCGGCC	0.602													c|||	1	0.000199681	0.0	0.0	5008	,	,		15813	0.0		0.0	False		,,,				2504	0.001					uc001atq.3																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27						c.(751-753)gaC>gaT		Homo sapiens tumor necrosis factor receptor superfamily, member 8 (TNFRSF8), transcript variant 1, mRNA.							51.0	49.0	49.0					1																	12172031		2203	4300	6503	SO:0001819	synonymous_variant	943				cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane		g.chr1:12172031C>T	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.753C>T	1.37:g.12172031C>T						TNFRSF8_uc010obc.2_Silent_p.D140D	p.D251D	NM_001243	NP_001234	P28908	TNR8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	6	975	+	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)	251					B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	37	c.753C>T	CCDS144.1																																																																																				0.602	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		
NT5C1A	84618	broad.mit.edu	37	1	40131873	40131873	+	Silent	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:40131873G>A	ENST00000235628.1	-	2	170	c.171C>T	c.(169-171)tcC>tcT	p.S57S		NM_032526.1	NP_115915.1	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	57					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|purine nucleobase metabolic process (GO:0006144)|purine nucleoside monophosphate catabolic process (GO:0009128)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			breast(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)	15	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGGCTCGGGAGGACACAGCGA	0.582																																						uc001cdq.1																			0				breast(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)	15						c.(169-171)tcC>tcT		Homo sapiens 5'-nucleotidase, cytosolic IA (NT5C1A), mRNA.							94.0	76.0	82.0					1																	40131873		2203	4300	6503	SO:0001819	synonymous_variant	84618				purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding	g.chr1:40131873G>A	AF331801	CCDS440.1	1p34.3-p33	2008-07-18			ENSG00000116981	ENSG00000116981			17819	protein-coding gene	gene with protein product	"""cytosolic 5' nucleotidase, type 1A"", ""AMP-specific 5'-NT"", ""cytosolic 5'-nucleotidase IA"""	610525				11133996, 11690631	Standard	NM_032526		Approved	CN-I, CN-IA, CN1A, CN1, MGC119199, MGC119201	uc001cdq.1	Q9BXI3	OTTHUMG00000009244	ENST00000235628.1:c.171C>T	1.37:g.40131873G>A							p.S57S	NM_032526	NP_115915	Q9BXI3	5NT1A_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		1	171	-	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	57					Q3SYB9|Q5TG98|Q9BWT8	Silent	SNP	ENST00000235628.1	37	c.171C>T	CCDS440.1																																																																																				0.582	NT5C1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025626.1	NM_032526	
MSH4	4438	broad.mit.edu	37	1	76272802	76272802	+	Silent	SNP	T	T	C			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:76272802T>C	ENST00000263187.3	+	3	668	c.564T>C	c.(562-564)ttT>ttC	p.F188F		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	188					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						TATCCCAGTTTGCAGACAACA	0.373								Mismatch excision repair (MMR)																														uc001dhd.2																			0				breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						c.(562-564)ttT>ttC	Mismatch excision repair (MMR)	Homo sapiens mutS homolog 4 (E. coli) (MSH4), mRNA.							107.0	116.0	113.0					1																	76272802		2203	4300	6503	SO:0001819	synonymous_variant	4438				chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding	g.chr1:76272802T>C	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.564T>C	1.37:g.76272802T>C							p.F188F	NM_002440	NP_002431	O15457	MSH4_HUMAN			2	679	+			188					Q5T4U6|Q8NEB3|Q9UNP8	Silent	SNP	ENST00000263187.3	37	c.564T>C	CCDS670.1																																																																																				0.373	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
ELTD1	64123	broad.mit.edu	37	1	79392712	79392712	+	Missense_Mutation	SNP	G	G	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:79392712G>T	ENST00000370742.3	-	8	1005	c.942C>A	c.(940-942)aaC>aaA	p.N314K		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	314					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TCAATAAGAAGTTGTCAGATG	0.318																																						uc001diq.4																			0				NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69						c.(940-942)aaC>aaA		Homo sapiens EGF, latrophilin and seven transmembrane domain containing 1 (ELTD1), mRNA.							80.0	75.0	76.0					1																	79392712		1812	4079	5891	SO:0001583	missense	64123				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity	g.chr1:79392712G>T	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.942C>A	1.37:g.79392712G>T	ENSP00000359778:p.Asn314Lys						p.N314K	NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN		COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)	7	1098	-			314					B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	c.942C>A	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	6.537	0.467259	0.12402	.	.	ENSG00000162618	ENST00000370742	T	0.09911	2.93	6.02	-0.0395	0.13875	Domain of unknown function DUF3497 (1);	0.312145	0.42548	N	0.000697	T	0.01592	0.0051	N	0.25647	0.755	0.09310	N	0.999994	B	0.10296	0.003	B	0.15484	0.013	T	0.46359	-0.9197	9	.	.	.	.	3.4041	0.07335	0.2296:0.1161:0.5357:0.1187	.	314	Q9HBW9	ELTD1_HUMAN	K	314	ENSP00000359778:N314K	.	N	-	3	2	ELTD1	79165300	0.981000	0.34729	0.677000	0.29947	0.390000	0.30446	1.168000	0.31859	0.079000	0.16929	0.544000	0.68410	AAC		0.318	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
TRMT13	54482	broad.mit.edu	37	1	100602642	100602643	+	Splice_Site	INS	-	-	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:100602642_100602643insT	ENST00000370141.2	+	3	267		c.e3+1		TRMT13_ENST00000370139.1_Splice_Site|TRMT13_ENST00000370143.1_Splice_Site	NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)						tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										ACCAAAACCTGTAAGTGTTTGA	0.337																																						uc001dsv.3																			0				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)	21						c.e3+1		Homo sapiens coiled-coil domain containing 76 (CCDC76), mRNA.																																				SO:0001630	splice_region_variant	54482				tRNA processing		metal ion binding|methyltransferase activity	g.chr1:100602642_100602643insT	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.261+1->T	1.37:g.100602643_100602643dupT						CCDC76_uc010ouf.2_Splice_Site|CCDC76_uc009wea.3_Splice_Site_p.P87_splice	p.P87_splice	NM_019083	NP_061956	Q9NUP7	TRM13_HUMAN		Epithelial(280;0.0814)|all cancers(265;0.133)|COAD - Colon adenocarcinoma(174;0.146)|Lung(183;0.194)	3	280	+		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)	87					Q5VVL0|Q9NW65	Splice_Site	INS	ENST00000370141.2	37	c.261_splice	CCDS765.1																																																																																				0.337	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	Intron
KCND3	3752	broad.mit.edu	37	1	112524445	112524445	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:112524445G>A	ENST00000315987.2	-	2	1383	c.904C>T	c.(904-906)Cgc>Tgc	p.R302C	KCND3_ENST00000369697.1_Missense_Mutation_p.R302C|KCND3_ENST00000302127.4_Missense_Mutation_p.R302C	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	302					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TGGGAGTGGCGGGAAAACTTG	0.582																																						uc001ebu.1																			0				NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49						c.(904-906)Cgc>Tgc		Homo sapiens potassium voltage-gated channel, Shal-related subfamily, member 3 (KCND3), transcript variant 1, mRNA.							74.0	79.0	78.0					1																	112524445		2203	4300	6503	SO:0001583	missense	3752					sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding	g.chr1:112524445G>A	AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6239	protein-coding gene	gene with protein product		605411	"""spinocerebellar ataxia 22"", ""spinocerebellar ataxia 19"""	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.904C>T	1.37:g.112524445G>A	ENSP00000319591:p.Arg302Cys					KCND3_uc001ebv.1_Missense_Mutation_p.R302C	p.R302C	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	1	1384	-		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)	302					O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	c.904C>T	CCDS843.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.771691	0.69992	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.98792	-5.14;-5.14;-5.14	5.49	4.56	0.56223	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99542	0.9836	H	0.99156	4.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97649	1.0153	10	0.87932	D	0	.	15.2585	0.73603	0.0:0.0:0.8583:0.1417	.	302;302	Q14D71;Q9UK17	.;KCND3_HUMAN	C	302	ENSP00000358711:R302C;ENSP00000319591:R302C;ENSP00000306923:R302C	ENSP00000306923:R302C	R	-	1	0	KCND3	112325968	1.000000	0.71417	0.907000	0.35723	0.996000	0.88848	7.990000	0.88215	1.286000	0.44565	0.655000	0.94253	CGC		0.582	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198	
LOC645166	645166	broad.mit.edu	37	1	148933289	148933289	+	lincRNA	SNP	A	A	G	rs9729175	byFrequency	TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:148933289A>G	ENST00000539543.1	+	0	176					NR_027355.2																						TGCTGCCCGCAGGATATTGTG	0.562													.|||	630	0.125799	0.112	0.1282	5008	,	,		27649	0.1796		0.0656	False		,,,				2504	0.1493					uc010pbc.1																			0											c.e3-2		Homo sapiens lymphocyte-specific protein 1 pseudogene (LOC645166), transcript variant 2, non-coding RNA.																																						645166							g.chr1:148933289A>G																													1.37:g.148933289A>G						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Splice_Site								3		+									Splice_Site	SNP	ENST00000539543.1	37	c.236_splice																																																																																					0.562	RP11-14N7.2-201	KNOWN	basic	lincRNA	lincRNA			
FLG	2312	broad.mit.edu	37	1	152283656	152283656	+	Missense_Mutation	SNP	G	G	A	rs144184134	byFrequency	TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:152283656G>A	ENST00000368799.1	-	3	3741	c.3706C>T	c.(3706-3708)Cgt>Tgt	p.R1236C	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1236	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCATGGTGACGTGACCCTGAG	0.562									Ichthyosis				G|||	5	0.000998403	0.0008	0.0	5008	,	,		19690	0.0		0.0	False		,,,				2504	0.0041					uc001ezu.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(3706-3708)Cgt>Tgt		Homo sapiens filaggrin (FLG), mRNA.		G	CYS/ARG	9,4397	15.5+/-35.6	0,9,2194	307.0	294.0	298.0		3706	-0.9	0.0	1	dbSNP_134	298	0,8600		0,0,4300	yes	missense	FLG	NM_002016.1	180	0,9,6494	AA,AG,GG		0.0,0.2043,0.0692	probably-damaging	1236/4062	152283656	9,12997	2203	4300	6503	SO:0001583	missense	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152283656G>A	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3706C>T	1.37:g.152283656G>A	ENSP00000357789:p.Arg1236Cys					AK056431_uc001ezv.3_5'Flank	p.R1236C	NM_002016	NP_002007	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	3742	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		1236			Ser-rich.		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	c.3706C>T	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	3.110	-0.182817	0.06340	0.002043	0.0	ENSG00000143631	ENST00000368799	T	0.02446	4.29	1.64	-0.916	0.10489	.	.	.	.	.	T	0.01029	0.0034	M	0.66939	2.045	0.09310	N	1	D	0.58620	0.983	B	0.36186	0.219	T	0.49437	-0.8940	9	0.56958	D	0.05	.	2.991	0.05983	0.0:0.2995:0.3988:0.3017	.	1236	P20930	FILA_HUMAN	C	1236	ENSP00000357789:R1236C	ENSP00000357789:R1236C	R	-	1	0	FLG	150550280	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.397000	0.20883	0.714000	0.32081	0.186000	0.17326	CGT		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG2	388698	broad.mit.edu	37	1	152328935	152328935	+	Missense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:152328935C>T	ENST00000388718.5	-	3	1399	c.1327G>A	c.(1327-1329)Gaa>Aaa	p.E443K	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	443	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACATGTTGTTCGAACCCAGAG	0.448																																						uc001ezw.4																			0		p.F442L(1)|p.E443V(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188						c.(1327-1329)Gaa>Aaa		Homo sapiens filaggrin family member 2 (FLG2), mRNA.							168.0	160.0	163.0					1																	152328935		2203	4300	6503	SO:0001583	missense	388698						calcium ion binding|structural molecule activity	g.chr1:152328935C>T	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1327G>A	1.37:g.152328935C>T	ENSP00000373370:p.Glu443Lys					AK056431_uc001ezv.3_Intron	p.E443K	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	1400	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		443			Ser-rich.		Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	c.1327G>A	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	1.393	-0.580373	0.03854	.	.	ENSG00000143520	ENST00000388718	T	0.22134	1.97	2.88	-4.05	0.03998	.	.	.	.	.	T	0.01387	0.0045	N	0.04508	-0.205	0.09310	N	1	B	0.23058	0.079	B	0.06405	0.002	T	0.42832	-0.9428	9	0.06757	T	0.87	.	4.202	0.10471	0.0:0.2999:0.3321:0.368	.	443	Q5D862	FILA2_HUMAN	K	443	ENSP00000373370:E443K	ENSP00000373370:E443K	E	-	1	0	FLG2	150595559	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.008000	0.03663	-0.922000	0.03789	0.561000	0.74099	GAA		0.448	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
SMCP	4184	broad.mit.edu	37	1	152857174	152857174	+	Silent	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:152857174G>A	ENST00000368765.3	+	2	426	c.276G>A	c.(274-276)ccG>ccA	p.P92P		NM_030663.2	NP_109588.2	P49901	MCSP_HUMAN	sperm mitochondria-associated cysteine-rich protein	92					penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)		p.P92P(1)		breast(1)|cervix(1)|endometrium(1)|lung(4)|urinary_tract(1)	8	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAACTCACCGCAAACTCAGG	0.537																																						uc021ozk.1																			1	Substitution - coding silent(1)	p.P92P(2)|p.P92L(1)	urinary_tract(1)	breast(1)|cervix(1)|endometrium(1)|lung(4)|urinary_tract(1)	8						c.(274-276)ccG>ccA		Homo sapiens sperm mitochondria-associated cysteine-rich protein (SMCP), nuclear gene encoding mitochondrial protein, mRNA.							116.0	108.0	110.0					1																	152857174		2203	4300	6503	SO:0001819	synonymous_variant	4184				penetration of zona pellucida|sperm motility	mitochondrial membrane		g.chr1:152857174G>A	BC014593	CCDS1029.1	1q21.3	2009-03-19	2005-10-06	2005-10-06	ENSG00000163206	ENSG00000163206			6962	protein-coding gene	gene with protein product		601148	"""mitochondrial capsule selenoprotein"""	MCSP		8833144	Standard	NM_030663		Approved		uc001fat.3	P49901	OTTHUMG00000012452	ENST00000368765.3:c.276G>A	1.37:g.152857174G>A						SMCP_uc001fat.3_Silent_p.P92P	p.P92P	NM_030663	NP_109588	P49901	MCSP_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.171)		0	276	+	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		92					Q96A42	Silent	SNP	ENST00000368765.3	37	c.276G>A	CCDS1029.1																																																																																				0.537	SMCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034665.1	NM_030663	
USH2A	7399	broad.mit.edu	37	1	215799138	215799138	+	Silent	SNP	T	T	C			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:215799138T>C	ENST00000307340.3	-	72	15980	c.15594A>G	c.(15592-15594)acA>acG	p.T5198T	USH2A_ENST00000366943.2_Silent_p.T5222T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5198					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGTGGGTGTCTGTGAATGTGG	0.463										HNSCC(13;0.011)																												uc001hku.1																			0				NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(15592-15594)acA>acG		Homo sapiens Usher syndrome 2A (autosomal recessive, mild) (USH2A), transcript variant 2, mRNA.							362.0	287.0	313.0					1																	215799138		2203	4300	6503	SO:0001819	synonymous_variant	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:215799138T>C	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15594A>G	1.37:g.215799138T>C		HNSCC(13;0.011)					p.T5198T	NM_206933	NP_996816	O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	71	15981	-			5198					Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	c.15594A>G	CCDS31025.1																																																																																				0.463	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
RYR2	6262	broad.mit.edu	37	1	237806746	237806746	+	Splice_Site	SNP	A	A	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr1:237806746A>T	ENST00000366574.2	+	48	7658	c.7341A>T	c.(7339-7341)aaA>aaT	p.K2447N	RYR2_ENST00000360064.6_Splice_Site_p.K2445N|RYR2_ENST00000542537.1_Splice_Site_p.K2431N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2447	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CAATAGCCAAAGGTAAGGCCA	0.438																																						uc001hyl.1																			0				NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586						c.e48+1		Homo sapiens ryanodine receptor 2 (cardiac) (RYR2), mRNA.							138.0	131.0	134.0					1																	237806746		1925	4114	6039	SO:0001630	splice_region_variant	6262				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding	g.chr1:237806746A>T	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7342+1A>T	1.37:g.237806746A>T							p.D2448_splice	NM_001035	NP_001026	Q92736	RYR2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		48	7462	+	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	2448			4 X approximate repeats.		Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	c.7342_splice	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249801	0.80024	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96619	-4.07;-4.07;-4.07	5.27	4.14	0.48551	.	0.000000	0.64402	D	0.000003	D	0.97536	0.9193	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96794	0.9584	10	0.52906	T	0.07	.	8.6013	0.33747	0.8505:0.0:0.1495:0.0	.	2447	Q92736	RYR2_HUMAN	N	2447;2445;2431	ENSP00000355533:K2447N;ENSP00000353174:K2445N;ENSP00000443798:K2431N	ENSP00000353174:K2445N	K	+	3	2	RYR2	235873369	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.235000	0.65348	0.948000	0.37687	0.460000	0.39030	AAA		0.438	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Missense_Mutation
PCDH15	65217	broad.mit.edu	37	10	55944974	55944974	+	Missense_Mutation	SNP	C	C	T	rs61735473	byFrequency	TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr10:55944974C>T	ENST00000320301.6	-	12	1754	c.1360G>A	c.(1360-1362)Gtc>Atc	p.V454I	PCDH15_ENST00000361849.3_Missense_Mutation_p.V454I|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.V454I|PCDH15_ENST00000395433.1_Missense_Mutation_p.V432I|PCDH15_ENST00000373955.1_Missense_Mutation_p.V454I|PCDH15_ENST00000395432.2_Missense_Mutation_p.V417I|PCDH15_ENST00000373965.2_Missense_Mutation_p.V461I|PCDH15_ENST00000395430.1_Missense_Mutation_p.V454I|PCDH15_ENST00000395445.1_Missense_Mutation_p.V461I|PCDH15_ENST00000437009.1_Missense_Mutation_p.V454I|PCDH15_ENST00000409834.1_Missense_Mutation_p.V65I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Missense_Mutation_p.V454I|PCDH15_ENST00000373957.3_Missense_Mutation_p.V432I|PCDH15_ENST00000414778.1_Missense_Mutation_p.V459I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	454	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.V454I(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTCTGTGTGACGGTGAAGACT	0.393										HNSCC(58;0.16)			C|||	63	0.0125799	0.0469	0.0014	5008	,	,		16201	0.0		0.0	False		,,,				2504	0.0					uc010qhy.1																			1	Substitution - Missense(1)	p.V454I(1)	pancreas(1)	NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237						c.(1375-1377)Gtc>Atc		Homo sapiens protocadherin-related 15 (PCDH15), transcript variant A, mRNA.		C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	158,4248	107.3+/-145.7	5,148,2050	171.0	151.0	158.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1375,1360,1360,1360,1249,1294,1396,1360,1375,1360,1294,1360	2.5	0.1	10	dbSNP_129	158	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	29,29,29,29,29,29,29,29,29,29,29,29	5,149,6349	TT,TC,CC		0.0116,3.586,1.2225	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	459/1963,454/1958,454/1887,454/1953,417/1916,432/1936,466/1791,454/1540,459/1683,454/1678,432/1933,454/1956	55944974	159,12847	2203	4300	6503	SO:0001583	missense	65217				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding	g.chr10:55944974C>T	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1360G>A	10.37:g.55944974C>T	ENSP00000322604:p.Val454Ile	HNSCC(58;0.16)				PCDH15_uc010qhq.2_Missense_Mutation_p.V459I|PCDH15_uc010qhr.2_Missense_Mutation_p.V454I|PCDH15_uc021pqv.1_Missense_Mutation_p.V454I|PCDH15_uc021pqw.1_Missense_Mutation_p.V466I|PCDH15_uc010qht.2_Missense_Mutation_p.V461I|PCDH15_uc021pqx.1_Missense_Mutation_p.V454I|PCDH15_uc001jjv.1_Missense_Mutation_p.V432I|PCDH15_uc021pqy.1_Missense_Mutation_p.V454I|PCDH15_uc021pqz.1_Missense_Mutation_p.V432I|PCDH15_uc010qhv.1_Missense_Mutation_p.V454I|PCDH15_uc010qhw.1_Missense_Mutation_p.V417I|PCDH15_uc010qhx.1_Missense_Mutation_p.V454I|PCDH15_uc010qhz.1_Missense_Mutation_p.V454I|PCDH15_uc010qia.1_Missense_Mutation_p.V432I|PCDH15_uc001jju.1_Missense_Mutation_p.V454I|PCDH15_uc010qib.1_Missense_Mutation_p.V432I|PCDH15_uc001jjw.3_Missense_Mutation_p.V454I	p.V459I	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN			12	1770	-		Melanoma(3;0.117)|Lung SC(717;0.238)	454			Cadherin 4.		A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	c.1375G>A	CCDS7248.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	C	3.054	-0.194630	0.06259	0.03586	1.16E-4	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60672	0.47;1.1;1.1;0.17;0.47;1.1;1.1;1.1;1.1;1.1;1.1;1.1;1.1;1.1	5.29	2.45	0.29901	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.13243	0.0321	L	0.49350	1.555	0.34867	D	0.743217	B;B;B;B;P;B;B;B;B;B;B;B;B;B;B	0.49358	0.302;0.302;0.195;0.195;0.923;0.302;0.302;0.033;0.05;0.101;0.115;0.115;0.011;0.115;0.195	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.42738	0.113;0.177;0.103;0.079;0.396;0.177;0.113;0.02;0.012;0.017;0.055;0.044;0.007;0.044;0.103	T	0.40701	-0.9549	9	0.27082	T	0.32	.	10.0916	0.42449	0.0:0.7752:0.0:0.2248	.	432;454;454;459;454;417;454;454;461;461;454;459;454;432;454	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	I	461;459;454;454;65;461;454;417;454;432;432;454;454;459;454;454	ENSP00000363076:V461I;ENSP00000410304:V459I;ENSP00000378826:V454I;ENSP00000386693:V65I;ENSP00000378832:V461I;ENSP00000378833:V454I;ENSP00000378820:V417I;ENSP00000354950:V454I;ENSP00000378821:V432I;ENSP00000363068:V432I;ENSP00000322604:V454I;ENSP00000378818:V454I;ENSP00000412628:V454I;ENSP00000363066:V454I	ENSP00000322604:V454I	V	-	1	0	PCDH15	55614980	0.889000	0.30405	0.053000	0.19242	0.791000	0.44710	1.599000	0.36751	0.329000	0.23460	-0.229000	0.12294	GTC		0.393	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
CFAP43	80217	broad.mit.edu	37	10	105928529	105928529	+	Silent	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr10:105928529C>T	ENST00000278064.2	-	21	2782	c.2457G>A	c.(2455-2457)tcG>tcA	p.S819S	WDR96_ENST00000357060.3_Silent_p.S888S|WDR96_ENST00000428666.1_Silent_p.S889S																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TCACAGCCATCGAATTCCAAC	0.373																																						uc001kxw.3																			0				NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						c.(2662-2664)tcG>tcA		Homo sapiens WD repeat domain 96 (WDR96), mRNA.							153.0	143.0	146.0					10																	105928529		2203	4300	6503	SO:0001819	synonymous_variant	80217							g.chr10:105928529C>T																												ENST00000278064.2:c.2457G>A	10.37:g.105928529C>T						WDR96_uc009xxq.3_Silent_p.S196S|WDR96_uc001kxx.4_Silent_p.S889S	p.S888S	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN			20	2780	-			888						Silent	SNP	ENST00000278064.2	37	c.2664G>A		.	.	.	.	.	.	.	.	.	.	C	0.022	-1.412046	0.01145	.	.	ENSG00000197748	ENST00000434629	.	.	.	5.43	-10.9	0.00192	.	.	.	.	.	T	0.42177	0.1191	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53563	-0.8421	4	.	.	.	.	5.9935	0.19480	0.1109:0.0854:0.3988:0.4048	.	.	.	.	Q	249	.	.	R	-	2	0	WDR96	105918519	0.003000	0.15002	0.029000	0.17559	0.057000	0.15508	-2.276000	0.01161	-3.142000	0.00233	-2.629000	0.00154	CGA		0.373	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1		
ADRB1	153	broad.mit.edu	37	10	115804336	115804336	+	Silent	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr10:115804336C>T	ENST00000369295.2	+	1	531	c.445C>T	c.(445-447)Ctg>Ttg	p.L149L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	149					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	CATCGAGACCCTGTGTGTCAT	0.682																																						uc001lba.3																			0				large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6						c.(445-447)Ctg>Ttg		Homo sapiens adrenergic, beta-1-, receptor (ADRB1), mRNA.	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Arbutamine(DB01102)|Atenolol(DB00335)|Betaxolol(DB00195)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Desipramine(DB01151)|Dobutamine(DB00841)|Dopamine(DB00988)|Epinephrine(DB00668)|Esmolol(DB00187)|Isoetharine(DB00221)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Metoprolol(DB00264)|Nadolol(DB01203)|Norepinephrine(DB00368)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Practolol(DB01297)|Propranolol(DB00571)|Risperidone(DB00734)|Timolol(DB00373)|Ziprasidone(DB00246)						100.0	110.0	107.0					10																	115804336		2203	4300	6503	SO:0001819	synonymous_variant	153				positive regulation of cAMP biosynthetic process	integral to plasma membrane	alpha-2A adrenergic receptor binding|beta1-adrenergic receptor activity|protein heterodimerization activity	g.chr10:115804336C>T	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.445C>T	10.37:g.115804336C>T							p.L149L	NM_000684	NP_000675	P08588	ADRB1_HUMAN		Epithelial(162;0.0124)|all cancers(201;0.0298)	0	531	+		Colorectal(252;0.172)|Breast(234;0.188)	149					B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	c.445C>T	CCDS7586.1																																																																																				0.682	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
CD6	923	broad.mit.edu	37	11	60780934	60780934	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr11:60780934G>A	ENST00000313421.7	+	7	1376	c.1190G>A	c.(1189-1191)cGg>cAg	p.R397Q	CD6_ENST00000545105.1_3'UTR|CD6_ENST00000346437.4_Missense_Mutation_p.R397Q|CD6_ENST00000344028.5_Missense_Mutation_p.R397Q|CD6_ENST00000352009.5_Missense_Mutation_p.R397Q|CD6_ENST00000452451.2_Missense_Mutation_p.R397Q	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	397					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						AAGGAATCTCGGGAGCTAATG	0.443																																					Pancreas(169;904 2017 4767 38890 42505)	uc001nqq.3																			0				endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						c.(1189-1191)cGg>cAg		Homo sapiens CD6 molecule (CD6), transcript variant 1, mRNA.							193.0	195.0	195.0					11																	60780934		2203	4299	6502	SO:0001583	missense	923				cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity	g.chr11:60780934G>A		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1190G>A	11.37:g.60780934G>A	ENSP00000323280:p.Arg397Gln					CD6_uc009yni.3_Missense_Mutation_p.R296Q|CD6_uc009ynj.3_Missense_Mutation_p.R274Q|CD6_uc001nqp.3_Missense_Mutation_p.R397Q|CD6_uc001nqs.3_Non-coding_Transcript|CD6_uc001nqr.3_Missense_Mutation_p.R397Q|CD6_uc001nqt.3_Missense_Mutation_p.R397Q	p.R397Q	NM_006725	NP_006716	P30203	CD6_HUMAN			6	1415	+			397					A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	c.1190G>A	CCDS7999.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.248|7.248	0.602669|0.602669	0.13939|0.13939	.|.	.|.	ENSG00000013725|ENSG00000013725	ENST00000538611|ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	.|T;T;T;T;T;T;T	.|0.01422	.|5.03;5.01;4.91;4.94;5.13;4.92;5.02	5.33|5.33	-1.79|-1.79	0.07932|0.07932	.|.	.|1.186040	.|0.06402	.|N	.|0.718920	T|T	0.01029|0.01029	0.0034|0.0034	L|L	0.39397|0.39397	1.21|1.21	0.09310|0.09310	N|N	1|1	.|P;B;B;B;B	.|0.45283	.|0.855;0.341;0.179;0.277;0.231	.|B;B;B;B;B	.|0.30782	.|0.12;0.024;0.024;0.026;0.013	T|T	0.50171|0.50171	-0.8859|-0.8859	5|10	.|0.13108	.|T	.|0.6	.|.	5.1186|5.1186	0.14849|0.14849	0.4143:0.0:0.4519:0.1337|0.4143:0.0:0.4519:0.1337	.|.	.|296;397;397;397;397	.|E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.|.;.;.;CD6_HUMAN;.	R|Q	140|397;397;397;274;296;397;397	.|ENSP00000344108:R397Q;ENSP00000345566:R397Q;ENSP00000323280:R397Q;ENSP00000440055:R274Q;ENSP00000410638:R296Q;ENSP00000390676:R397Q;ENSP00000340628:R397Q	.|ENSP00000323280:R397Q	G|R	+|+	1|2	0|0	CD6|CD6	60537510|60537510	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.012000|0.012000	0.07955|0.07955	-1.650000|-1.650000	0.01991|0.01991	-0.634000|-0.634000	0.05538|0.05538	-0.857000|-0.857000	0.03018|0.03018	GGG|CGG		0.443	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
PPP2R5B	5526	broad.mit.edu	37	11	64695622	64695622	+	Missense_Mutation	SNP	G	G	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr11:64695622G>T	ENST00000164133.2	+	5	1205	c.583G>T	c.(583-585)Gtc>Ttc	p.V195F		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	195					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						TCAAAAGTTTGTCCTGATGGT	0.582																																						uc001obz.3																			0				central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						c.(583-585)Gtc>Ttc		Homo sapiens protein phosphatase 2, regulatory subunit B', beta (PPP2R5B), mRNA.							107.0	103.0	104.0					11																	64695622		2201	4297	6498	SO:0001583	missense	5526				signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity	g.chr11:64695622G>T	L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9310	protein-coding gene	gene with protein product	"""PP2A, B subunit, B' beta isoform"", ""PP2A, B subunit, B56 beta isoform"", ""PP2A, B subunit, PR61 beta isoform"", ""PP2A, B subunit, R5 beta isoform"", ""serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"""	601644	"""protein phosphatase 2, regulatory subunit B (B56), beta isoform"", ""protein phosphatase 2, regulatory subunit B', beta isoform"""			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.583G>T	11.37:g.64695622G>T	ENSP00000164133:p.Val195Phe					PPP2R5B_uc001oby.3_Missense_Mutation_p.V195F	p.V195F	NM_006244	NP_006235	Q15173	2A5B_HUMAN			3	876	+			195					Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	c.583G>T	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.613186	0.87359	.	.	ENSG00000068971	ENST00000164133;ENST00000359279;ENST00000532850;ENST00000527441	.	.	.	3.56	3.56	0.40772	Armadillo-type fold (1);	0.146450	0.44285	D	0.000479	T	0.80793	0.4691	M	0.88979	2.995	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.84336	0.0524	8	.	.	.	-7.1572	13.5415	0.61676	0.0:0.0:1.0:0.0	.	195	Q15173	2A5B_HUMAN	F	195;222;109;195	.	.	V	+	1	0	PPP2R5B	64452198	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.137000	0.94496	2.322000	0.78497	0.549000	0.68633	GTC		0.582	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244	
SNX32	254122	broad.mit.edu	37	11	65617743	65617744	+	Splice_Site	INS	-	-	T	rs375818666		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr11:65617743_65617744insT	ENST00000308342.6	+	4	799		c.e4+1			NM_152760.2	NP_689973.2	Q86XE0	SNX32_HUMAN	sorting nexin 32						intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				READ - Rectum adenocarcinoma(159;0.171)		AGCTGGAAGCGTGAGTGCCCCC	0.554																																						uc001ofr.3																			0				endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						c.e4+1		Homo sapiens sorting nexin 32 (SNX32), mRNA.																																				SO:0001630	splice_region_variant	254122				cell communication|protein transport		phosphatidylinositol binding	g.chr11:65617743_65617744insT	AK055496	CCDS8113.2	11q13.1	2008-03-11	2008-03-11	2008-03-11	ENSG00000172803	ENSG00000172803		"""Sorting nexins"""	26423	protein-coding gene	gene with protein product			"""sorting nexin 6B"""	SNX6B		16782399	Standard	XM_005273871		Approved	FLJ30934	uc001ofr.3	Q86XE0	OTTHUMG00000128491	ENST00000308342.6:c.374+1->T	11.37:g.65617744_65617744dupT						SNX32_uc010rop.1_3'UTR	p.A125_splice	NM_152760	NP_689973	Q86XE0	SNX32_HUMAN		READ - Rectum adenocarcinoma(159;0.171)	4	501	+			125			PX.		Q8IW53|Q96NG4	Splice_Site	INS	ENST00000308342.6	37	c.374_splice	CCDS8113.2																																																																																				0.554	SNX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250295.3	NM_152760	Intron
CABP4	57010	broad.mit.edu	37	11	67222962	67222962	+	Missense_Mutation	SNP	C	C	T	rs371921931		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr11:67222962C>T	ENST00000325656.5	+	1	145	c.68C>T	c.(67-69)gCg>gTg	p.A23V	CABP4_ENST00000542025.2_3'UTR|CABP4_ENST00000438189.2_Intron|GPR152_ENST00000312457.2_5'Flank	NM_145200.3	NP_660201.1	P57796	CABP4_HUMAN	calcium binding protein 4	23					photoreceptor cell morphogenesis (GO:0008594)|phototransduction (GO:0007602)|retinal bipolar neuron differentiation (GO:0060040)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytosol (GO:0005829)|extracellular region (GO:0005576)|synapse (GO:0045202)|terminal bouton (GO:0043195)	calcium ion binding (GO:0005509)			central_nervous_system(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)	11			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			AAGCCCCCTGCGGGGGTTGTG	0.632																																						uc001olo.3																			0				central_nervous_system(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)	11						c.(67-69)gCg>gTg		Homo sapiens calcium binding protein 4 (CABP4), mRNA.		C	VAL/ALA	0,4354		0,0,2177	10.0	13.0	12.0		68	-4.7	0.0	11		12	1,8501		0,1,4250	no	missense	CABP4	NM_145200.3	64	0,1,6427	TT,TC,CC		0.0118,0.0,0.0078	benign	23/276	67222962	1,12855	2177	4251	6428	SO:0001583	missense	57010				visual perception	cytoplasm|extracellular region|terminal button	calcium ion binding	g.chr11:67222962C>T	AC005849	CCDS8166.1, CCDS73333.1	11q13.2	2013-09-20			ENSG00000175544	ENSG00000175544		"""EF-hand domain containing"""	1386	protein-coding gene	gene with protein product		608965				10625670, 16960802	Standard	NM_145200		Approved	CSNB2B	uc001olo.3	P57796	OTTHUMG00000168033	ENST00000325656.5:c.68C>T	11.37:g.67222962C>T	ENSP00000324960:p.Ala23Val					GPR152_uc001olm.3_5'Flank|CABP4_uc001oln.3_Intron	p.A23V	NM_145200	NP_660201	P57796	CABP4_HUMAN	BRCA - Breast invasive adenocarcinoma(15;8.18e-06)		0	145	+			23					Q8N4Z2|Q8WWY5	Missense_Mutation	SNP	ENST00000325656.5	37	c.68C>T	CCDS8166.1	.	.	.	.	.	.	.	.	.	.	C	7.173	0.587989	0.13812	0.0	1.18E-4	ENSG00000175544	ENST00000325656	T	0.66995	-0.24	4.62	-4.66	0.03329	.	1.907910	0.02844	N	0.128297	T	0.32793	0.0841	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17992	-1.0351	10	0.14252	T	0.57	-0.7757	3.4879	0.07626	0.4265:0.2544:0.0:0.3191	.	23	P57796	CABP4_HUMAN	V	23	ENSP00000324960:A23V	ENSP00000324960:A23V	A	+	2	0	CABP4	66979538	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.976000	0.03786	-1.092000	0.03062	0.436000	0.28706	GCG		0.632	CABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397624.2		
AMOTL1	154810	broad.mit.edu	37	11	94554698	94554698	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr11:94554698G>A	ENST00000433060.2	+	4	1265	c.1124G>A	c.(1123-1125)cGc>cAc	p.R375H	AMOTL1_ENST00000317837.9_Missense_Mutation_p.R375H|AMOTL1_ENST00000539727.1_3'UTR|AMOTL1_ENST00000317829.8_Missense_Mutation_p.R325H	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	375					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CCTTGCAGCCGCCCATGCCAA	0.602																																						uc001pfb.3																			0				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36						c.(1123-1125)cGc>cAc		Homo sapiens angiomotin like 1 (AMOTL1), mRNA.							27.0	33.0	31.0					11																	94554698		2144	4244	6388	SO:0001583	missense	154810					cytoplasm|tight junction	identical protein binding	g.chr11:94554698G>A	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1124G>A	11.37:g.94554698G>A	ENSP00000387739:p.Arg375His					AMOTL1_uc001pfc.3_Missense_Mutation_p.R325H	p.R375H	NM_130847	NP_570899	Q8IY63	AMOL1_HUMAN			3	1294	+		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)	375					Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	c.1124G>A	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.913356	0.52439	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000317837;ENST00000433060	T;T;T	0.13089	2.62;2.62;2.62	5.68	5.68	0.88126	.	0.076575	0.56097	D	0.000032	T	0.33789	0.0875	M	0.66939	2.045	0.51482	D	0.999926	D;D	0.76494	0.999;0.996	D;P	0.65323	0.934;0.67	T	0.02813	-1.1107	10	0.13853	T	0.58	-25.1937	19.7951	0.96477	0.0:0.0:1.0:0.0	.	325;375	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	H	325;381;375;375	ENSP00000320968:R325H;ENSP00000323474:R375H;ENSP00000387739:R375H	ENSP00000320968:R325H	R	+	2	0	AMOTL1	94194346	1.000000	0.71417	1.000000	0.80357	0.607000	0.37147	5.190000	0.65104	2.698000	0.92095	0.561000	0.74099	CGC		0.602	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
IL26	55801	broad.mit.edu	37	12	68619233	68619233	+	Missense_Mutation	SNP	C	C	G			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr12:68619233C>G	ENST00000229134.4	-	2	283	c.219G>C	c.(217-219)aaG>aaC	p.K73N	IFNG-AS1_ENST00000536914.1_RNA	NM_018402.1	NP_060872.1	Q9NPH9	IL26_HUMAN	interleukin 26	73					cell-cell signaling (GO:0007267)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000515)		CCATAAACTGCTTTTTTGTTT	0.274																																						uc001stx.1																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	12						c.(217-219)aaG>aaC		Homo sapiens interleukin 26 (IL26), mRNA.							46.0	49.0	48.0					12																	68619233		2192	4297	6489	SO:0001583	missense	55801				cell-cell signaling|negative regulation of epithelial cell proliferation|positive regulation of cytokine secretion|positive regulation of ERK1 and ERK2 cascade|positive regulation of JAK-STAT cascade|positive regulation of protein kinase B signaling cascade|positive regulation of stress-activated MAPK cascade|positive regulation of transcription from RNA polymerase II promoter	cytosol|extracellular space|soluble fraction	cytokine activity	g.chr12:68619233C>G	AJ251549	CCDS8981.1	12q15	2008-08-04			ENSG00000111536	ENSG00000111536		"""Interleukins and interleukin receptors"""	17119	protein-coding gene	gene with protein product		605679				10729163, 11528524	Standard	NM_018402		Approved	AK155, IL-26	uc001stx.1	Q9NPH9	OTTHUMG00000169114	ENST00000229134.4:c.219G>C	12.37:g.68619233C>G	ENSP00000229134:p.Lys73Asn						p.K73N	NM_018402	NP_060872	Q9NPH9	IL26_HUMAN	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000515)	1	254	-			73						Missense_Mutation	SNP	ENST00000229134.4	37	c.219G>C	CCDS8981.1	.	.	.	.	.	.	.	.	.	.	C	5.762	0.324968	0.10900	.	.	ENSG00000111536	ENST00000229134	T	0.76839	-1.05	5.08	-0.475	0.12104	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.510935	0.19110	N	0.122472	T	0.54255	0.1847	N	0.19112	0.55	0.25392	N	0.98852	B	0.10296	0.003	B	0.10450	0.005	T	0.27640	-1.0068	9	.	.	.	-18.257	3.0652	0.06212	0.1284:0.4677:0.2506:0.1533	.	73	Q9NPH9	IL26_HUMAN	N	73	ENSP00000229134:K73N	.	K	-	3	2	IL26	66905500	0.968000	0.33430	0.443000	0.26883	0.641000	0.38312	0.780000	0.26760	0.003000	0.14656	0.462000	0.41574	AAG		0.274	IL26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402302.1	NM_018402	
RCBTB1	55213	broad.mit.edu	37	13	50140816	50140816	+	Missense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr13:50140816C>T	ENST00000378302.2	-	4	475	c.215G>A	c.(214-216)tGt>tAt	p.C72Y	RCBTB1_ENST00000546015.1_Missense_Mutation_p.C72Y|RCBTB1_ENST00000258646.3_Missense_Mutation_p.C72Y	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	72					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		CTTCTTTCCACATAAGCCTTC	0.408																																						uc001vde.1																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16						c.(214-216)tGt>tAt		Homo sapiens regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1 (RCBTB1), mRNA.							151.0	139.0	143.0					13																	50140816		2203	4300	6503	SO:0001583	missense	55213				cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus		g.chr13:50140816C>T	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.215G>A	13.37:g.50140816C>T	ENSP00000367552:p.Cys72Tyr						p.C72Y	NM_018191	NP_060661	Q8NDN9	RCBT1_HUMAN	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)	3	476	-		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	72					Q8IY29|Q969U9	Missense_Mutation	SNP	ENST00000378302.2	37	c.215G>A	CCDS9418.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294497	0.40594	.	.	ENSG00000136144	ENST00000258646;ENST00000378302;ENST00000546015	D;D;D	0.84589	-1.87;-1.87;-1.87	5.61	4.77	0.60923	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.165139	0.64402	D	0.000002	D	0.90170	0.6928	M	0.69358	2.11	0.33739	D	0.619167	D	0.53151	0.958	P	0.56398	0.797	D	0.93175	0.6569	10	0.59425	D	0.04	-10.5236	18.6055	0.91264	0.0:0.7775:0.2224:0.0	.	72	Q8NDN9	RCBT1_HUMAN	Y	72	ENSP00000258646:C72Y;ENSP00000367552:C72Y;ENSP00000443293:C72Y	ENSP00000258646:C72Y	C	-	2	0	RCBTB1	49038817	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.744000	0.55112	0.849000	0.35215	-1.273000	0.01405	TGT		0.408	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
ABCC4	10257	broad.mit.edu	37	13	95715080	95715080	+	Missense_Mutation	SNP	T	T	C			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr13:95715080T>C	ENST00000376887.4	-	26	3358	c.3244A>G	c.(3244-3246)Agt>Ggt	p.S1082G	ABCC4_ENST00000412704.1_Missense_Mutation_p.S1035G	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1082	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	ATGAGGGAACTTTTTCCAGCT	0.398																																						uc001vmd.4																			0				breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						c.(3244-3246)Agt>Ggt		Homo sapiens ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), transcript variant 1, mRNA.	Cefazolin(DB01327)						73.0	74.0	74.0					13																	95715080		2203	4300	6503	SO:0001583	missense	10257				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity	g.chr13:95715080T>C	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3244A>G	13.37:g.95715080T>C	ENSP00000366084:p.Ser1082Gly					ABCC4_uc010afj.3_5'UTR|ABCC4_uc010afk.3_Missense_Mutation_p.S1035G	p.S1082G	NM_005845	NP_005836	O15439	MRP4_HUMAN			25	3363	-	all_neural(89;0.0878)|Medulloblastoma(90;0.163)		1082			ABC transporter 2.		A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	37	c.3244A>G	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.751734	0.69533	.	.	ENSG00000125257	ENST00000412704;ENST00000376887	D;D	0.97831	-4.56;-4.56	6.14	6.14	0.99180	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98261	0.9424	H	0.99074	4.42	0.80722	D	1	B;P	0.38048	0.38;0.616	B;B	0.26517	0.042;0.07	D	0.98194	1.0464	10	0.87932	D	0	.	16.7723	0.85541	0.0:0.0:0.0:1.0	.	1035;1082	O15439-2;O15439	.;MRP4_HUMAN	G	1035;1082	ENSP00000388657:S1035G;ENSP00000366084:S1082G	ENSP00000366084:S1082G	S	-	1	0	ABCC4	94513081	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.690000	0.84178	2.360000	0.80028	0.519000	0.50382	AGT		0.398	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
POTEM	641455	broad.mit.edu	37	14	20010235	20010235	+	Missense_Mutation	SNP	A	A	G	rs113380635		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr14:20010235A>G	ENST00000551509.1	-	5	974	c.923T>C	c.(922-924)gTt>gCt	p.V308A	RP11-244H18.1_ENST00000547584.1_lincRNA|RNU6-1268P_ENST00000391214.1_RNA	NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	308										endometrium(4)|kidney(1)|lung(4)	9						AAGTATGAGAACAGTTCTAAA	0.368																																						uc001vwc.3																			0				endometrium(4)|kidney(1)|lung(4)	9						c.(922-924)gTt>gCt		Homo sapiens POTE ankyrin domain family, member M (POTEM), mRNA.							42.0	37.0	39.0					14																	20010235		365	763	1128	SO:0001583	missense	641455							g.chr14:20010235A>G		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.923T>C	14.37:g.20010235A>G	ENSP00000452296:p.Val308Ala					POTEM_uc001vwb.3_Non-coding_Transcript|P712P_uc001vwd.3_Non-coding_Transcript	p.V308A	NM_001145442	NP_001138914	A6NI47	POTEM_HUMAN			4	975	-			308						Missense_Mutation	SNP	ENST00000551509.1	37	c.923T>C	CCDS45076.1	.	.	.	.	.	.	.	.	.	.	g	5.617	0.298596	0.10622	.	.	ENSG00000187537	ENST00000551509;ENST00000439503;ENST00000344684	T	0.60040	0.22	0.906	0.906	0.19314	Ankyrin repeat-containing domain (4);	0.000000	0.32655	N	0.005811	T	0.10723	0.0262	N	0.00039	-2.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	8	.	.	.	.	3.4158	0.07375	0.2955:0.0:0.7045:0.0	.	308	A6NI47	POTEM_HUMAN	A	308;393;308	ENSP00000452296:V308A	.	V	-	2	0	POTEM	19080235	0.621000	0.27077	0.813000	0.32504	0.042000	0.13812	0.922000	0.28734	-0.020000	0.14032	-1.160000	0.01791	GTT		0.368	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442	
RYR3	6263	broad.mit.edu	37	15	33873724	33873724	+	Missense_Mutation	SNP	G	G	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr15:33873724G>T	ENST00000389232.4	+	14	1523	c.1453G>T	c.(1453-1455)Gtc>Ttc	p.V485F	RYR3_ENST00000415757.3_Missense_Mutation_p.V485F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	485					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GTTGGCCCTTGTCTTAAATTG	0.438																																						uc001zhi.3																			0				NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311						c.(1453-1455)Gtc>Ttc		Homo sapiens ryanodine receptor 3 (RYR3), transcript variant 1, mRNA.							133.0	132.0	132.0					15																	33873724		1927	4146	6073	SO:0001583	missense	6263				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr15:33873724G>T		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.1453G>T	15.37:g.33873724G>T	ENSP00000373884:p.Val485Phe					RYR3_uc010bar.3_Missense_Mutation_p.V485F	p.V485F	NM_001036	NP_001027	Q15413	RYR3_HUMAN		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	13	1523	+		all_lung(180;7.18e-09)	485					O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	c.1453G>T	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725196	0.68959	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.97752	-4.52;-4.52	5.51	5.51	0.81932	Intracellular calcium-release channel (1);	0.180388	0.37530	N	0.002058	D	0.98330	0.9446	M	0.83953	2.67	0.47949	D	0.999555	D;D	0.56746	0.977;0.968	P;P	0.53450	0.656;0.726	D	0.99285	1.0897	10	0.87932	D	0	.	19.4206	0.94720	0.0:0.0:1.0:0.0	.	485;485	Q15413-2;Q15413	.;RYR3_HUMAN	F	485	ENSP00000373884:V485F;ENSP00000399610:V485F	ENSP00000354735:V485F	V	+	1	0	RYR3	31661016	1.000000	0.71417	0.852000	0.33557	0.992000	0.81027	3.924000	0.56476	2.582000	0.87167	0.563000	0.77884	GTC		0.438	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
SLTM	79811	broad.mit.edu	37	15	59181723	59181723	+	Missense_Mutation	SNP	G	G	C			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr15:59181723G>C	ENST00000380516.2	-	16	2197	c.2110C>G	c.(2110-2112)Cga>Gga	p.R704G	AC025918.2_ENST00000452467.1_RNA|SLTM_ENST00000536328.1_Missense_Mutation_p.R273G	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	704	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TCTCTTTCTCGAGCAATCCGT	0.413																																						uc002afp.3																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(2110-2112)Cga>Gga		Homo sapiens SAFB-like, transcription modulator (SLTM), transcript variant 1, mRNA.							239.0	197.0	211.0					15																	59181723		2192	4292	6484	SO:0001583	missense	79811				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding	g.chr15:59181723G>C	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.2110C>G	15.37:g.59181723G>C	ENSP00000369887:p.Arg704Gly					SLTM_uc002afn.3_Missense_Mutation_p.R246G|SLTM_uc002afo.3_Missense_Mutation_p.R686G|SLTM_uc002afq.3_Missense_Mutation_p.R273G|SLTM_uc010bgd.3_Missense_Mutation_p.R273G	p.R704G	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN			15	2198	-			704			Arg/Glu-rich.		A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	37	c.2110C>G	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204693	0.58234	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328	T	0.22134	1.97	5.62	4.69	0.59074	.	0.000000	0.45126	D	0.000390	T	0.45478	0.1344	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.43589	-0.9382	10	0.52906	T	0.07	.	15.8756	0.79159	0.0:0.0:0.8634:0.1366	.	704;273	Q9NWH9;A8K5V8	SLTM_HUMAN;.	G	704;270;273	ENSP00000369887:R704G	ENSP00000369887:R704G	R	-	1	2	SLTM	56969015	1.000000	0.71417	0.986000	0.45419	0.976000	0.68499	6.080000	0.71299	1.356000	0.45884	0.655000	0.94253	CGA		0.413	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755	
CYP1A2	1544	broad.mit.edu	37	15	75042328	75042328	+	Silent	SNP	G	G	A	rs17861153	byFrequency	TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr15:75042328G>A	ENST00000343932.4	+	2	312	c.249G>A	c.(247-249)acG>acA	p.T83T		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	83			T -> M (in allele CYP1A2*9). {ECO:0000269|PubMed:14563787}.		alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.T83T(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	TTGGCTCCACGCCCGTGCTGG	0.667																																						uc002ayr.1																			1	Substitution - coding silent(1)	p.T83T(2)	kidney(1)	breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33						c.(247-249)acG>acA		Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2 (CYP1A2), mRNA.	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315)	G		2,4392	4.2+/-10.8	0,2,2195	51.0	46.0	47.0		249	-9.9	0.0	15	dbSNP_123	47	13,8579	9.8+/-36.6	0,13,4283	no	coding-synonymous	CYP1A2	NM_000761.3		0,15,6478	AA,AG,GG		0.1513,0.0455,0.1155		83/517	75042328	15,12971	2197	4296	6493	SO:0001819	synonymous_variant	1544				alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding	g.chr15:75042328G>A	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.249G>A	15.37:g.75042328G>A							p.T83T	NM_000761	NP_000752	P05177	CP1A2_HUMAN			1	313	+			83		T -> M (in allele CYP1A2*9).			Q16754|Q6NWU5|Q9BXX7|Q9UK49	Silent	SNP	ENST00000343932.4	37	c.249G>A	CCDS32293.1																																																																																				0.667	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
IL4R	3566	broad.mit.edu	37	16	27374339	27374339	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr16:27374339C>T	ENST00000395762.2	+	11	1925	c.1666C>T	c.(1666-1668)Cga>Tga	p.R556*	IL4R_ENST00000380922.3_Nonsense_Mutation_p.R541*|IL4R_ENST00000170630.2_Nonsense_Mutation_p.R556*|IL4R_ENST00000543915.2_Nonsense_Mutation_p.R556*	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	556	Required for IRS1 activation and IL4- induced cell growth.				defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GATCCTCCGCCGAAATGTCCT	0.637																																						uc002don.3																			0				breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						c.(1666-1668)Cga>Tga		Homo sapiens interleukin 4 receptor (IL4R), transcript variant 1, mRNA.							29.0	33.0	31.0					16																	27374339		2196	4300	6496	SO:0001587	stop_gained	3566				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity	g.chr16:27374339C>T	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1666C>T	16.37:g.27374339C>T	ENSP00000379111:p.Arg556*					IL4R_uc002dop.4_Nonsense_Mutation_p.R541*|IL4R_uc010bxy.3_Nonsense_Mutation_p.R556*|IL4R_uc002doo.3_Nonsense_Mutation_p.R396*	p.R556*	NM_000418	NP_000409	P24394	IL4RA_HUMAN			10	1908	+			556			Required for IRS1 activation and IL4- induced cell growth.		B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Nonsense_Mutation	SNP	ENST00000395762.2	37	c.1666C>T	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	C	37	6.259888	0.97421	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	.	.	.	5.16	3.14	0.36123	.	6.252000	0.00166	N	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-6.6276	6.1989	0.20565	0.1908:0.7127:0.0:0.0965	.	.	.	.	X	556;556;541;556	.	ENSP00000170630:R556X	R	+	1	2	IL4R	27281840	0.010000	0.17322	0.005000	0.12908	0.109000	0.19521	1.471000	0.35365	0.532000	0.28657	0.555000	0.69702	CGA		0.637	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
IRX6	79190	broad.mit.edu	37	16	55361572	55361572	+	Missense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr16:55361572C>T	ENST00000290552.7	+	4	1820	c.488C>T	c.(487-489)gCc>gTc	p.A163V	IRX6_ENST00000558315.1_3'UTR|RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	163					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						ACACTCAAGGCCTGGCTCAAC	0.592																																						uc002ehy.3																			0				breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						c.(487-489)gCc>gTc		Homo sapiens iroquois homeobox 6 (IRX6), mRNA.							111.0	84.0	93.0					16																	55361572		2198	4300	6498	SO:0001583	missense	79190					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr16:55361572C>T	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"""Homeoboxes / TALE class"""	14675	protein-coding gene	gene with protein product		606196	"""iroquois homeobox protein 7"", ""iroquois homeobox protein 6"""	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.488C>T	16.37:g.55361572C>T	ENSP00000290552:p.Ala163Val					IRX6_uc002ehx.3_Missense_Mutation_p.A163V|IRX6_uc010ccb.1_Non-coding_Transcript	p.A163V	NM_024335	NP_077311	P78412	IRX6_HUMAN			3	1021	+			163					B2RN06|Q7Z2K0	Missense_Mutation	SNP	ENST00000290552.7	37	c.488C>T	CCDS32449.1	.	.	.	.	.	.	.	.	.	.	C	36	5.947897	0.97134	.	.	ENSG00000159387	ENST00000290552	D	0.84660	-1.88	5.97	5.97	0.96955	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.053328	0.85682	D	0.000000	D	0.92084	0.7491	M	0.85542	2.76	0.80722	D	1	D;D	0.62365	0.976;0.991	P;P	0.56042	0.625;0.79	D	0.92578	0.6072	10	0.87932	D	0	-26.6319	20.023	0.97509	0.0:1.0:0.0:0.0	.	163;62	P78412;Q9BZI2	IRX6_HUMAN;.	V	163	ENSP00000290552:A163V	ENSP00000290552:A163V	A	+	2	0	IRX6	53919073	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.728000	0.84847	2.837000	0.97791	0.655000	0.94253	GCC		0.592	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335	
SOX9	6662	broad.mit.edu	37	17	70118954	70118954	+	Missense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr17:70118954C>T	ENST00000245479.2	+	2	898	c.526C>T	c.(526-528)Ccg>Tcg	p.P176S		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	176					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CAAGTACCAGCCGCGGCGGAG	0.652																																					Pancreas(42;83 1041 2320 35205 39456)	uc002jiw.3																			0				breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26						c.(526-528)Ccg>Tcg		Homo sapiens SRY (sex determining region Y)-box 9 (SOX9), mRNA.							58.0	61.0	60.0					17																	70118954		2203	4300	6503	SO:0001583	missense	6662				cAMP-mediated signaling|negative regulation of transcription, DNA-dependent|positive regulation of branching involved in ureteric bud morphogenesis|protein complex assembly|renal vesicle induction	nucleus|protein complex	core promoter sequence-specific DNA binding|enhancer binding|protein kinase A catalytic subunit binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	g.chr17:70118954C>T	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"""SRY (sex determining region Y)-boxes"""	11204	protein-coding gene	gene with protein product		608160	"""campomelic dysplasia, autosomal sex-reversal"""	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.526C>T	17.37:g.70118954C>T	ENSP00000245479:p.Pro176Ser					AK094963_uc002jiv.3_5'Flank	p.P176S	NM_000346	NP_000337	P48436	SOX9_HUMAN	STAD - Stomach adenocarcinoma(260;0.119)		1	898	+		Colorectal(1115;0.245)	176					Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	37	c.526C>T	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	C	32	5.135321	0.94517	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	D	0.94457	-3.43	4.7	3.73	0.42828	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);	0.000000	0.85682	D	0.000000	D	0.97860	0.9297	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98210	1.0472	10	0.87932	D	0	.	12.4406	0.55623	0.0:0.9183:0.0:0.0817	.	176	P48436	SOX9_HUMAN	S	176	ENSP00000245479:P176S	ENSP00000245479:P176S	P	+	1	0	SOX9	67630549	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.610000	0.82949	0.974000	0.38366	0.561000	0.74099	CCG		0.652	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346	
OTOP3	347741	broad.mit.edu	37	17	72943010	72943010	+	Missense_Mutation	SNP	G	G	A	rs372869932		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr17:72943010G>A	ENST00000328801.4	+	6	1060	c.1060G>A	c.(1060-1062)Gtc>Atc	p.V354I		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	354						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					AGGTGTGTGCGTCTTTGTGCT	0.627																																						uc010wrr.2																			0				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						c.(1060-1062)Gtc>Atc		Homo sapiens otopetrin 3 (OTOP3), mRNA.		A	ILE/VAL	0,4406		0,0,2203	55.0	47.0	50.0		1060	-0.1	0.5	17		50	1,8599	1.2+/-3.3	0,1,4299	no	missense	OTOP3	NM_178233.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	354/597	72943010	1,13005	2203	4300	6503	SO:0001583	missense	347741					integral to membrane|intracellular	zinc ion binding	g.chr17:72943010G>A	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.1060G>A	17.37:g.72943010G>A	ENSP00000328090:p.Val354Ile					OTOP3_uc010wrq.2_Missense_Mutation_p.V336I	p.V354I	NM_178233	NP_839947	Q7RTS5	OTOP3_HUMAN			5	1060	+	all_lung(278;0.151)|Lung NSC(278;0.185)		354						Missense_Mutation	SNP	ENST00000328801.4	37	c.1060G>A	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	g	2.634	-0.285602	0.05605	0.0	1.16E-4	ENSG00000182938	ENST00000328801	T	0.23348	1.91	4.4	-0.139	0.13460	.	0.407810	0.23889	N	0.043566	T	0.17874	0.0429	L	0.35854	1.095	0.09310	N	0.999997	B	0.21381	0.055	B	0.20577	0.03	T	0.18999	-1.0319	10	0.30854	T	0.27	-25.2045	10.8716	0.46887	0.3768:0.0:0.6232:0.0	.	354	Q7RTS5	OTOP3_HUMAN	I	354	ENSP00000328090:V354I	ENSP00000328090:V354I	V	+	1	0	OTOP3	70454605	0.001000	0.12720	0.536000	0.28039	0.027000	0.11550	-0.097000	0.11042	-0.246000	0.09611	-1.295000	0.01343	GTC		0.627	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
EPB41L3	23136	broad.mit.edu	37	18	5395093	5395093	+	Silent	SNP	C	C	A	rs144676596		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr18:5395093C>A	ENST00000341928.2	-	21	3466	c.3126G>T	c.(3124-3126)acG>acT	p.T1042T	EPB41L3_ENST00000400111.3_Silent_p.T820T|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000342933.3_Silent_p.T1042T|EPB41L3_ENST00000540638.2_Silent_p.T820T|EPB41L3_ENST00000544123.1_Silent_p.T873T|EPB41L3_ENST00000542146.1_Silent_p.T347T|EPB41L3_ENST00000427684.2_Silent_p.T339T	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1042	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.T1042T(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CTGCATCCCCCGTGATGACTA	0.448																																						uc002kmt.1																			1	Substitution - coding silent(1)	p.T1042T(2)	lung(1)	breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						c.(3124-3126)acG>acT		Homo sapiens erythrocyte membrane protein band 4.1-like 3 (EPB41L3), mRNA.							150.0	128.0	136.0					18																	5395093		2203	4300	6503	SO:0001819	synonymous_variant	23136				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity	g.chr18:5395093C>A	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.3126G>T	18.37:g.5395093C>A						EPB41L3_uc010wzh.1_Silent_p.T873T|EPB41L3_uc002kmu.1_Silent_p.T820T|EPB41L3_uc010dkq.1_Silent_p.T711T|EPB41L3_uc002kms.1_Silent_p.T277T|EPB41L3_uc010wze.1_Silent_p.T347T|EPB41L3_uc010wzf.1_Silent_p.T339T|EPB41L3_uc010wzg.1_Silent_p.T314T|EPB41L3_uc010dkr.2_Silent_p.T434T	p.T1042T	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN			20	3212	-			1042			Carboxyl-terminal (CTD).		B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	37	c.3126G>T	CCDS11838.1																																																																																				0.448	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
FBXO15	201456	broad.mit.edu	37	18	71791770	71791770	+	Missense_Mutation	SNP	G	G	C			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr18:71791770G>C	ENST00000419743.2	-	7	1028	c.949C>G	c.(949-951)Cat>Gat	p.H317D	FBXO15_ENST00000269500.5_Missense_Mutation_p.H241D	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	317						SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		TGATGAAAATGAAGATTTGCC	0.328																																						uc002llf.2																			0				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27						c.(949-951)Cat>Gat		Homo sapiens F-box protein 15 (FBXO15), transcript variant 2, mRNA.							166.0	161.0	162.0					18																	71791770		2203	4300	6503	SO:0001583	missense	201456							g.chr18:71791770G>C	AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"""F-boxes /  ""other"""""	13617	protein-coding gene	gene with protein product		609093	"""F-box only protein 15"""			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.949C>G	18.37:g.71791770G>C	ENSP00000393154:p.His317Asp					FBXO15_uc002lle.2_Missense_Mutation_p.H241D	p.H317D	NM_001142958	NP_689889	Q8NCQ5	FBX15_HUMAN		BRCA - Breast invasive adenocarcinoma(31;0.143)	6	1029	-		Esophageal squamous(42;0.103)|Prostate(75;0.173)	241					B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	c.949C>G	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867520	0.72065	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.53640	0.63;0.61	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.70911	0.3278	M	0.80183	2.485	0.51767	D	0.999938	D;D	0.89917	0.999;1.0	D;D	0.85130	0.997;0.997	T	0.75309	-0.3363	10	0.87932	D	0	-16.1319	16.4476	0.83942	0.0:0.0:1.0:0.0	.	317;241	B3KST3;Q8NCQ5	.;FBX15_HUMAN	D	241;317	ENSP00000269500:H241D;ENSP00000393154:H317D	ENSP00000269500:H241D	H	-	1	0	FBXO15	69942750	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.918000	0.69996	2.476000	0.83614	0.563000	0.77884	CAT		0.328	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676	
FUT5	2527	broad.mit.edu	37	19	5867028	5867028	+	Missense_Mutation	SNP	G	G	A	rs200537067		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:5867028G>A	ENST00000588525.1	-	2	796	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	FUT5_ENST00000252675.5_Missense_Mutation_p.R237C	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	237					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						TTGTGGGAGCGTCCGTACACG	0.622																																						uc002mdo.4																			0				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						c.(709-711)Cgc>Tgc		Homo sapiens fucosyltransferase 5 (alpha (1,3) fucosyltransferase) (FUT5), mRNA.							45.0	45.0	45.0					19																	5867028		2184	4269	6453	SO:0001583	missense	2527				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity|alpha(1,3)-fucosyltransferase activity	g.chr19:5867028G>A		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.709C>T	19.37:g.5867028G>A	ENSP00000466880:p.Arg237Cys					FUT5_uc010duo.3_Missense_Mutation_p.R237C|FUT5_uc021uno.1_Missense_Mutation_p.R237C	p.R237C	NM_002034	NP_002025	Q11128	FUT5_HUMAN			1	880	-			237					A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	37	c.709C>T	CCDS12154.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.985566	0.35036	.	.	ENSG00000130383	ENST00000252675	T	0.26518	1.73	2.13	-4.27	0.03744	.	4.826560	0.01040	U	0.004297	T	0.49218	0.1544	M	0.88842	2.985	0.09310	N	1	D	0.57899	0.981	P	0.55161	0.77	T	0.59894	-0.7368	10	0.87932	D	0	.	9.7326	0.40370	0.0:0.0:0.3169:0.6831	.	237	Q11128	FUT5_HUMAN	C	237	ENSP00000252675:R237C	ENSP00000252675:R237C	R	-	1	0	FUT5	5818028	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.832000	0.04400	-0.770000	0.04614	-0.800000	0.03216	CGC		0.622	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
MUC16	94025	broad.mit.edu	37	19	9091524	9091524	+	Silent	SNP	G	G	A	rs375390174	byFrequency	TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:9091524G>A	ENST00000397910.4	-	1	494	c.291C>T	c.(289-291)tcC>tcT	p.S97S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	97	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTTTGCTCGGAGTGTGTCA	0.537													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19717	0.0		0.0	False		,,,				2504	0.0					uc002mkp.3																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(289-291)tcC>tcT		Homo sapiens mucin 16, cell surface associated (MUC16), mRNA.		G		29,3943		0,29,1957	138.0	136.0	137.0		291	-2.0	0.0	19		137	1,8329		0,1,4164	no	coding-synonymous	MUC16	NM_024690.2		0,30,6121	AA,AG,GG		0.012,0.7301,0.2439		97/14508	9091524	30,12272	1986	4165	6151	SO:0001819	synonymous_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9091524G>A	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.291C>T	19.37:g.9091524G>A							p.S97S	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			0	495	-			97			Thr-rich.		Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	c.291C>T	CCDS54212.1																																																																																				0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF833P	401898	broad.mit.edu	37	19	11796063	11796063	+	lincRNA	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:11796063G>A	ENST00000344893.3	+	0	2062					NR_028594.1		Q6ZTB9	ZN833_HUMAN	zinc finger protein 833, pseudogene								metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5						CAGTGAAGATGAACCTTATAA	0.353																																						uc021upi.1																			0				endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5						c.(1-3)atG>atA		Homo sapiens zinc finger protein 833, pseudogene (ZNF833P), non-coding RNA.							86.0	91.0	90.0					19																	11796063		2203	4300	6503			401898							g.chr19:11796063G>A	BC137336		19p13.2	2010-08-03	2010-08-03	2010-08-03	ENSG00000197332	ENSG00000197332			33819	pseudogene	pseudogene			"""zinc finger protein 833"""	ZNF833			Standard	NR_028594		Approved		uc021upi.1	Q6ZTB9	OTTHUMG00000156530		19.37:g.11796063G>A						ZNF833P_uc002msl.4_Non-coding_Transcript	p.M1I							2	679	+								B2RPA0	Missense_Mutation	SNP	ENST00000344893.3	37	c.3G>A																																																																																					0.353	ZNF833P-001	KNOWN	basic|readthrough_transcript	lincRNA	lincRNA	OTTHUMT00000458891.1	NM_001013691	
LYPD4	147719	broad.mit.edu	37	19	42342222	42342222	+	Missense_Mutation	SNP	C	C	T	rs142442476	byFrequency	TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:42342222C>T	ENST00000330743.3	-	4	1536	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	LYPD4_ENST00000343055.4_Missense_Mutation_p.V74I|LYPD4_ENST00000601246.1_Missense_Mutation_p.V74I|AC020956.3_ENST00000593354.1_lincRNA	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	109						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						GACCGGCAGACGCGACTGTAG	0.522													-|||	4	0.000798722	0.0015	0.0029	5008	,	,		17852	0.0		0.0	False		,,,				2504	0.0					uc002orp.1																			0				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						c.(325-327)Gtc>Atc		Homo sapiens LY6/PLAUR domain containing 4 (LYPD4), mRNA.			ILE/VAL	13,4393	20.2+/-43.8	0,13,2190	142.0	122.0	129.0		325	-0.4	0.2	19	dbSNP_134	129	3,8597	3.0+/-9.4	0,3,4297	no	missense	LYPD4	NM_173506.4	29	0,16,6487	TT,TC,CC		0.0349,0.2951,0.123	benign	109/247	42342222	16,12990	2203	4300	6503	SO:0001583	missense	147719					anchored to membrane|plasma membrane		g.chr19:42342222C>T	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.325G>A	19.37:g.42342222C>T	ENSP00000328737:p.Val109Ile					LYPD4_uc002orq.1_Missense_Mutation_p.V74I	p.V109I	NM_173506	NP_775777	Q6UWN0	LYPD4_HUMAN			3	1309	-			109					Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	37	c.325G>A	CCDS12587.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	c	10.47	1.359659	0.24598	0.002951	3.49E-4	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.13778	3.27;2.56	4.03	-0.44	0.12261	.	0.469748	0.18111	N	0.151362	T	0.10078	0.0247	L	0.52126	1.63	0.19300	N	0.999971	B;B	0.27791	0.189;0.119	B;B	0.17722	0.019;0.008	T	0.20273	-1.0280	10	0.36615	T	0.2	-8.3817	6.2763	0.20983	0.0:0.5602:0.0:0.4398	.	74;109	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	I	109;74	ENSP00000328737:V109I;ENSP00000339568:V74I	ENSP00000328737:V109I	V	-	1	0	LYPD4	47034062	0.073000	0.21202	0.181000	0.23098	0.724000	0.41520	0.022000	0.13511	0.028000	0.15324	-0.389000	0.06534	GTC		0.522	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506	
PSG2	5670	broad.mit.edu	37	19	43576027	43576027	+	Silent	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:43576027C>T	ENST00000406487.1	-	4	887	c.789G>A	c.(787-789)gcG>gcA	p.A263A		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	263	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.A263A(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				GGTTAGAGTTCGCGAAGCAAG	0.443																																						uc002ovr.3																			1	Substitution - coding silent(1)	p.A263A(2)|p.A263V(1)	lung(1)	central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49						c.(787-789)gcG>gcA		Homo sapiens pregnancy specific beta-1-glycoprotein 2 (PSG2), mRNA.							184.0	193.0	190.0					19																	43576027		2202	4299	6501	SO:0001819	synonymous_variant	5670				cell migration|female pregnancy	extracellular region		g.chr19:43576027C>T		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.789G>A	19.37:g.43576027C>T						PSG4_uc010xwk.1_Intron	p.A263A	NM_031246	NP_112536	P11465	PSG2_HUMAN			3	961	-		Prostate(69;0.00682)	263			Ig-like C2-type 2.		Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	c.789G>A	CCDS12616.1																																																																																				0.443	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
PSG4	5672	broad.mit.edu	37	19	43708378	43708378	+	Silent	SNP	C	C	T	rs533600298		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:43708378C>T	ENST00000405312.3	-	2	327	c.90G>A	c.(88-90)ccG>ccA	p.P30P	PSG4_ENST00000244295.9_Silent_p.P30P|PSG4_ENST00000433626.2_Silent_p.P30P	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	30					female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)		p.P30P(2)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				CAGTTGTGGGCGGATTCCAGA	0.468													C|||	1	0.000199681	0.0	0.0014	5008	,	,		15815	0.0		0.0	False		,,,				2504	0.0					uc002ovy.3																			2	Substitution - coding silent(2)	p.P30P(3)	large_intestine(2)	central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24						c.(88-90)ccG>ccA		Homo sapiens pregnancy specific beta-1-glycoprotein 4 (PSG4), transcript variant 1, mRNA.							118.0	131.0	127.0					19																	43708378		2137	4270	6407	SO:0001819	synonymous_variant	5672				defense response|female pregnancy	extracellular region		g.chr19:43708378C>T		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.90G>A	19.37:g.43708378C>T						PSG4_uc002ovz.3_Silent_p.P30P|PSG4_uc002owb.3_Silent_p.P30P	p.P30P	NM_002780	NP_002771	Q00888	PSG4_HUMAN			1	192	-		Prostate(69;0.00682)	30					E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	c.90G>A	CCDS46093.1																																																																																				0.468	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
NLRP4	147945	broad.mit.edu	37	19	56370207	56370207	+	Nonsense_Mutation	SNP	T	T	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:56370207T>A	ENST00000301295.6	+	3	1870	c.1448T>A	c.(1447-1449)tTg>tAg	p.L483*	NLRP4_ENST00000346986.5_Nonsense_Mutation_p.L483*|NLRP4_ENST00000587891.1_Nonsense_Mutation_p.L408*	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	483					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GTACAGGAATTGCTAGTTGCC	0.423																																						uc002qmd.4																			0		p.E482K(1)|p.L483F(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42						c.(1447-1449)tTg>tAg		Homo sapiens NLR family, pyrin domain containing 4 (NLRP4), mRNA.							134.0	137.0	136.0					19																	56370207		2203	4300	6503	SO:0001587	stop_gained	147945						ATP binding	g.chr19:56370207T>A	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1448T>A	19.37:g.56370207T>A	ENSP00000301295:p.Leu483*					NLRP4_uc002qmf.3_Nonsense_Mutation_p.L408*|NLRP4_uc010etf.3_Nonsense_Mutation_p.L314*	p.L483*	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN		GBM - Glioblastoma multiforme(193;0.0606)	2	1870	+		Colorectal(82;0.0002)|Ovarian(87;0.221)	483					Q86W87|Q96AY6	Nonsense_Mutation	SNP	ENST00000301295.6	37	c.1448T>A	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	T	38	7.071727	0.98044	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	.	.	.	3.56	3.56	0.40772	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.8059	0.34938	0.0:0.0:0.0:1.0	.	.	.	.	X	483	.	ENSP00000301295:L483X	L	+	2	0	NLRP4	61062019	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.505000	0.22642	1.840000	0.53500	0.533000	0.62120	TTG		0.423	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	G	T	rs201682072		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr19:58385546G>T	ENST00000435989.2	-	3	1446	c.1212C>A	c.(1210-1212)gaC>gaA	p.D404E	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D404E(10)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AATGTTTTTTGTCAGTGTGAA	0.393																																						uc002qqo.2																			10	Substitution - Missense(10)	p.D404E(20)	urinary_tract(3)|kidney(3)|prostate(2)|NS(1)|skin(1)	NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						c.(1210-1212)gaC>gaA		Homo sapiens zinc finger protein 814 (ZNF814), mRNA.							117.0	93.0	100.0					19																	58385546		692	1591	2283	SO:0001583	missense	730051				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:58385546G>T		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1212C>A	19.37:g.58385546G>T	ENSP00000410545:p.Asp404Glu					ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.2_Intron	p.D404E	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN			2	1484	-			404					A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	c.1212C>A	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.12	1.545823	0.27652	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.14640	2.49	2.33	-4.66	0.03329	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04363	0.0120	N	0.03177	-0.4	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.33574	-0.9863	9	0.54805	T	0.06	.	1.2175	0.01917	0.3897:0.3041:0.1331:0.1731	.	404	B7Z6K7	ZN814_HUMAN	E	404;266	ENSP00000410545:D404E	ENSP00000365378:D266E	D	-	3	2	ZNF814	63077358	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-1.489000	0.02306	-2.531000	0.00491	-1.292000	0.01352	GAC		0.393	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
RAD51AP2	729475	broad.mit.edu	37	2	17692095	17692095	+	Silent	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr2:17692095G>A	ENST00000399080.2	-	3	3479	c.3456C>T	c.(3454-3456)taC>taT	p.Y1152Y		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	1152	Interaction with RAD51.									endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTAAGTTTCCGTAACACATTT	0.338																																						uc002rcl.1																			0				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						c.(3454-3456)taC>taT		Homo sapiens RAD51 associated protein 2 (RAD51AP2), mRNA.							83.0	74.0	77.0					2																	17692095		1807	4070	5877	SO:0001819	synonymous_variant	729475							g.chr2:17692095G>A	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.3456C>T	2.37:g.17692095G>A						RAD51AP2_uc010exn.1_Silent_p.Y1143Y	p.Y1152Y	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN			2	3480	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)		1152			Interaction with RAD51.			Silent	SNP	ENST00000399080.2	37	c.3456C>T	CCDS42656.1																																																																																				0.338	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
TMEM17	200728	broad.mit.edu	37	2	62728426	62728426	+	Missense_Mutation	SNP	C	C	T	rs561991904		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr2:62728426C>T	ENST00000335390.5	-	4	726	c.515G>A	c.(514-516)cGt>cAt	p.R172H		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	172					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GAGGTGGAAACGAACTGCCAA	0.423													C|||	1	0.000199681	0.0	0.0	5008	,	,		20736	0.0		0.0	False		,,,				2504	0.001					uc002sbt.2																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9						c.(514-516)cGt>cAt		Homo sapiens transmembrane protein 17 (TMEM17), mRNA.							144.0	137.0	139.0					2																	62728426		2203	4300	6503	SO:0001583	missense	200728					integral to membrane		g.chr2:62728426C>T		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.515G>A	2.37:g.62728426C>T	ENSP00000335094:p.Arg172His					TMEM17_uc002sbu.2_3'UTR|TMEM17_uc002sbv.1_3'UTR	p.R172H	NM_198276	NP_938017	Q86X19	TMM17_HUMAN	LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)		3	855	-	Lung NSC(7;0.0274)|all_lung(7;0.0568)		172					Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	37	c.515G>A	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.590260	0.46214	.	.	ENSG00000186889	ENST00000335390	T	0.49139	0.79	5.6	2.81	0.32909	.	0.353194	0.33057	N	0.005327	T	0.30947	0.0781	N	0.19112	0.55	0.31902	N	0.61588	B	0.11235	0.004	B	0.04013	0.001	T	0.28138	-1.0053	10	0.41790	T	0.15	-2.2764	10.8395	0.46706	0.0:0.7347:0.0:0.2653	.	172	Q86X19	TMM17_HUMAN	H	172	ENSP00000335094:R172H	ENSP00000335094:R172H	R	-	2	0	TMEM17	62581930	0.428000	0.25522	1.000000	0.80357	0.998000	0.95712	0.334000	0.19787	0.735000	0.32537	0.650000	0.86243	CGT		0.423	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
TGFA	7039	broad.mit.edu	37	2	70683568	70683568	+	Missense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr2:70683568C>T	ENST00000295400.6	-	4	515	c.268G>A	c.(268-270)Gtg>Atg	p.V90M	TGFA_ENST00000418333.2_Missense_Mutation_p.V89M|AC017084.1_ENST00000401177.2_RNA|TGFA_ENST00000445399.1_Missense_Mutation_p.V89M|TGFA_ENST00000450929.1_Missense_Mutation_p.V95M|TGFA_ENST00000460808.1_5'UTR|TGFA_ENST00000444975.1_Missense_Mutation_p.V96M	NM_001099691.2|NM_003236.3	NP_001093161.1|NP_003227.1	P01135	TGFA_HUMAN	transforming growth factor, alpha	90					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|mammary gland alveolus development (GO:0060749)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell division (GO:0051781)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mitosis (GO:0045840)|response to drug (GO:0042493)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)	p.V90M(1)		haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						GCAGCCACCACGGCCAGGAGG	0.577																																						uc002sgs.4																			1	Substitution - Missense(1)	p.V90M(2)	prostate(1)	haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						c.(268-270)Gtg>Atg		Homo sapiens transforming growth factor, alpha (TGFA), transcript variant 1, mRNA.							63.0	49.0	54.0					2																	70683568		2203	4298	6501	SO:0001583	missense	7039				activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity	g.chr2:70683568C>T		CCDS1905.1, CCDS46316.1	2p13	2012-10-02			ENSG00000163235	ENSG00000163235			11765	protein-coding gene	gene with protein product		190170				3459638, 10552925	Standard	NM_003236		Approved		uc002sgs.4	P01135	OTTHUMG00000129669	ENST00000295400.6:c.268G>A	2.37:g.70683568C>T	ENSP00000295400:p.Val90Met					TGFA_uc010fdq.3_Missense_Mutation_p.V96M|TGFA_uc010fdr.3_Missense_Mutation_p.V95M|TGFA_uc002sgt.4_Missense_Mutation_p.V89M|TGFA_uc002sgu.3_Missense_Mutation_p.V89M|TGFA_uc002sgv.3_Missense_Mutation_p.V90M|TGFA_uc002sgw.3_Missense_Mutation_p.V89M	p.V90M	NM_003236	NP_003227	P01135	TGFA_HUMAN			3	516	-			90					A8K286|Q15577|Q53SK7|Q9BS56|Q9UEI3|Q9UKM1|Q9UKM2|Q9UKM3	Missense_Mutation	SNP	ENST00000295400.6	37	c.268G>A	CCDS1905.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934367	0.92458	.	.	ENSG00000163235	ENST00000295400;ENST00000445399;ENST00000418333;ENST00000450929;ENST00000444975;ENST00000394241	T;T;T;T;T;T	0.13657	2.57;2.57;2.57;2.57;2.57;2.57	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.39759	0.1090	M	0.76328	2.33	0.50039	D	0.999846	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.998;0.998;0.984;0.984;0.999	T	0.16719	-1.0393	10	0.87932	D	0	.	16.9667	0.86287	0.0:1.0:0.0:0.0	.	95;96;89;90;89;89;90	E7EPT6;F8VNR3;P01135-5;Q9UKM3;P01135-3;P01135-2;P01135	.;.;.;.;.;.;TGFA_HUMAN	M	90;89;89;95;96;89	ENSP00000295400:V90M;ENSP00000387493:V89M;ENSP00000404099:V89M;ENSP00000414127:V95M;ENSP00000404131:V96M;ENSP00000377787:V89M	ENSP00000295400:V90M	V	-	1	0	TGFA	70537076	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.249000	0.78278	2.608000	0.88229	0.561000	0.74099	GTG		0.577	TGFA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251870.2		
RGPD3	653489	broad.mit.edu	37	2	107040566	107040566	+	Missense_Mutation	SNP	T	T	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr2:107040566T>A	ENST00000409886.3	-	20	3944	c.3857A>T	c.(3856-3858)gAt>gTt	p.D1286V	RGPD3_ENST00000304514.7_Missense_Mutation_p.D1286V	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1286					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TGTTGACTCATCAAAGTGGAA	0.408																																						uc010ywi.1																			0				breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						c.(3856-3858)gAt>gTt		Homo sapiens RANBP2-like and GRIP domain containing 3 (RGPD3), mRNA.							167.0	124.0	137.0					2																	107040566		660	1515	2175	SO:0001583	missense	653489				intracellular transport		binding	g.chr2:107040566T>A		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.3857A>T	2.37:g.107040566T>A	ENSP00000386588:p.Asp1286Val						p.D1286V	NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN			19	3914	-			1286					B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	c.3857A>T	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	5.864	0.343502	0.11069	.	.	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.39229	1.09;1.09	2.35	2.35	0.29111	.	.	.	.	.	T	0.20495	0.0493	N	0.08118	0	0.50813	D	0.99989	P	0.37176	0.586	B	0.34873	0.191	T	0.04454	-1.0950	9	0.59425	D	0.04	-17.4495	7.1563	0.25639	0.0:0.8506:0.0:0.1494	.	1286	A6NKT7	RGPD3_HUMAN	V	1286	ENSP00000386588:D1286V;ENSP00000303659:D1286V	ENSP00000303659:D1286V	D	-	2	0	RGPD3	106406998	1.000000	0.71417	0.997000	0.53966	0.031000	0.12232	5.868000	0.69605	0.328000	0.23435	-1.128000	0.01989	GAT		0.408	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
JAG1	182	broad.mit.edu	37	20	10644609	10644612	+	Splice_Site	DEL	ACGA	ACGA	-			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr20:10644609_10644612delACGA	ENST00000254958.5	-	3	953_955	c.438_440delTCGT	c.(436-441)gttcgt>gtt	p.R147fs	JAG1_ENST00000423891.2_5'Flank	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	147					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						AGCGATACTTACGAACGGTGTCAT	0.466									Alagille Syndrome																													uc002wnw.2																			0				biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44	GRCh37	CM061812|CS003182	JAG1	M|S		c.e3+1		Homo sapiens jagged 1 (JAG1), mRNA.																																				SO:0001630	splice_region_variant	182	Alagille Syndrome	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity	g.chr20:10644609_10644612delACGA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.439+1TCGT>-	20.37:g.10644609_10644612delACGA							p.Q147_splice	NM_000214	NP_000205	P78504	JAG1_HUMAN			3	955	-			147					A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Splice_Site	DEL	ENST00000254958.5	37	c.439_splice	CCDS13112.1																																																																																				0.466	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	Frame_Shift_Del
RALGAPA2	57186	broad.mit.edu	37	20	20493785	20493785	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr20:20493785G>A	ENST00000202677.7	-	32	4235	c.4228C>T	c.(4228-4230)Cat>Tat	p.H1410Y		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1410					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						CCTTCCACATGGGCATTGTCA	0.547																																						uc002wrz.3																			0				endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						c.(4228-4230)Cat>Tat		Homo sapiens Ral GTPase activating protein, alpha subunit 2 (catalytic) (RALGAPA2), mRNA.							49.0	47.0	48.0					20																	20493785		1968	4149	6117	SO:0001583	missense	57186				activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity	g.chr20:20493785G>A	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4228C>T	20.37:g.20493785G>A	ENSP00000202677:p.His1410Tyr					RALGAPA2_uc002wry.3_Missense_Mutation_p.H1025Y|RALGAPA2_uc010zsg.2_Missense_Mutation_p.H858Y|RALGAPA2_uc002wsa.1_Missense_Mutation_p.H182Y	p.H1410Y	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN			31	4371	-			1410					Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	c.4228C>T	CCDS46584.1	.	.	.	.	.	.	.	.	.	.	G	3.990	-0.004705	0.07773	.	.	ENSG00000188559	ENST00000202677	D	0.94576	-3.46	5.62	4.45	0.53987	.	0.059706	0.64402	D	0.000002	T	0.81297	0.4793	N	0.03071	-0.42	0.40334	D	0.978962	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.74399	-0.3678	9	.	.	.	.	4.1809	0.10374	0.3122:0.0:0.6878:0.0	.	1248;1410;1410	A8MSM5;Q2PPJ7-2;Q2PPJ7	.;.;RGPA2_HUMAN	Y	1410	ENSP00000202677:H1410Y	.	H	-	1	0	RALGAPA2	20441785	1.000000	0.71417	0.119000	0.21687	0.910000	0.53928	6.423000	0.73361	2.803000	0.96430	0.591000	0.81541	CAT		0.547	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
MYH7B	57644	broad.mit.edu	37	20	33584258	33584258	+	Missense_Mutation	SNP	A	A	G			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr20:33584258A>G	ENST00000262873.7	+	27	3271	c.3179A>G	c.(3178-3180)cAg>cGg	p.Q1060R		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1018						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGTGACCTGCAGGCCGAGGAG	0.672																																						uc002xbi.2																			0				NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						c.(3178-3180)cAg>cGg		Homo sapiens myosin, heavy chain 7B, cardiac muscle, beta (MYH7B), mRNA.							29.0	34.0	32.0					20																	33584258		2201	4299	6500	SO:0001583	missense	57644					membrane|myosin filament	actin binding|ATP binding|motor activity	g.chr20:33584258A>G	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.3179A>G	20.37:g.33584258A>G	ENSP00000262873:p.Gln1060Arg						p.Q1060R	NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.00691)		28	3496	+			1018					Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	c.3179A>G	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018656	0.54576	.	.	ENSG00000078814	ENST00000262873	D	0.86956	-2.19	4.68	4.68	0.58851	.	0.000000	0.35936	N	0.002898	D	0.88291	0.6397	M	0.86178	2.8	0.51012	D	0.999904	B	0.16166	0.016	B	0.11329	0.006	D	0.87094	0.2174	10	0.59425	D	0.04	.	14.6158	0.68547	1.0:0.0:0.0:0.0	.	1018	A7E2Y1	MYH7B_HUMAN	R	1060	ENSP00000262873:Q1060R	ENSP00000262873:Q1060R	Q	+	2	0	MYH7B	33047919	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.322000	0.79097	2.107000	0.64212	0.533000	0.62120	CAG		0.672	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
HMGB1P1	10357	broad.mit.edu	37	20	56063608	56063609	+	IGR	DEL	AT	AT	-			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr20:56063608_56063609delAT								RBM38 (79219 upstream) : CTCFL (7425 downstream)																							ATATGCAGCAATATCCTTTTCG	0.436																																																									0																																																	SO:0001628	intergenic_variant	10357							g.chr20:56063608_56063609delAT																													20.37:g.56063610_56063611delAT						MIR5095 (65330 upstream) : CTCFL (270 downstream)																			Frame_Shift_Del	DEL		37																																																																																					0	0.436								
NPBWR2	2832	broad.mit.edu	37	20	62737704	62737704	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr20:62737704G>A	ENST00000369768.1	-	1	820	c.481C>T	c.(481-483)Cgg>Tgg	p.R161W		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	161					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)	p.R161W(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					TTCGCCCCCCGGTAGGTGCGC	0.632																																						uc011abt.2																			1	Substitution - Missense(1)	p.R161W(2)|p.R161Q(1)	upper_aerodigestive_tract(1)	haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						c.(481-483)Cgg>Tgg		Homo sapiens neuropeptides B/W receptor 2 (NPBWR2), mRNA.							20.0	22.0	21.0					20																	62737704		2192	4269	6461	SO:0001583	missense	2832					plasma membrane	opioid receptor activity|protein binding	g.chr20:62737704G>A	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.481C>T	20.37:g.62737704G>A	ENSP00000358783:p.Arg161Trp						p.R161W	NM_005286	NP_005277	P48146	NPBW2_HUMAN			0	481	-	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)		161					Q6NWQ6|Q9H4K3	Missense_Mutation	SNP	ENST00000369768.1	37	c.481C>T	CCDS13557.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.451033	0.26074	.	.	ENSG00000125522	ENST00000369768	T	0.42900	0.96	3.51	1.27	0.21489	GPCR, rhodopsin-like superfamily (1);	0.090637	0.45361	U	0.000374	T	0.62159	0.2405	M	0.84511	2.7	0.33843	D	0.631693	D	0.89917	1.0	D	0.68765	0.96	T	0.71958	-0.4435	10	0.44086	T	0.13	.	10.9593	0.47376	0.0:0.0:0.6622:0.3378	.	161	P48146	NPBW2_HUMAN	W	161	ENSP00000358783:R161W	ENSP00000358783:R161W	R	-	1	2	NPBWR2	62208148	0.983000	0.35010	0.000000	0.03702	0.071000	0.16799	0.607000	0.24209	0.403000	0.25479	-0.500000	0.04577	CGG		0.632	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
MME	4311	broad.mit.edu	37	3	154832945	154832945	+	Splice_Site	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr3:154832945G>A	ENST00000460393.1	+	4	478		c.e4+1		MME_ENST00000462745.1_Splice_Site|MME_ENST00000493237.1_Splice_Site|MME_ENST00000492661.1_Splice_Site|MME_ENST00000360490.2_Splice_Site	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase						angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	GTTTTGAAAGGTTAGTAGAGA	0.378																																						uc010hvr.1																			0				central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64						c.e4+1		Homo sapiens membrane metallo-endopeptidase (MME), transcript variant 2b, mRNA.	Candoxatril(DB00616)						93.0	89.0	90.0					3																	154832945		2203	4300	6503	SO:0001630	splice_region_variant	4311				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding	g.chr3:154832945G>A		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.358+1G>A	3.37:g.154832945G>A						MME_uc003fab.1_Splice_Site_p.D120_splice|MME_uc003fac.1_Splice_Site_p.D120_splice|MME_uc003fad.1_Splice_Site_p.D120_splice|MME_uc003fae.1_Splice_Site_p.D120_splice	p.D120_splice	NM_007289	NP_009220	P08473	NEP_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		4	569	+		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	120					A8K6U6|D3DNJ9|Q3MIX4	Splice_Site	SNP	ENST00000460393.1	37	c.358_splice	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.206804	0.79127	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000481828;ENST00000462745;ENST00000493237;ENST00000360490;ENST00000462837	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6107	0.95606	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MME	156315639	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	9.731000	0.98807	2.648000	0.89879	0.655000	0.94253	.		0.378	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	Intron
PLD1	5337	broad.mit.edu	37	3	171330189	171330189	+	Missense_Mutation	SNP	C	C	G			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr3:171330189C>G	ENST00000351298.4	-	25	2888	c.2762G>C	c.(2761-2763)gGa>gCa	p.G921A	PLD1_ENST00000342215.6_3'UTR|PLD1_ENST00000340989.4_Missense_Mutation_p.G921A|PLD1_ENST00000356327.5_Missense_Mutation_p.G883A	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	921	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GTCACGCTTTCCCAGCATGCT	0.507																																					NSCLC(149;2174 3517 34058)	uc003fhs.3																			0		p.G921*(2)|p.L920L(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63						c.(2761-2763)gGa>gCa		Homo sapiens phospholipase D1, phosphatidylcholine-specific (PLD1), transcript variant 1, mRNA.	Choline(DB00122)						127.0	108.0	115.0					3																	171330189		2203	4300	6503	SO:0001583	missense	5337				cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity	g.chr3:171330189C>G	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.2762G>C	3.37:g.171330189C>G	ENSP00000342793:p.Gly921Ala					PLD1_uc003fht.3_Missense_Mutation_p.G883A|PLD1_uc003fhu.4_Missense_Mutation_p.G215A	p.G921A	NM_002662	NP_002653	Q13393	PLD1_HUMAN	LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		24	3109	-	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		921			Catalytic.			Missense_Mutation	SNP	ENST00000351298.4	37	c.2762G>C	CCDS3216.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.5|28.5	4.923721|4.923721	0.92319|0.92319	.|.	.|.	ENSG00000075651|ENSG00000075651	ENST00000446289|ENST00000356327;ENST00000351298;ENST00000340989	.|T;T;T	.|0.23754	.|1.89;1.89;1.89	5.57|5.57	5.57|5.57	0.84162|0.84162	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66886|0.66886	0.2835|0.2835	H|H	0.96142|0.96142	3.775|3.775	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.994;1.0;1.0	.|D;D;D	.|0.97110	.|0.965;1.0;1.0	T|T	0.77643|0.77643	-0.2511|-0.2511	5|10	.|0.62326	.|D	.|0.03	-23.2722|-23.2722	19.5547|19.5547	0.95338|0.95338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|921;906;921	.|Q13393-4;Q59EA4;Q13393	.|.;.;PLD1_HUMAN	Q|A	184|883;921;921	.|ENSP00000348681:G883A;ENSP00000342793:G921A;ENSP00000340326:G921A	.|ENSP00000340326:G921A	E|G	-|-	1|2	0|0	PLD1|PLD1	172812883|172812883	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.969000|0.969000	0.65631|0.65631	7.792000|7.792000	0.85828|0.85828	2.606000|2.606000	0.88127|0.88127	0.650000|0.650000	0.86243|0.86243	GAA|GGA		0.507	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
LPHN3	23284	broad.mit.edu	37	4	62452954	62452954	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr4:62452954G>A	ENST00000514591.1	+	4	394	c.65G>A	c.(64-66)cGt>cAt	p.R22H	LPHN3_ENST00000506700.1_Missense_Mutation_p.R22H|LPHN3_ENST00000514996.1_Missense_Mutation_p.R22H|LPHN3_ENST00000508946.1_Missense_Mutation_p.R22H|LPHN3_ENST00000506746.1_Missense_Mutation_p.R90H|LPHN3_ENST00000512091.2_Missense_Mutation_p.R22H|LPHN3_ENST00000514157.1_Missense_Mutation_p.R22H|LPHN3_ENST00000506720.1_Missense_Mutation_p.R90H|LPHN3_ENST00000504896.1_Missense_Mutation_p.R22H|LPHN3_ENST00000511324.1_Missense_Mutation_p.R90H|LPHN3_ENST00000507164.1_Missense_Mutation_p.R90H|LPHN3_ENST00000545650.1_Missense_Mutation_p.R22H|LPHN3_ENST00000508693.1_Missense_Mutation_p.R90H|LPHN3_ENST00000507625.1_Missense_Mutation_p.R90H|LPHN3_ENST00000509896.1_Missense_Mutation_p.R90H			Q9HAR2	LPHN3_HUMAN	latrophilin 3	22					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GCTTTCAGCCGTGCCCCAATT	0.453																																						uc010ihh.3																			0				breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						c.(64-66)cGt>cAt		Homo sapiens latrophilin 3 (LPHN3), mRNA.							37.0	39.0	38.0					4																	62452954		1909	4114	6023	SO:0001583	missense	23284				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	g.chr4:62452954G>A	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.65G>A	4.37:g.62452954G>A	ENSP00000422533:p.Arg22His					LPHN3_uc003hcq.4_Missense_Mutation_p.R22H|LPHN3_uc010ihg.1_Missense_Mutation_p.R90H	p.R22H	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN			1	238	+			22					E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	c.65G>A	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.256124	0.80246	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72282	-0.56;-0.54;-0.57;-0.57;-0.55;-0.54;-0.58;-0.58;-0.57;-0.56;-0.56;-0.61;-0.64;-0.64;-0.6	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.78059	0.4224	L	0.29908	0.895	0.54753	D	0.999987	D;D;D	0.71674	0.995;0.998;0.997	P;D;P	0.72075	0.719;0.976;0.855	T	0.79834	-0.1636	10	0.87932	D	0	.	19.0468	0.93022	0.0:0.0:1.0:0.0	.	22;90;22	E9PE04;E7EN28;Q9HAR2-2	.;.;.	H	22;22;90;90;22;22;22;22;22;90;90;90;22;22;22;90;90;22	ENSP00000423388:R22H;ENSP00000422533:R22H;ENSP00000423787:R90H;ENSP00000425033:R90H;ENSP00000424120:R22H;ENSP00000439831:R22H;ENSP00000421476:R90H;ENSP00000424030:R90H;ENSP00000421372:R90H;ENSP00000425201:R22H;ENSP00000423434:R22H;ENSP00000421627:R22H;ENSP00000420931:R90H;ENSP00000425884:R90H;ENSP00000424258:R22H	ENSP00000280009:R22H	R	+	2	0	LPHN3	62135549	1.000000	0.71417	0.993000	0.49108	0.330000	0.28571	9.608000	0.98331	2.741000	0.93983	0.650000	0.86243	CGT		0.453	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
CXCL1	2919	broad.mit.edu	37	4	74735288	74735288	+	Splice_Site	SNP	G	G	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr4:74735288G>T	ENST00000395761.3	+	1	167		c.e1+1		CXCL1_ENST00000509101.1_Splice_Site	NM_001511.3	NP_001502.1	P09341	GROA_HUMAN	chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)						actin cytoskeleton organization (GO:0030036)|cell chemotaxis (GO:0060326)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|enzyme activator activity (GO:0008047)|receptor binding (GO:0005102)			lung(2)	2	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CGCGCAGCAGGTGGGTACCGG	0.726																																						uc003hhh.2																			0				lung(2)	2						c.e1+1		Homo sapiens chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) (CXCL1), transcript variant 1, mRNA.							9.0	13.0	11.0					4																	74735288		2059	4173	6232	SO:0001630	splice_region_variant	2919				actin cytoskeleton organization|cell proliferation|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|intracellular signal transduction|negative regulation of cell proliferation|nervous system development	extracellular space|intracellular	chemokine activity|enzyme activator activity|growth factor activity	g.chr4:74735288G>T	J03561	CCDS47074.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163739		"""Endogenous ligands"""	4602	protein-coding gene	gene with protein product		155730	"""GRO1 oncogene (melanoma growth stimulating activity, alpha)"", ""fibroblast secretory protein"""	MGSA, GRO1, FSP		2217207	Standard	NM_001511		Approved	SCYB1, GROa, MGSA-a, NAP-3	uc003hhh.3	P09341		ENST00000395761.3:c.100+1G>T	4.37:g.74735288G>T							p.G34_splice	NM_001511	NP_001502	P09341	GROA_HUMAN	all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)		1	179	+	Breast(15;0.00102)		34					Q9UCR7	Splice_Site	SNP	ENST00000395761.3	37	c.100_splice	CCDS47074.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.750339	0.30955	.	.	ENSG00000163739	ENST00000395761	.	.	.	3.82	2.97	0.34412	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3137	0.26489	0.1244:0.0:0.8756:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CXCL1	74954152	1.000000	0.71417	0.383000	0.26132	0.066000	0.16364	2.287000	0.43505	0.940000	0.37473	0.467000	0.42956	.		0.726	CXCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362734.1		Intron
EPGN	255324	broad.mit.edu	37	4	75174232	75174232	+	5'UTR	SNP	A	A	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr4:75174232A>T	ENST00000413830.1	+	0	43				EPGN_ENST00000509145.1_5'Flank|EPGN_ENST00000502358.1_5'Flank|EPGN_ENST00000505212.1_5'Flank|EPGN_ENST00000514968.1_5'Flank|EPGN_ENST00000332112.4_5'UTR|EPGN_ENST00000503098.1_5'Flank	NM_001270989.1	NP_001257918.1	Q6UW88	EPGN_HUMAN	epithelial mitogen						activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)			breast(3)|liver(1)|lung(1)|skin(1)	6			Lung(101;0.196)			AGAGAAAGAAAGTTAAGCAAC	0.363																																						uc003hic.1																			0				breast(3)|liver(1)|lung(1)|skin(1)	6								Homo sapiens epithelial mitogen homolog (mouse) (EPGN), mRNA.							151.0	153.0	152.0					4																	75174232		2203	4300	6503	SO:0001623	5_prime_UTR_variant	255324				activation of MAPK activity|angiogenesis|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	extracellular region|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity	g.chr4:75174232A>T		CCDS59475.1, CCDS59476.1, CCDS59477.1, CCDS59478.1, CCDS59479.1	4q13.3	2012-12-07	2012-12-07						17470	protein-coding gene	gene with protein product			"""epithelial mitogen homolog (mouse)"""				Standard	NM_001270989		Approved	epigen, EPG, PRO9904, ALGV3072	uc003hic.2	Q6UW88		ENST00000413830.1:c.-19A>T	4.37:g.75174232A>T						BC016361_uc003hhv.1_Intron|EPGN_uc003hhw.3_5'UTR|EPGN_uc003hib.1_5'UTR|EPGN_uc003hhy.1_5'UTR|EPGN_uc003hhz.1_5'UTR|EPGN_uc010iin.1_5'UTR|EPGN_uc003hhx.1_Non-coding_Transcript|EPGN_uc003hia.1_5'UTR				Q6UW88	EPGN_HUMAN	Lung(101;0.196)		0		+								A1BMM3|A1BMM4|A1BMM5|A1BMM6|A1BMM7|A1BMM8|A8K090	Translation_Start_Site	SNP	ENST00000413830.1	37		CCDS59478.1																																																																																				0.363	EPGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362738.1	NM_001013442	
PDHA2	5161	broad.mit.edu	37	4	96761394	96761394	+	Silent	SNP	C	C	T	rs143281239		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr4:96761394C>T	ENST00000295266.4	+	1	156	c.93C>T	c.(91-93)gaC>gaT	p.D31D		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	31					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.D31E(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		CCTCAAATGACGCTACATTTG	0.502																																						uc003htr.4																			1	Substitution - Missense(1)	p.D31E(2)	lung(1)	NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46						c.(91-93)gaC>gaT		Homo sapiens pyruvate dehydrogenase (lipoamide) alpha 2 (PDHA2), mRNA.	NADH(DB00157)	C		1,4405	2.1+/-5.4	0,1,2202	58.0	58.0	58.0		93	-9.3	0.0	4	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	PDHA2	NM_005390.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		31/389	96761394	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5161				glycolysis	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity	g.chr4:96761394C>T		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.93C>T	4.37:g.96761394C>T							p.D31D	NM_005390	NP_005381	P29803	ODPAT_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	0	156	+		Hepatocellular(203;0.114)	31					B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Silent	SNP	ENST00000295266.4	37	c.93C>T	CCDS3644.1																																																																																				0.502	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1		
PRMT9	90826	broad.mit.edu	37	4	148591889	148591889	+	Missense_Mutation	SNP	G	G	A	rs201783758		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr4:148591889G>A	ENST00000322396.6	-	5	991	c.749C>T	c.(748-750)tCc>tTc	p.S250F	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.S137F	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		250	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TACAACTAGGGACACTCTATA	0.328																																						uc003ilc.3																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						c.(748-750)tCc>tTc		Homo sapiens protein arginine methyltransferase 10 (putative) (PRMT10), mRNA.							97.0	100.0	99.0					4																	148591889		2203	4300	6503	SO:0001583	missense	90826					cytoplasm	binding|protein methyltransferase activity	g.chr4:148591889G>A																												ENST00000322396.6:c.749C>T	4.37:g.148591889G>A	ENSP00000314396:p.Ser250Phe					PRMT10_uc003ild.3_Missense_Mutation_p.S137F	p.S250F	NM_138364	NP_612373	Q6P2P2	ANM10_HUMAN			4	891	-			250					A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	c.749C>T	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629348	0.87560	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.22539	1.95;1.95	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.54271	0.1848	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59392	-0.7463	10	0.87932	D	0	-6.288	19.8241	0.96610	0.0:0.0:1.0:0.0	.	250	Q6P2P2	ANM10_HUMAN	F	250;137	ENSP00000314396:S250F;ENSP00000439508:S137F	ENSP00000314396:S250F	S	-	2	0	PRMT10	148811339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.205000	0.95048	2.758000	0.94735	0.655000	0.94253	TCC		0.328	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
PIK3R1	5295	broad.mit.edu	37	5	67592121	67592121	+	Missense_Mutation	SNP	T	T	C			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr5:67592121T>C	ENST00000521381.1	+	15	2553	c.1937T>C	c.(1936-1938)tTt>tCt	p.F646S	PIK3R1_ENST00000396611.1_Missense_Mutation_p.F654S|PIK3R1_ENST00000521657.1_Missense_Mutation_p.F646S|PIK3R1_ENST00000523872.1_Missense_Mutation_p.F283S|PIK3R1_ENST00000274335.5_Missense_Mutation_p.F646S|PIK3R1_ENST00000320694.8_Missense_Mutation_p.F346S|PIK3R1_ENST00000336483.5_Missense_Mutation_p.F376S	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	646	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	GATGGCACTTTTCTTGTCCGG	0.453			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												uc003jva.3				Rec	yes		5	5q13.1	5295	"""Mis, F, O"""	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""			"""E, O"""			"""gliobastoma, ovarian, colorectal"""		2	Whole gene deletion(1)|Unknown(1)	p.0?(1)|p.?(1)	large_intestine(1)|lung(1)	breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178						c.(1936-1938)tTt>tCt		Homo sapiens phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1), transcript variant 1, mRNA.	Isoproterenol(DB01064)						172.0	165.0	167.0					5																	67592121		2203	4300	6503	SO:0001583	missense	5295				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	g.chr5:67592121T>C	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1937T>C	5.37:g.67592121T>C	ENSP00000428056:p.Phe646Ser	TCGA GBM(4;<1E-08)				PIK3R1_uc003jvc.3_Missense_Mutation_p.F346S|PIK3R1_uc003jvd.3_Missense_Mutation_p.F376S|PIK3R1_uc003jve.3_Missense_Mutation_p.F325S|PIK3R1_uc021xzn.1_Missense_Mutation_p.F283S	p.F646S	NM_181523	NP_852664	P27986	P85A_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	14	2517	+		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)	646			SH2 2.		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	c.1937T>C	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.950495	0.92660	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000523872	D;D;D;D;D;D;D	0.96967	-4.19;-4.19;-4.19;-4.19;-4.19;-4.19;-4.19	5.15	5.15	0.70609	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.99052	0.9675	H	0.99454	4.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.98897	1.0775	10	0.87932	D	0	-18.8473	15.1338	0.72545	0.0:0.0:0.0:1.0	.	376;346;646	P27986-2;P27986-3;P27986	.;.;P85A_HUMAN	S	646;646;654;646;346;376;283	ENSP00000428056:F646S;ENSP00000429277:F646S;ENSP00000379855:F654S;ENSP00000274335:F646S;ENSP00000323512:F346S;ENSP00000338554:F376S;ENSP00000430098:F283S	ENSP00000274335:F646S	F	+	2	0	PIK3R1	67627877	1.000000	0.71417	0.881000	0.34555	0.992000	0.81027	7.868000	0.87116	2.171000	0.68590	0.528000	0.53228	TTT		0.453	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
LNPEP	4012	broad.mit.edu	37	5	96320900	96320900	+	Missense_Mutation	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr5:96320900C>T	ENST00000231368.5	+	3	1669	c.977C>T	c.(976-978)aCc>aTc	p.T326I	LNPEP_ENST00000395770.3_Missense_Mutation_p.T312I	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	326					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		GAGCAATACACCGCTTTATCA	0.378																																						uc003kmv.1																			0				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34						c.(976-978)aCc>aTc		Homo sapiens leucyl/cystinyl aminopeptidase (LNPEP), transcript variant 1, mRNA.							129.0	125.0	126.0					5																	96320900		2203	4300	6503	SO:0001583	missense	4012				cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding	g.chr5:96320900C>T	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.977C>T	5.37:g.96320900C>T	ENSP00000231368:p.Thr326Ile					LNPEP_uc003kmw.1_Missense_Mutation_p.T312I	p.T326I	NM_005575	NP_787116	Q9UIQ6	LCAP_HUMAN		COAD - Colon adenocarcinoma(37;0.072)	2	1491	+		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)	326					O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	c.977C>T	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	C	3.546	-0.092761	0.07053	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.04603	3.59;3.59	5.34	5.34	0.76211	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.424075	0.26553	N	0.023725	T	0.04861	0.0131	L	0.37466	1.105	0.25957	N	0.98268	B	0.06786	0.001	B	0.09377	0.004	T	0.36939	-0.9727	10	0.17369	T	0.5	.	12.386	0.55333	0.0:0.9216:0.0:0.0784	.	326	Q9UIQ6	LCAP_HUMAN	I	326;312	ENSP00000231368:T326I;ENSP00000379117:T312I	ENSP00000231368:T326I	T	+	2	0	LNPEP	96346656	0.956000	0.32656	0.993000	0.49108	0.972000	0.66771	3.156000	0.50708	2.667000	0.90743	0.643000	0.83706	ACC		0.378	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
FAT2	2196	broad.mit.edu	37	5	150925630	150925630	+	Silent	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr5:150925630G>A	ENST00000261800.5	-	9	5070	c.5058C>T	c.(5056-5058)agC>agT	p.S1686S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1686	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTCAGAGGGGCTCATAGCAG	0.443																																						uc003lue.4																			0		p.M1685V(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196						c.(5056-5058)agC>agT		Homo sapiens FAT tumor suppressor homolog 2 (Drosophila) (FAT2), mRNA.							65.0	72.0	70.0					5																	150925630		2203	4300	6503	SO:0001819	synonymous_variant	2196				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding	g.chr5:150925630G>A	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.5058C>T	5.37:g.150925630G>A							p.S1686S	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		8	5071	-		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	1686			Cadherin 15.		O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	c.5058C>T	CCDS4317.1																																																																																				0.443	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
ENPP4	22875	broad.mit.edu	37	6	46107513	46107513	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr6:46107513G>A	ENST00000321037.4	+	2	423	c.193G>A	c.(193-195)Gtt>Att	p.V65I		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	65					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TGTTAAAAATGTTTTTATCAC	0.363																																						uc003oxy.3																			0				central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						c.(193-195)Gtt>Att		Homo sapiens ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative) (ENPP4), mRNA.							64.0	66.0	65.0					6																	46107513		2203	4299	6502	SO:0001583	missense	22875					integral to membrane	hydrolase activity	g.chr6:46107513G>A	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.193G>A	6.37:g.46107513G>A	ENSP00000318066:p.Val65Ile						p.V65I	NM_014936	NP_055751	Q9Y6X5	ENPP4_HUMAN			1	452	+			65					A8K5G1|Q7L2N1	Missense_Mutation	SNP	ENST00000321037.4	37	c.193G>A	CCDS34468.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.679225	0.47886	.	.	ENSG00000001561	ENST00000321037;ENST00000371401	T	0.73258	-0.73	5.96	5.96	0.96718	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.108203	0.64402	D	0.000008	T	0.57784	0.2077	L	0.47190	1.495	0.43593	D	0.995944	P	0.36330	0.548	B	0.37304	0.246	T	0.56768	-0.7924	10	0.24483	T	0.36	-23.8661	20.4192	0.99033	0.0:0.0:1.0:0.0	.	65	Q9Y6X5	ENPP4_HUMAN	I	65	ENSP00000318066:V65I	ENSP00000318066:V65I	V	+	1	0	ENPP4	46215472	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.184000	0.50926	2.831000	0.97527	0.650000	0.86243	GTT		0.363	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
KIF25	3834	broad.mit.edu	37	6	168443353	168443353	+	Silent	SNP	G	G	A	rs147561163		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr6:168443353G>A	ENST00000443060.2	+	9	1333	c.942G>A	c.(940-942)ccG>ccA	p.P314P	KIF25_ENST00000351261.3_Intron|KIF25_ENST00000354419.2_Silent_p.P314P			Q9UIL4	KIF25_HUMAN	kinesin family member 25	314	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P314P(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCCATGCCCCGTACCGGAACA	0.652																																						uc003qwk.1																			1	Substitution - coding silent(1)	p.P314P(2)	cervix(1)	NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29						c.(940-942)ccG>ccA		Homo sapiens kinesin family member 25 (KIF25), transcript variant 1, mRNA.		G	,	0,4406		0,0,2203	112.0	107.0	109.0		,942	-8.2	0.0	6	dbSNP_134	109	3,8597	3.0+/-9.4	0,3,4297	no	intron,coding-synonymous	KIF25	NM_005355.3,NM_030615.2	,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,	,314/385	168443353	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	3834				microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity	g.chr6:168443353G>A	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.942G>A	6.37:g.168443353G>A						KIF25_uc003qwl.1_Intron	p.P314P	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)	7	1204	+		Breast(66;1.07e-05)|Ovarian(120;0.0728)	314					O94775|Q5SZU9	Silent	SNP	ENST00000443060.2	37	c.942G>A	CCDS5305.1																																																																																				0.652	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1		
SDK1	221935	broad.mit.edu	37	7	4153898	4153898	+	Missense_Mutation	SNP	G	G	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr7:4153898G>A	ENST00000404826.2	+	25	3954	c.3815G>A	c.(3814-3816)cGg>cAg	p.R1272Q	SDK1_ENST00000389531.3_Missense_Mutation_p.R1272Q	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1272	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGCCGGACGCGGGAGTCAGGT	0.652																																						uc003smx.3																			0				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153						c.(3814-3816)cGg>cAg		Homo sapiens sidekick cell adhesion molecule 1 (SDK1), transcript variant 1, mRNA.							18.0	18.0	18.0					7																	4153898		2197	4297	6494	SO:0001583	missense	221935				cell adhesion	integral to membrane		g.chr7:4153898G>A	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3815G>A	7.37:g.4153898G>A	ENSP00000385899:p.Arg1272Gln					SDK1_uc010kso.3_Missense_Mutation_p.R548Q	p.R1272Q	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)	24	3954	+		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)	1272					Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	c.3815G>A	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.855984	0.71834	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.52983	0.64;0.64	5.38	5.38	0.77491	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.086696	0.46758	D	0.000265	T	0.61211	0.2329	L	0.39326	1.205	0.22728	N	0.998805	D;D	0.76494	0.999;0.988	D;B	0.65443	0.935;0.421	T	0.57341	-0.7828	10	0.72032	D	0.01	.	19.1613	0.93533	0.0:0.0:1.0:0.0	.	1272;1272	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	Q	1272	ENSP00000385899:R1272Q;ENSP00000374182:R1272Q	ENSP00000374182:R1272Q	R	+	2	0	SDK1	4120424	1.000000	0.71417	0.508000	0.27688	0.448000	0.32197	6.207000	0.72159	2.507000	0.84556	0.655000	0.94253	CGG		0.652	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
HGF	3082	broad.mit.edu	37	7	81386513	81386513	+	Silent	SNP	G	G	A	rs367553438		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr7:81386513G>A	ENST00000222390.5	-	4	700	c.474C>T	c.(472-474)caC>caT	p.H158H	HGF_ENST00000423064.2_Silent_p.H158H|HGF_ENST00000354224.6_Silent_p.H158H|HGF_ENST00000457544.2_Silent_p.H158H|HGF_ENST00000453411.1_Silent_p.H158H|HGF_ENST00000453018.1_Silent_p.H55H|HGF_ENST00000444829.2_Silent_p.H158H	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	158	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						ACCTGTGTTCGTGTGGTATCA	0.393																																						uc003uhl.3																			0				NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						c.(472-474)caC>caT		Homo sapiens hepatocyte growth factor (hepapoietin A; scatter factor) (HGF), transcript variant 1, mRNA.		G	,,,,	1,4405	2.1+/-5.4	0,1,2202	172.0	157.0	162.0		474,474,474,474,474	-6.2	0.9	7		162	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HGF	NM_000601.4,NM_001010931.1,NM_001010932.1,NM_001010933.1,NM_001010934.1	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	158/729,158/291,158/724,158/286,158/211	81386513	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3082				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity	g.chr7:81386513G>A		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"""hepatopoietin A"", ""fibroblast-derived tumor cytotoxic factor"", ""scatter factor"", ""lung fibroblast-derived mitogen"""	142409	"""deafness, autosomal recessive 39"""	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.474C>T	7.37:g.81386513G>A						HGF_uc003uhm.3_Silent_p.H158H|HGF_uc003uhn.1_Silent_p.H158H|HGF_uc003uho.1_Silent_p.H158H|HGF_uc003uhp.3_Silent_p.H158H|HGF_uc022agw.1_Silent_p.H158H	p.H158H	NM_000601	NP_000592	P14210	HGF_HUMAN			3	639	-			158			Kringle 1.		A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Silent	SNP	ENST00000222390.5	37	c.474C>T	CCDS5597.1																																																																																				0.393	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601	
SAMD12	401474	broad.mit.edu	37	8	119452171	119452171	+	Silent	SNP	C	C	G			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr8:119452171C>G	ENST00000314727.4	-	3	358	c.222G>C	c.(220-222)gtG>gtC	p.V74V	SAMD12_ENST00000409003.4_Silent_p.V74V	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	74										endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			TCCATAGAGCCACCGGTTTAG	0.428																																						uc003yom.2																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9						c.(220-222)gtG>gtC		Homo sapiens sterile alpha motif domain containing 12 (SAMD12), transcript variant 2, mRNA.							139.0	122.0	128.0					8																	119452171		2203	4300	6503	SO:0001819	synonymous_variant	401474							g.chr8:119452171C>G	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"""Sterile alpha motif (SAM) domain containing"""	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.222G>C	8.37:g.119452171C>G						SAMD12_uc010mda.1_Silent_p.V74V|SAMD12_uc010mdb.1_Non-coding_Transcript	p.V74V	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	STAD - Stomach adenocarcinoma(47;0.00391)		2	351	-	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		74					Q0P502	Silent	SNP	ENST00000314727.4	37	c.222G>C	CCDS6325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.685|9.685	1.150421|1.150421	0.21371|0.21371	.|.	.|.	ENSG00000177570|ENSG00000177570	ENST00000453675|ENST00000526765	.|.	.|.	.|.	5.68|5.68	4.79|4.79	0.61399|0.61399	.|.	.|.	.|.	.|.	.|.	T|T	0.60676|0.60676	0.2287|0.2287	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.58787|0.58787	-0.7575|-0.7575	4|4	.|.	.|.	.|.	-11.8271|-11.8271	9.9162|9.9162	0.41436|0.41436	0.1372:0.7922:0.0:0.0705|0.1372:0.7922:0.0:0.0705	.|.	.|.	.|.	.|.	R|S	71|89	.|.	.|.	G|W	-|-	1|2	0|0	SAMD12|SAMD12	119521352|119521352	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	0.967000|0.967000	0.29344|0.29344	1.369000|1.369000	0.46134|0.46134	0.561000|0.561000	0.74099|0.74099	GGC|TGG		0.428	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506	
CELP	1057	broad.mit.edu	37	9	135961717	135961717	+	RNA	SNP	C	C	T	rs538477299		TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chr9:135961717C>T	ENST00000411440.2	+	0	552					NR_001275.2				carboxyl ester lipase pseudogene																		GGGTGGGGGCCGACCATAGAG	0.602													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14612	0.0		0.0	False		,,,				2504	0.0					uc011mcu.1																			0											c.(457-459)gcC>gcT		Homo sapiens carboxyl ester lipase pseudogene (CELP), non-coding RNA.																																						1057							g.chr9:135961717C>T	L14813		9q34.2	2014-03-18	2003-02-28	2003-03-07	ENSG00000170827	ENSG00000170827			1849	pseudogene	pseudogene			"""carboxyl ester lipase-like (bile salt-stimulated lipase-like)"""	CELL		1639390	Standard	NR_001275		Approved		uc011mcu.1		OTTHUMG00000020857		9.37:g.135961717C>T							p.A153A							3	552	+									Silent	SNP	ENST00000411440.2	37	c.459C>T																																																																																					0.602	CELP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000339837.1	NM_001808	
WWC3	55841	broad.mit.edu	37	X	10106937	10106937	+	Silent	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chrX:10106937C>T	ENST00000380861.4	+	21	3436	c.3045C>T	c.(3043-3045)gaC>gaT	p.D1015D	WWC3_ENST00000454666.1_Silent_p.D1015D	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	1015					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TGCTTCGGGACGAGCGGCTCC	0.711																																						uc004csx.4																			0				NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						c.(3043-3045)gaC>gaT		Homo sapiens WWC family member 3 (WWC3), mRNA.							17.0	17.0	17.0					X																	10106937		2188	4276	6464	SO:0001819	synonymous_variant	55841							g.chrX:10106937C>T	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.3045C>T	X.37:g.10106937C>T						WWC3_uc010nds.3_Silent_p.D679D|WWC3_uc010ndt.3_Non-coding_Transcript	p.D1015D	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN			20	3243	+			1015					A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	c.3045C>T	CCDS14136.1																																																																																				0.711	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
MAGED2	10916	broad.mit.edu	37	X	54841851	54841851	+	Silent	SNP	C	C	T			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chrX:54841851C>T	ENST00000375068.1	+	12	1790	c.1557C>T	c.(1555-1557)gaC>gaT	p.D519D	MAGED2_ENST00000375060.1_Silent_p.D434D|MAGED2_ENST00000347546.4_Silent_p.D501D|MAGED2_ENST00000218439.4_Silent_p.D519D|MAGED2_ENST00000396224.1_Silent_p.D519D|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375058.1_Silent_p.D519D|MAGED2_ENST00000375062.4_Silent_p.D434D|MAGED2_ENST00000375053.2_Silent_p.D519D			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	519						membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						GCAACTGGGACGAAGCTGATA	0.617																																						uc004dtk.1																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						c.(1555-1557)gaC>gaT		Homo sapiens melanoma antigen family D, 2 (MAGED2), transcript variant 2, mRNA.							23.0	23.0	23.0					X																	54841851		2203	4296	6499	SO:0001819	synonymous_variant	10916							g.chrX:54841851C>T	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1557C>T	X.37:g.54841851C>T						MAGED2_uc004dtl.1_Silent_p.D519D|MAGED2_uc004dtm.1_Silent_p.D434D|MAGED2_uc004dtn.1_Silent_p.D519D|MAGED2_uc004dto.1_Silent_p.D493D	p.D519D	NM_177433	NP_957516	Q9UNF1	MAGD2_HUMAN			11	1651	+			519					A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	37	c.1557C>T	CCDS14362.1																																																																																				0.617	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
NLGN3	54413	broad.mit.edu	37	X	70368006	70368006	+	Missense_Mutation	SNP	A	A	G			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chrX:70368006A>G	ENST00000358741.3	+	2	710	c.407A>G	c.(406-408)gAg>gGg	p.E136G	NLGN3_ENST00000536169.1_Missense_Mutation_p.E136G|NLGN3_ENST00000374051.3_Missense_Mutation_p.E136G	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	136					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					TACATCCAGGAGCCCAACGAA	0.612																																					Esophageal Squamous(103;760 1488 16849 22250 40351)	uc004dzd.2																			0				biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37						c.(406-408)gAg>gGg		Homo sapiens neuroligin 3 (NLGN3), transcript variant 1, mRNA.							145.0	94.0	111.0					X																	70368006		2203	4300	6503	SO:0001583	missense	54413				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	neurexin binding|receptor activity	g.chrX:70368006A>G	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.407A>G	X.37:g.70368006A>G	ENSP00000351591:p.Glu136Gly					NLGN3_uc004dzb.3_Missense_Mutation_p.E136G|NLGN3_uc011mps.2_Missense_Mutation_p.E136G|NLGN3_uc004dzc.3_Missense_Mutation_p.E19G|NLGN3_uc011mpr.1_Missense_Mutation_p.E136G	p.E136G	NM_181303	NP_851820	Q9NZ94	NLGN3_HUMAN			1	741	+	Renal(35;0.156)		136					B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Missense_Mutation	SNP	ENST00000358741.3	37	c.407A>G	CCDS55441.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.568065	0.45798	.	.	ENSG00000196338	ENST00000536169;ENST00000542063;ENST00000374051;ENST00000395855;ENST00000358741	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	4.79	4.79	0.61399	.	0.294316	0.39687	N	0.001291	T	0.47432	0.1445	N	0.16790	0.44	0.58432	D	0.99999	B;B;B	0.32781	0.017;0.384;0.014	B;B;B	0.39935	0.065;0.314;0.039	T	0.52866	-0.8518	10	0.54805	T	0.06	.	13.5479	0.61715	1.0:0.0:0.0:0.0	.	136;136;136	D3DVV1;B7Z5Y1;Q9NZ94-2	.;.;.	G	136;19;136;136;136	ENSP00000445298:E136G;ENSP00000363163:E136G;ENSP00000379196:E136G;ENSP00000351591:E136G	ENSP00000351591:E136G	E	+	2	0	NLGN3	70284731	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.761000	0.91691	1.771000	0.52183	0.417000	0.27973	GAG		0.612	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977	
ATRX	546	broad.mit.edu	37	X	76937694	76937694	+	Missense_Mutation	SNP	C	C	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chrX:76937694C>A	ENST00000373344.5	-	9	3268	c.3054G>T	c.(3052-3054)aaG>aaT	p.K1018N	ATRX_ENST00000395603.3_Missense_Mutation_p.K980N|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1018					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GCTCAGGTAACTTTTCAGTGC	0.308			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															uc004ecp.4				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(3052-3054)aaG>aaT		Homo sapiens alpha thalassemia/mental retardation syndrome X-linked (ATRX), transcript variant 1, mRNA.	Phosphatidylserine(DB00144)						69.0	72.0	71.0					X																	76937694		2198	4285	6483	SO:0001583	missense	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76937694C>A	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.3054G>T	X.37:g.76937694C>A	ENSP00000362441:p.Lys1018Asn					ATRX_uc004ecq.4_Missense_Mutation_p.K980N|ATRX_uc004eco.4_Missense_Mutation_p.K803N|ATRX_uc004ecr.2_Missense_Mutation_p.K950N|ATRX_uc010nlx.1_Missense_Mutation_p.K989N|ATRX_uc010nly.1_Missense_Mutation_p.K963N	p.K1018N	NM_000489	NP_000480	P46100	ATRX_HUMAN			8	3286	-			1018					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	c.3054G>T	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254656	0.22965	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.93659	-3.26;-3.26	5.56	0.695	0.18070	.	0.398362	0.25514	N	0.030159	D	0.90796	0.7110	L	0.34521	1.04	0.39136	D	0.961958	P;D;P;P	0.56746	0.883;0.977;0.928;0.883	B;P;P;B	0.52856	0.444;0.711;0.647;0.444	D	0.88938	0.3378	10	0.66056	D	0.02	-11.8485	9.5098	0.39069	0.0:0.4138:0.0:0.5862	.	1018;950;980;1018	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	N	1018;980;945	ENSP00000362441:K1018N;ENSP00000378967:K980N	ENSP00000362441:K1018N	K	-	3	2	ATRX	76824350	0.154000	0.22792	0.649000	0.29536	0.964000	0.63967	-0.122000	0.10627	0.256000	0.21614	0.513000	0.50165	AAG		0.308	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
STAG2	10735	broad.mit.edu	37	X	123205085	123205085	+	Nonsense_Mutation	SNP	T	T	A			TCGA-06-6388-01A-12D-1845-08	TCGA-06-6388-10A-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9214f8b-6684-4e29-812c-2a44963e8914	4c5eb4d1-3046-4691-99de-dd448adc1dfc	g.chrX:123205085T>A	ENST00000371160.1	+	25	2735	c.2445T>A	c.(2443-2445)taT>taA	p.Y815*	STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.Y815*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.Y815*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.Y815*|STAG2_ENST00000371145.3_Nonsense_Mutation_p.Y815*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.Y746*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	815					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CATTAGTGTATACCCCTGATT	0.363																																						uc004eua.3																			0				breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						c.(2443-2445)taT>taA		Homo sapiens stromal antigen 2 (STAG2), transcript variant 1, mRNA.							224.0	194.0	204.0					X																	123205085		2203	4300	6503	SO:0001587	stop_gained	10735				cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding	g.chrX:123205085T>A	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2445T>A	X.37:g.123205085T>A	ENSP00000360202:p.Tyr815*					STAG2_uc004etz.4_Nonsense_Mutation_p.Y815*|STAG2_uc004eub.3_Nonsense_Mutation_p.Y815*|STAG2_uc004euc.3_Nonsense_Mutation_p.Y815*|STAG2_uc004eud.3_Nonsense_Mutation_p.Y815*|STAG2_uc004eue.3_Nonsense_Mutation_p.Y815*	p.Y815*	NM_001042749	NP_001036215	Q8N3U4	STAG2_HUMAN			24	2849	+			815					B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	37	c.2445T>A	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	T	41	9.072606	0.99057	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.44	0.632	0.17705	.	0.129187	0.53938	D	0.000045	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0362	9.4512	0.38727	0.0:0.5612:0.0:0.4388	.	.	.	.	X	815;746;815;815;815;815	.	ENSP00000218089:Y815X	Y	+	3	2	STAG2	123032766	0.995000	0.38212	0.980000	0.43619	0.824000	0.46624	0.443000	0.21644	-0.346000	0.08312	-1.174000	0.01732	TAT		0.363	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
