#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
FAF1	11124	broad.mit.edu	37	1	51001131	51001131	+	Splice_Site	SNP	T	T	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr1:51001131T>C	ENST00000396153.2	-	15	1857		c.e15-2		FAF1_ENST00000545823.1_Splice_Site|FAF1_ENST00000371778.4_Splice_Site	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1						apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TTGTGTTCCCTAAAAACATAT	0.323																																						uc009vyx.1																			1	Whole gene deletion(1)		thyroid(1)	ovary(1)|pancreas(1)	2						c.e16-1		FAS-associated factor 1							116.0	111.0	112.0					1																	51001131		2203	4300	6503	SO:0001630	splice_region_variant	11124				apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	g.chr1:51001131T>C	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.1406-2A>G	1.37:g.51001131T>C						FAF1_uc009vyw.1_Splice_Site|FAF1_uc001cse.1_Splice_Site_p.G469_splice|FAF1_uc010onc.1_Splice_Site_p.G227_splice	p.G469_splice	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN		GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)	16	1469	-								Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Splice_Site	SNP	ENST00000396153.2	37	c.1406_splice	CCDS554.1	.	.	.	.	.	.	.	.	.	.	T	16.78	3.217086	0.58560	.	.	ENSG00000185104	ENST00000396153;ENST00000371778;ENST00000545823;ENST00000371780;ENST00000543607	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.158	0.72759	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAF1	50773719	1.000000	0.71417	0.994000	0.49952	0.556000	0.35491	7.671000	0.83941	1.979000	0.57680	0.482000	0.46254	.		0.323	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051	Intron
MAB21L3	126868	broad.mit.edu	37	1	116666896	116666896	+	Silent	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr1:116666896C>T	ENST00000369500.3	+	4	664	c.399C>T	c.(397-399)atC>atT	p.I133I	MAB21L3_ENST00000464946.1_3'UTR	NM_152367.2	NP_689580.2	Q8N8X9	MB213_HUMAN	mab-21-like 3 (C. elegans)	133										breast(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|urinary_tract(1)	19						ATGTGAACATCGACGGAGACA	0.557																																						uc001egc.1																			0					0						c.(397-399)ATC>ATT		hypothetical protein LOC126868							121.0	110.0	114.0					1																	116666896		2203	4300	6503	SO:0001819	synonymous_variant	126868							g.chr1:116666896C>T	AK096035	CCDS886.1	1p13.1	2011-02-23	2011-02-23	2011-02-23	ENSG00000173212	ENSG00000173212			26787	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 161"""	C1orf161		14702039	Standard	NM_152367		Approved	FLJ38716	uc001egc.1	Q8N8X9	OTTHUMG00000012110	ENST00000369500.3:c.399C>T	1.37:g.116666896C>T							p.I133I	NM_152367	NP_689580	Q8N8X9	MB213_HUMAN		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)	4	664	+	Lung SC(450;0.184)	all_cancers(81;0.00142)|all_lung(203;0.000139)|all_epithelial(167;0.000401)|Lung NSC(69;0.000705)	133					Q5TDL7	Silent	SNP	ENST00000369500.3	37	c.399C>T	CCDS886.1																																																																																				0.557	MAB21L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033486.1	NM_152367	
ASTN1	460	broad.mit.edu	37	1	176993825	176993825	+	Silent	SNP	C	C	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr1:176993825C>A	ENST00000367654.3	-	6	1375	c.1164G>T	c.(1162-1164)ctG>ctT	p.L388L	ASTN1_ENST00000367657.3_Silent_p.L388L|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Silent_p.L388L|ASTN1_ENST00000361833.2_Silent_p.L388L	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	388					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TGATGCTGATCAGGGTCAAGG	0.512																																						uc001glc.2																			0				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						c.(1162-1164)CTG>CTT		astrotactin isoform 1							159.0	125.0	137.0					1																	176993825		2203	4300	6503	SO:0001819	synonymous_variant	460				cell migration|neuron cell-cell adhesion	integral to membrane		g.chr1:176993825C>A	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1164G>T	1.37:g.176993825C>A						ASTN1_uc001glb.1_Silent_p.L388L|ASTN1_uc001gld.1_Silent_p.L388L|ASTN1_uc009wwx.1_Silent_p.L388L|ASTN1_uc001gle.3_RNA	p.L388L	NM_004319	NP_004310	O14525	ASTN1_HUMAN			6	1376	-			388			Helical; (Potential).		A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37	c.1164G>T																																																																																					0.512	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
PROX1	5629	broad.mit.edu	37	1	214209144	214209144	+	Silent	SNP	C	C	G			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr1:214209144C>G	ENST00000366958.4	+	5	2789	c.2181C>G	c.(2179-2181)tcC>tcG	p.S727S	PROX1_ENST00000435016.1_Silent_p.S727S|PROX1_ENST00000261454.4_Silent_p.S727S|PROX1_ENST00000498508.2_Silent_p.S727S	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	727	Essential for nuclear localization, interaction with RORG, repression of RORG transcriptional activator activity. {ECO:0000250|UniProtKB:P48437}.|Prospero-like.				aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		TTTTCAAATCCCCGAACTGCC	0.423																																						uc001hkh.2																			0				ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6						c.(2179-2181)TCC>TCG		prospero homeobox 1							81.0	73.0	76.0					1																	214209144		2203	4300	6503	SO:0001819	synonymous_variant	5629				aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding	g.chr1:214209144C>G	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"""Homeoboxes / PROS class"""	9459	protein-coding gene	gene with protein product		601546	"""prospero-related homeobox 1"""			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.2181C>G	1.37:g.214209144C>G							p.S727S	NM_002763	NP_002754	Q92786	PROX1_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)	5	2453	+			727			Prospero-like.		A6NK29|A8K2B1|Q5SW76|Q8TB91	Silent	SNP	ENST00000366958.4	37	c.2181C>G	CCDS31021.1																																																																																				0.423	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763	
PARP1	142	broad.mit.edu	37	1	226558164	226558164	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr1:226558164C>T	ENST00000366794.5	-	15	2268	c.2125G>A	c.(2125-2127)Gca>Aca	p.A709T	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	709	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		ATGGAGTATGCGGCCTGGATC	0.597								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																														uc001hqd.3																			0				lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10						c.(2125-2127)GCA>ACA	Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA	poly (ADP-ribose) polymerase family, member 1							169.0	149.0	156.0					1																	226558164		2203	4300	6503	SO:0001583	missense	142				cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding	g.chr1:226558164C>T	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2125G>A	1.37:g.226558164C>T	ENSP00000355759:p.Ala709Thr						p.A709T	NM_001618	NP_001609	P09874	PARP1_HUMAN		GBM - Glioblastoma multiforme(131;0.0531)	15	2296	-	Breast(184;0.133)		709			PARP alpha-helical.		B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	c.2125G>A	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	C	34	5.328090	0.95733	.	.	ENSG00000143799	ENST00000366794	T	0.58940	0.3	5.79	5.79	0.91817	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.000000	0.85682	D	0.000000	D	0.82912	0.5140	M	0.93062	3.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86063	0.1533	10	0.72032	D	0.01	.	20.0413	0.97592	0.0:1.0:0.0:0.0	.	709	P09874	PARP1_HUMAN	T	709	ENSP00000355759:A709T	ENSP00000355759:A709T	A	-	1	0	PARP1	224624787	1.000000	0.71417	0.183000	0.23137	0.738000	0.42128	7.484000	0.81180	2.751000	0.94390	0.650000	0.86243	GCA		0.597	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
AKR1C4	1109	broad.mit.edu	37	10	5238864	5238864	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr10:5238864G>A	ENST00000380448.1	+	3	287	c.34G>A	c.(34-36)Gat>Aat	p.D12N	U8_ENST00000516100.1_RNA|AKR1CL1_ENST00000445191.1_Intron|AKR1C4_ENST00000263126.1_Missense_Mutation_p.D12N			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	12					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						AGAGCTAAATGATGGTCACTT	0.418																																						uc001ihw.2																			0				ovary(1)	1						c.(34-36)GAT>AAT		aldo-keto reductase family 1, member C4	NADH(DB00157)						272.0	222.0	239.0					10																	5238864		2203	4300	6503	SO:0001583	missense	1109				androgen metabolic process|bile acid biosynthetic process	cytosol	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid transmembrane transporter activity|chlordecone reductase activity|electron carrier activity	g.chr10:5238864G>A	M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.34G>A	10.37:g.5238864G>A	ENSP00000369814:p.Asp12Asn						p.D12N	NM_001818	NP_001809	P17516	AK1C4_HUMAN			1	67	+			12					Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	c.34G>A	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.058404	0.36277	.	.	ENSG00000198610	ENST00000380448;ENST00000263126;ENST00000397357	T;T	0.48836	0.8;0.8	2.92	2.92	0.33932	NADP-dependent oxidoreductase domain (2);	0.000000	0.64402	D	0.000019	T	0.40297	0.1111	L	0.35854	1.095	0.36894	D	0.890051	P	0.41008	0.735	P	0.44561	0.453	T	0.40232	-0.9574	10	0.21540	T	0.41	.	12.0413	0.53454	0.0:0.0:1.0:0.0	.	12	P17516	AK1C4_HUMAN	N	12	ENSP00000369814:D12N;ENSP00000263126:D12N	ENSP00000263126:D12N	D	+	1	0	AKR1C4	5228864	1.000000	0.71417	0.635000	0.29338	0.310000	0.27922	5.503000	0.66962	1.565000	0.49641	0.591000	0.81541	GAT		0.418	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	
TAF3	83860	broad.mit.edu	37	10	8006394	8006394	+	Silent	SNP	A	A	G			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr10:8006394A>G	ENST00000344293.5	+	3	1127	c.921A>G	c.(919-921)aaA>aaG	p.K307K		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	307					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						CTGTATCCAAAGAAAAGAAAT	0.493																																						uc010qbd.1																			0				ovary(1)	1						c.(919-921)AAA>AAG		RNA polymerase II transcription factor TAFII140							55.0	54.0	55.0					10																	8006394		1871	4087	5958	SO:0001819	synonymous_variant	83860				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding	g.chr10:8006394A>G	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.921A>G	10.37:g.8006394A>G							p.K307K	NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN			3	921	+			307					Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Silent	SNP	ENST00000344293.5	37	c.921A>G	CCDS41487.1																																																																																				0.493	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
OPN4	94233	broad.mit.edu	37	10	88419055	88419055	+	Splice_Site	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr10:88419055C>T	ENST00000241891.5	+	5	797	c.630C>T	c.(628-630)agC>agT	p.S210S	OPN4_ENST00000372071.2_Splice_Site_p.S221S	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	210					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GGCTCCCAGGCGCCTACGTGC	0.622																																						uc001kdq.2																			0				ovary(1)	1						c.(628-630)AGC>AGT		opsin 4 isoform 1							107.0	92.0	97.0					10																	88419055		2203	4300	6503	SO:0001630	splice_region_variant	94233				phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity	g.chr10:88419055C>T	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.629-1C>T	10.37:g.88419055C>T						OPN4_uc001kdp.2_Silent_p.S221S|OPN4_uc010qmk.1_Silent_p.S221S|OPN4_uc009xsx.1_5'Flank	p.S210S	NM_033282	NP_150598	Q9UHM6	OPN4_HUMAN			5	857	+			210			Extracellular (Potential).		B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	37	c.630C>T	CCDS7376.1																																																																																				0.622	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	Silent
RPEL1	729020	broad.mit.edu	37	10	105005758	105005758	+	Missense_Mutation	SNP	C	C	T	rs532886573		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr10:105005758C>T	ENST00000441178.2	+	1	115	c.5C>T	c.(4-6)gCg>gTg	p.A2V		NM_001143909.1	NP_001137381.1																					AGCGGTATGGCGTCGGGCTGC	0.522																																						uc009xxi.2																			0					0						c.(4-6)GCG>GTG		rcRPE protein							57.0	51.0	53.0					10																	105005758		692	1591	2283	SO:0001583	missense	729020				carbohydrate metabolic process		ribulose-phosphate 3-epimerase activity	g.chr10:105005758C>T																												ENST00000441178.2:c.5C>T	10.37:g.105005758C>T	ENSP00000476672:p.Ala2Val					uc001kwr.2_Intron	p.A2V	NM_001143909	NP_001137381	Q2QD12	Q2QD12_HUMAN			1	115	+			2						Missense_Mutation	SNP	ENST00000441178.2	37	c.5C>T																																																																																					0.522	RP11-332O19.5-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050120.2		
OR52M1	119772	broad.mit.edu	37	11	4566916	4566916	+	Missense_Mutation	SNP	C	C	T	rs201510674	byFrequency	TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr11:4566916C>T	ENST00000360213.1	+	1	496	c.496C>T	c.(496-498)Cgc>Tgc	p.R166C		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTGATGATCCGCCTGCGGCT	0.522													C|||	9	0.00179712	0.0	0.0	5008	,	,		18785	0.0		0.001	False		,,,				2504	0.0082					uc010qyf.1																			0					0						c.(496-498)CGC>TGC		olfactory receptor, family 52, subfamily M,							101.0	102.0	102.0					11																	4566916		2201	4298	6499	SO:0001583	missense	119772				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:4566916C>T	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.496C>T	11.37:g.4566916C>T	ENSP00000353343:p.Arg166Cys						p.R166C	NM_001004137	NP_001004137	Q8NGK5	O52M1_HUMAN		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)	1	496	+		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)	166			Extracellular (Potential).			Missense_Mutation	SNP	ENST00000360213.1	37	c.496C>T	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.258228	0.59321	.	.	ENSG00000197790	ENST00000360213	T	0.00152	8.66	4.98	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.142760	0.32593	N	0.005884	T	0.00328	0.0010	M	0.79011	2.435	0.35917	D	0.831551	D	0.76494	0.999	D	0.63192	0.912	T	0.71978	-0.4429	10	0.87932	D	0	.	5.771	0.18253	0.0:0.6425:0.1629:0.1946	.	166	Q8NGK5	O52M1_HUMAN	C	166	ENSP00000353343:R166C	ENSP00000353343:R166C	R	+	1	0	OR52M1	4523492	0.000000	0.05858	0.950000	0.38849	0.952000	0.60782	-2.552000	0.00927	1.385000	0.46445	0.650000	0.86243	CGC		0.522	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
MRVI1	10335	broad.mit.edu	37	11	10647541	10647541	+	Missense_Mutation	SNP	C	C	G	rs373767088		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr11:10647541C>G	ENST00000436272.1	-	8	1337	c.1259G>C	c.(1258-1260)cGg>cCg	p.R420P	MRVI1_ENST00000541483.1_Intron|MRVI1_ENST00000558540.1_Missense_Mutation_p.R132P|MRVI1_ENST00000531107.1_Missense_Mutation_p.R439P|MRVI1_ENST00000423302.2_Missense_Mutation_p.R447P|MRVI1_ENST00000547195.1_Missense_Mutation_p.R356P|MRVI1_ENST00000421747.1_Missense_Mutation_p.R438P|MRVI1_ENST00000424001.1_Missense_Mutation_p.R132P|MRVI1_ENST00000552103.1_Missense_Mutation_p.R356P|MRVI1_ENST00000545852.1_Missense_Mutation_p.R132P|MRVI1_ENST00000527509.2_Missense_Mutation_p.R356P|MRVI1_ENST00000534266.2_Missense_Mutation_p.R132P			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	420					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TTTCTGCATCCGCACGGGCTG	0.597																																						uc010rcc.1																			0				ovary(2)|central_nervous_system(1)	3						c.(1339-1341)CGG>CCG		JAW1-related protein isoform c							12.0	13.0	12.0					11																	10647541		1923	4107	6030	SO:0001583	missense	10335				platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum		g.chr11:10647541C>G	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"""inositol 1,4,5-triphosphate-associated cGMP kinase substrate"", ""IP3R-associated cGMP kinase substrate"""	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1259G>C	11.37:g.10647541C>G	ENSP00000412229:p.Arg420Pro					MRVI1_uc001miw.2_Missense_Mutation_p.R438P|MRVI1_uc010rcb.1_Missense_Mutation_p.R439P|MRVI1_uc009ygb.1_Missense_Mutation_p.R132P|MRVI1_uc001mix.2_Missense_Mutation_p.R132P|MRVI1_uc001miz.2_Missense_Mutation_p.R356P|MRVI1_uc009ygc.1_Missense_Mutation_p.R356P|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_Missense_Mutation_p.R132P|MRVI1_uc010rce.1_Intron	p.R447P	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN		all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)	9	1726	-			420					B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	37	c.1340G>C		.	.	.	.	.	.	.	.	.	.	C	22.9	4.346580	0.82022	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T	0.26223	2.9;2.9;2.33;2.33;1.75;1.75;2.73;2.9;2.33	5.71	5.71	0.89125	.	0.210436	0.40302	N	0.001136	T	0.49864	0.1582	L	0.60455	1.87	0.46260	D	0.998959	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.70016	0.967;0.952;0.921	T	0.42732	-0.9434	10	0.62326	D	0.03	-14.9475	19.8534	0.96748	0.0:1.0:0.0:0.0	.	420;439;438	Q9Y6F6;E9PQY6;Q9Y6F6-4	MRVI1_HUMAN;.;.	P	438;421;420;356;356;132;132;447;439;356	ENSP00000414598:R438P;ENSP00000412229:R420P;ENSP00000448278:R356P;ENSP00000446764:R356P;ENSP00000441971:R132P;ENSP00000401205:R132P;ENSP00000412130:R447P;ENSP00000432436:R439P;ENSP00000432067:R356P	ENSP00000307885:R421P	R	-	2	0	MRVI1	10604117	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.374000	0.52402	2.711000	0.92665	0.563000	0.77884	CGG		0.597	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579	
HTR3A	3359	broad.mit.edu	37	11	113853896	113853896	+	Silent	SNP	C	C	T	rs573001897		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr11:113853896C>T	ENST00000504030.2	+	5	874	c.429C>T	c.(427-429)ggC>ggT	p.G143G	HTR3A_ENST00000506841.2_Silent_p.G143G|HTR3A_ENST00000375498.2_Silent_p.G149G|HTR3A_ENST00000355556.2_Silent_p.G149G|HTR3A_ENST00000299961.5_Silent_p.G128G|HTR3A_ENST00000535865.1_5'UTR			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	143					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	GGCATCAAGGCGAAGTTCAGA	0.537													C|||	1	0.000199681	0.0	0.0	5008	,	,		19985	0.001		0.0	False		,,,				2504	0.0					uc010rxb.1																			0					0						c.(445-447)GGC>GGT		5-hydroxytryptamine (serotonin) receptor 3A	Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)						183.0	162.0	169.0					11																	113853896		2201	4296	6497	SO:0001819	synonymous_variant	3359				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity	g.chr11:113853896C>T	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.429C>T	11.37:g.113853896C>T						HTR3A_uc010rxa.1_Silent_p.G149G|HTR3A_uc009yyx.2_RNA|HTR3A_uc010rxc.1_Silent_p.G128G	p.G149G	NM_213621	NP_998786	P46098	5HT3A_HUMAN		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	5	680	+		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)	143			Extracellular (Potential).		B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Silent	SNP	ENST00000504030.2	37	c.447C>T																																																																																					0.537	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
CPNE8	144402	broad.mit.edu	37	12	39155951	39155951	+	Missense_Mutation	SNP	T	T	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr12:39155951T>A	ENST00000331366.5	-	9	739	c.643A>T	c.(643-645)Atc>Ttc	p.I215F	CPNE8_ENST00000360449.3_Missense_Mutation_p.I203F	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	215	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				CTGACTGAGATCTTGAATGCT	0.308																																						uc001rls.1																			0				pancreas(1)	1						c.(643-645)ATC>TTC		copine VIII							114.0	107.0	109.0					12																	39155951		2203	4299	6502	SO:0001583	missense	144402							g.chr12:39155951T>A	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.643A>T	12.37:g.39155951T>A	ENSP00000329748:p.Ile215Phe						p.I215F	NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN			9	727	-	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)	215			C2 2.		Q2TB41|Q86VY2	Missense_Mutation	SNP	ENST00000331366.5	37	c.643A>T	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.888766	0.52014	.	.	ENSG00000139117	ENST00000331366;ENST00000360449	T;T	0.58060	0.36;0.36	4.05	2.9	0.33743	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.117906	0.56097	D	0.000026	T	0.43211	0.1237	L	0.33668	1.02	0.80722	D	1	B	0.22983	0.078	B	0.33799	0.17	T	0.34850	-0.9812	10	0.52906	T	0.07	-10.4735	8.9067	0.35528	0.0:0.094:0.0:0.906	.	215	Q86YQ8	CPNE8_HUMAN	F	215;203	ENSP00000329748:I215F;ENSP00000353633:I203F	ENSP00000329748:I215F	I	-	1	0	CPNE8	37442218	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.683000	0.84093	0.696000	0.31696	-0.256000	0.11100	ATC		0.308	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634	
KIF21A	55605	broad.mit.edu	37	12	39726188	39726188	+	Missense_Mutation	SNP	C	C	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr12:39726188C>A	ENST00000361418.5	-	21	2894	c.2879G>T	c.(2878-2880)aGa>aTa	p.R960I	KIF21A_ENST00000541463.2_Missense_Mutation_p.R924I|KIF21A_ENST00000544797.2_Missense_Mutation_p.R947I|KIF21A_ENST00000395670.3_Missense_Mutation_p.R960I|KIF21A_ENST00000361961.3_Missense_Mutation_p.R947I			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	960					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TTTCTCTCGTCTTTTTGTGAG	0.398																																						uc001rly.2																			0				ovary(4)|pancreas(1)|lung(1)|skin(1)	7						c.(2878-2880)AGA>ATA		kinesin family member 21A							197.0	185.0	190.0					12																	39726188		2203	4300	6503	SO:0001583	missense	55605				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity	g.chr12:39726188C>A	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2879G>T	12.37:g.39726188C>A	ENSP00000354878:p.Arg960Ile					KIF21A_uc001rlv.2_5'UTR|KIF21A_uc001rlw.2_Missense_Mutation_p.R277I|KIF21A_uc001rlx.2_Missense_Mutation_p.R947I|KIF21A_uc001rlz.2_Missense_Mutation_p.R924I|KIF21A_uc010skl.1_Missense_Mutation_p.R947I	p.R960I	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN			21	3025	-		Lung NSC(34;0.179)|all_lung(34;0.213)	960			Potential.		A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	c.2879G>T	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.0|26.0	4.699546|4.699546	0.88830|0.88830	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000552961|ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.|T;T;T;T;T;T	.|0.71579	.|-0.57;-0.53;0.25;-0.58;-0.47;-0.53	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	.|0.104775	.|0.42172	.|D	.|0.000746	D|D	0.82486|0.82486	0.5047|0.5047	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|P;D;B;B;D	.|0.69078	.|0.937;0.997;0.286;0.328;0.976	.|P;D;B;B;D	.|0.80764	.|0.735;0.994;0.15;0.085;0.918	T|T	0.82051|0.82051	-0.0649|-0.0649	5|10	.|0.49607	.|T	.|0.09	.|.	19.4615|19.4615	0.94920|0.94920	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|947;924;960;947;960	.|F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3	.|.;.;KI21A_HUMAN;.;.	Y|I	308|947;960;960;14;8;947;960;924	.|ENSP00000354851:R947I;ENSP00000379029:R960I;ENSP00000448792:R8I;ENSP00000445606:R947I;ENSP00000354878:R960I;ENSP00000438075:R924I	.|ENSP00000344501:R960I	D|R	-|-	1|2	0|0	KIF21A|KIF21A	38012455|38012455	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.917000|5.917000	0.69989|0.69989	2.576000|2.576000	0.86940|0.86940	0.557000|0.557000	0.71058|0.71058	GAC|AGA		0.398	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
GRIP1	23426	broad.mit.edu	37	12	66838466	66838466	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr12:66838466C>T	ENST00000398016.3	-	12	1497	c.1429G>A	c.(1429-1431)Gga>Aga	p.G477R	GRIP1_ENST00000286445.7_Missense_Mutation_p.G529R|GRIP1_ENST00000359742.4_Missense_Mutation_p.G529R	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GTTGGAATTCCATTGATGGCC	0.458																																						uc001stk.2																			0				ovary(2)	2						c.(1429-1431)GGA>AGA		glutamate receptor interacting protein 1							136.0	132.0	133.0					12																	66838466		1964	4134	6098	SO:0001583	missense	23426				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity	g.chr12:66838466C>T	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1429G>A	12.37:g.66838466C>T	ENSP00000381098:p.Gly477Arg					GRIP1_uc010sta.1_Missense_Mutation_p.G421R|GRIP1_uc001stj.2_Missense_Mutation_p.G259R|GRIP1_uc001stl.1_Missense_Mutation_p.G369R|GRIP1_uc001stm.2_Missense_Mutation_p.G477R	p.G477R	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)	12	1670	-			529			PDZ 4.		B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	c.1429G>A	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.902495|4.902495	0.92035|0.92035	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215|ENST00000538164	T;T;T;T;T;T|.	0.81078|.	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45|.	5.57|5.57	5.57|5.57	0.84162|0.84162	PDZ/DHR/GLGF (4);|.	0.110664|.	0.64402|.	D|.	0.000010|.	D|D	0.88040|0.88040	0.6330|0.6330	H|H	0.95611|0.95611	3.695|3.695	0.80722|0.80722	D|D	1|1	D;D;P;D|.	0.71674|.	0.997;0.969;0.944;0.998|.	D;D;D;D|.	0.78314|.	0.991;0.989;0.918;0.988|.	D|D	0.91138|0.91138	0.4943|0.4943	9|5	.|.	.|.	.|.	-15.8353|-15.8353	19.6192|19.6192	0.95649|0.95649	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	477;529;477;529|.	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2|.	.;GRIP1_HUMAN;.;.|.	R|I	477;529;529;477;421;369|343	ENSP00000381098:G477R;ENSP00000352780:G529R;ENSP00000286445:G529R;ENSP00000446047:G477R;ENSP00000446024:G421R;ENSP00000446011:G369R|.	.|.	G|M	-|-	1|3	0|0	GRIP1|GRIP1	65124733|65124733	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	7.484000|7.484000	0.81180|0.81180	2.637000|2.637000	0.89404|0.89404	0.539000|0.539000	0.68188|0.68188	GGA|ATG		0.458	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		
OAS2	4939	broad.mit.edu	37	12	113435338	113435338	+	Missense_Mutation	SNP	T	T	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr12:113435338T>A	ENST00000342315.4	+	4	855	c.641T>A	c.(640-642)aTc>aAc	p.I214N	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.I214N	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	214	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CAGAAAAAAATCAAGGATTTA	0.488																																					Pancreas(199;709 2232 18410 33584 35052)	uc001tuj.2																			0				ovary(1)	1						c.(640-642)ATC>AAC		2'-5'-oligoadenylate synthetase 2 isoform 1							88.0	77.0	81.0					12																	113435338		2203	4300	6503	SO:0001583	missense	4939				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|membrane|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding	g.chr12:113435338T>A	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.641T>A	12.37:g.113435338T>A	ENSP00000342278:p.Ile214Asn					OAS2_uc001tui.1_Missense_Mutation_p.I214N	p.I214N	NM_016817	NP_058197	P29728	OAS2_HUMAN			4	781	+			214			OAS domain 1.		A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	37	c.641T>A	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	T	7.023	0.559140	0.13436	.	.	ENSG00000111335	ENST00000342315;ENST00000392583;ENST00000552756	T;T;T	0.41065	1.01;1.01;1.01	4.06	-8.13	0.01073	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	16.749600	0.00166	N	0.000001	T	0.22589	0.0545	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.09907	-1.0653	10	0.23302	T	0.38	-20.9936	8.5433	0.33406	0.2251:0.0:0.597:0.1779	.	214;214	P29728;P29728-2	OAS2_HUMAN;.	N	214;214;139	ENSP00000342278:I214N;ENSP00000376362:I214N;ENSP00000446977:I139N	ENSP00000342278:I214N	I	+	2	0	OAS2	111919721	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.548000	0.06048	-1.669000	0.01470	-1.952000	0.00485	ATC		0.488	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
ULK1	8408	broad.mit.edu	37	12	132379629	132379629	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr12:132379629C>T	ENST00000321867.4	+	1	434	c.83C>T	c.(82-84)gCg>gTg	p.A28V		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	28	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GGCGCCTTCGCGGTGGTCTTC	0.751																																						uc001uje.2																			0				ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4						c.(82-84)GCG>GTG		Unc-51-like kinase 1							9.0	7.0	8.0					12																	132379629		2096	4132	6228	SO:0001583	missense	8408				autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity	g.chr12:132379629C>T	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.83C>T	12.37:g.132379629C>T	ENSP00000324560:p.Ala28Val						p.A28V	NM_003565	NP_003556	O75385	ULK1_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)	1	351	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)		28			Protein kinase.|ATP (By similarity).		Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	c.83C>T	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	N	17.97	3.518865	0.64634	.	.	ENSG00000177169	ENST00000321867	T	0.27256	1.68	4.13	3.23	0.37069	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.075709	0.51477	U	0.000082	T	0.55768	0.1941	M	0.92219	3.285	0.80722	D	1	D	0.65815	0.995	D	0.63597	0.916	T	0.66488	-0.5911	10	0.87932	D	0	.	12.2938	0.54833	0.1709:0.829:0.0:0.0	.	28	O75385	ULK1_HUMAN	V	28	ENSP00000324560:A28V	ENSP00000324560:A28V	A	+	2	0	ULK1	130945582	0.998000	0.40836	0.993000	0.49108	0.726000	0.41606	4.012000	0.57131	0.851000	0.35264	0.154000	0.16183	GCG		0.751	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
KLHL1	57626	broad.mit.edu	37	13	70314591	70314591	+	Silent	SNP	T	T	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr13:70314591T>C	ENST00000377844.4	-	8	2496	c.1737A>G	c.(1735-1737)caA>caG	p.Q579Q	KLHL1_ENST00000545028.1_Silent_p.Q386Q	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	579					actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		CAAATGTCCATTGTTGACTCT	0.413																																						uc001vip.2																			0					0						c.(1735-1737)CAA>CAG		kelch-like 1 protein							99.0	87.0	91.0					13																	70314591		2203	4300	6503	SO:0001819	synonymous_variant	57626				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding	g.chr13:70314591T>C	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"""Kelch-like"", ""BTB/POZ domain containing"""	6352	protein-coding gene	gene with protein product	"""Kelch-like protein 1"", ""Mayven-related protein 2"""	605332	"""kelch (Drosophila)-like 1"", ""kelch-like 1 (Drosophila)"""			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.1737A>G	13.37:g.70314591T>C						KLHL1_uc010thm.1_Silent_p.Q518Q	p.Q579Q	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)	8	2531	-		Breast(118;0.000162)	579			Kelch 3.		A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Silent	SNP	ENST00000377844.4	37	c.1737A>G	CCDS9445.1																																																																																				0.413	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866	
CLEC14A	161198	broad.mit.edu	37	14	38723832	38723832	+	Missense_Mutation	SNP	C	C	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr14:38723832C>A	ENST00000342213.2	-	1	1742	c.1396G>T	c.(1396-1398)Gtc>Ttc	p.V466F		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	466						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		CAGTCCCCGACTTTCACCCCA	0.602																																						uc001wum.1																			0				ovary(3)|skin(1)	4						c.(1396-1398)GTC>TTC		C-type lectin domain family 14, member A							75.0	77.0	76.0					14																	38723832		2203	4300	6503	SO:0001583	missense	161198					integral to membrane	sugar binding	g.chr14:38723832C>A		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"""C-type lectin domain containing"""	19832	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 27"""	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.1396G>T	14.37:g.38723832C>A	ENSP00000353013:p.Val466Phe						p.V466F	NM_175060	NP_778230	Q86T13	CLC14_HUMAN	Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)	1	1743	-	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		466			Cytoplasmic (Potential).		Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	37	c.1396G>T	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.128184	0.37533	.	.	ENSG00000176435	ENST00000342213	T	0.76709	-1.04	4.6	0.355	0.16069	.	2.302870	0.02364	N	0.077161	T	0.64494	0.2603	N	0.24115	0.695	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.51482	-0.8700	10	0.72032	D	0.01	3.0E-4	2.1515	0.03801	0.1542:0.5096:0.1503:0.1858	.	466	Q86T13	CLC14_HUMAN	F	466	ENSP00000353013:V466F	ENSP00000353013:V466F	V	-	1	0	CLEC14A	37793583	0.000000	0.05858	0.007000	0.13788	0.127000	0.20565	0.017000	0.13399	-0.048000	0.13401	0.563000	0.77884	GTC		0.602	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060	
NR2F2	7026	broad.mit.edu	37	15	96877485	96877485	+	Missense_Mutation	SNP	G	G	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr15:96877485G>C	ENST00000394166.3	+	2	2012	c.623G>C	c.(622-624)gGt>gCt	p.G208A	MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000421109.2_Missense_Mutation_p.G75A|NR2F2_ENST00000453270.2_Missense_Mutation_p.G55A|NR2F2_ENST00000394171.2_Missense_Mutation_p.G55A	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	208	Interaction with ZFPM2. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			AACATCATGGGTATCGAGAAC	0.602																																						uc010uri.1																			0				ovary(2)|breast(1)	3						c.(622-624)GGT>GCT		nuclear receptor subfamily 2, group F, member 2							166.0	159.0	162.0					15																	96877485		2197	4298	6495	SO:0001583	missense	7026				lipid metabolic process|negative regulation of cyclin-dependent protein kinase activity|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment	nucleus	ligand-regulated transcription factor activity|protein homodimerization activity|retinoic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity|zinc ion binding	g.chr15:96877485G>C	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"""Nuclear hormone receptors"""	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.623G>C	15.37:g.96877485G>C	ENSP00000377721:p.Gly208Ala					NR2F2_uc002btp.2_Missense_Mutation_p.G75A|NR2F2_uc010urj.1_Missense_Mutation_p.G55A|NR2F2_uc010urk.1_Missense_Mutation_p.G55A	p.G208A	NM_021005	NP_066285	P24468	COT2_HUMAN	OV - Ovarian serous cystadenocarcinoma(32;0.0856)		2	1847	+	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		208			Interaction with ZFPM2 (By similarity).|Ligand-binding (By similarity).		B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	37	c.623G>C	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018004	0.93404	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17	4.96	4.96	0.65561	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.96531	0.8868	L	0.36672	1.1	0.80722	D	1	D;P	0.89917	1.0;0.529	D;P	0.97110	1.0;0.654	D	0.94775	0.7948	10	0.14656	T	0.56	.	18.1811	0.89779	0.0:0.0:1.0:0.0	.	208;75	P24468;Q3KQR7	COT2_HUMAN;.	A	75;208;55;55	ENSP00000401674:G75A;ENSP00000377721:G208A;ENSP00000377726:G55A;ENSP00000389853:G55A	ENSP00000377721:G208A	G	+	2	0	NR2F2	94678489	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.866000	0.99616	2.306000	0.77630	0.561000	0.74099	GGT		0.602	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1		
KRTAP4-7	100132476	broad.mit.edu	37	17	39240900	39240900	+	Missense_Mutation	SNP	T	T	G	rs61746948	byFrequency	TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr17:39240900T>G	ENST00000391417.4	+	1	442	c.442T>G	c.(442-444)Ttg>Gtg	p.L148V		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	203	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						TCCCCGCCCCTTGTGCTGTGC	0.627																																						uc010wfn.1																			0					0						c.(442-444)TTG>GTG		keratin associated protein 4-7							84.0	82.0	82.0					17																	39240900		692	1591	2283	SO:0001583	missense	100132476							g.chr17:39240900T>G	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.442T>G	17.37:g.39240900T>G	ENSP00000375236:p.Leu148Val						p.L148V	NM_033061	NP_149050					1	442	+								A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	c.442T>G	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.836702	0.00069	.	.	ENSG00000240871	ENST00000391417	T	0.00584	6.4	3.99	-3.22	0.05125	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40136	-0.9579	8	0.02654	T	1	.	6.1576	0.20346	0.6045:0.0:0.2635:0.132	.	203	Q9BYR0	KRA47_HUMAN	V	148	ENSP00000375236:L148V	ENSP00000375236:L148V	L	+	1	2	KRTAP4-7	36494426	0.000000	0.05858	0.598000	0.28837	0.004000	0.04260	-0.333000	0.07894	-2.223000	0.00726	-4.761000	0.00003	TTG		0.627	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
KRTAP4-7	100132476	broad.mit.edu	37	17	39240908	39240908	+	Silent	SNP	T	T	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr17:39240908T>C	ENST00000391417.4	+	1	450	c.450T>C	c.(448-450)tgT>tgC	p.C150C		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	205	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C150C(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						CCTTGTGCTGTGCCTCCTCTT	0.607																																						uc010wfn.1																			1	Substitution - coding silent(1)		lung(1)		0						c.(448-450)TGT>TGC		keratin associated protein 4-7							90.0	87.0	88.0					17																	39240908		692	1591	2283	SO:0001819	synonymous_variant	100132476							g.chr17:39240908T>C	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.450T>C	17.37:g.39240908T>C							p.C150C	NM_033061	NP_149050					1	450	+								A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	c.450T>C	CCDS45673.1																																																																																				0.607	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
KRTAP4-9	100132386	broad.mit.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	A	T	rs113059833		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr17:39261693A>T	ENST00000391415.1	+	1	110	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	18					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.D18V(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						TGCGGCCAAGACCTCTGTCAG	0.627																																						uc010wfp.1																			1	Substitution - Missense(1)		endometrium(1)		0						c.(52-54)GAC>GTC		keratin associated protein 4-9							18.0	22.0	21.0					17																	39261693		692	1590	2282	SO:0001583	missense	100132386					keratin filament		g.chr17:39261693A>T	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.53A>T	17.37:g.39261693A>T	ENSP00000375234:p.Asp18Val						p.D18V	NM_001146041	NP_001139513	Q9BYQ8	KRA49_HUMAN			1	53	+			18						Missense_Mutation	SNP	ENST00000391415.1	37	c.53A>T	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	6.082	0.383461	0.11524	.	.	ENSG00000212722	ENST00000391415;ENST00000333994	T	0.32272	1.46	2.51	0.174	0.15040	.	.	.	.	.	T	0.25865	0.0630	M	0.64404	1.975	0.30580	P	0.762648	B	0.17852	0.024	B	0.14023	0.01	T	0.23154	-1.0196	8	0.45353	T	0.12	.	3.5681	0.07907	0.2702:0.2037:0.5261:0.0	.	18	Q9BYQ8	KRA49_HUMAN	V	18	ENSP00000375234:D18V	ENSP00000334461:D18V	D	+	2	0	KRTAP4-9	36515219	0.000000	0.05858	0.388000	0.26195	0.320000	0.28249	0.098000	0.15189	-0.245000	0.09625	0.155000	0.16302	GAC		0.627	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
CDKN2D	1032	broad.mit.edu	37	19	10678076	10678076	+	Silent	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr19:10678076G>A	ENST00000393599.2	-	2	483	c.159C>T	c.(157-159)agC>agT	p.S53S	KRI1_ENST00000361821.5_5'Flank|CDKN2D_ENST00000335766.2_Silent_p.S53S|KRI1_ENST00000537964.1_5'Flank|KRI1_ENST00000312962.6_5'Flank	NM_001800.3|NM_079421.2	NP_001791.1|NP_524145.1	P55273	CDN2D_HUMAN	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	53					autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to retinoic acid (GO:0032526)|response to UV (GO:0009411)|response to vitamin D (GO:0033280)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)			endometrium(3)|lung(2)|ovary(1)	6			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			CGATGGCGGTGCTGCCAAACA	0.592																																						uc002mpa.2																			0					0						c.(157-159)AGC>AGT		cyclin-dependent kinase inhibitor 2D							118.0	116.0	116.0					19																	10678076		2203	4300	6503	SO:0001819	synonymous_variant	1032	Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System			anti-apoptosis|autophagic cell death|cell cycle arrest|DNA synthesis involved in DNA repair|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|negative regulation of caspase activity|negative regulation of cell growth|negative regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity|response to retinoic acid|response to UV|response to vitamin D	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|protein kinase binding	g.chr19:10678076G>A		CCDS12244.1	19p13	2013-01-10				ENSG00000129355		"""Ankyrin repeat domain containing"""	1790	protein-coding gene	gene with protein product		600927				8575754	Standard	NM_079421		Approved	INK4D, p19	uc002mpa.3	P55273		ENST00000393599.2:c.159C>T	19.37:g.10678076G>A						KRI1_uc002mox.1_5'Flank|KRI1_uc002moy.1_5'Flank|CDKN2D_uc002mpb.2_Silent_p.S53S	p.S53S	NM_001800	NP_001791	P55273	CDN2D_HUMAN	Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)		2	461	-			53			ANK 1.		Q13102|Q6FGE9	Silent	SNP	ENST00000393599.2	37	c.159C>T	CCDS12244.1																																																																																				0.592	CDKN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452030.1	NM_079421	
CYP4F11	57834	broad.mit.edu	37	19	16025181	16025181	+	Missense_Mutation	SNP	C	C	T	rs200410691		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr19:16025181C>T	ENST00000402119.4	-	11	1757	c.1331G>A	c.(1330-1332)cGt>cAt	p.R444H	CYP4F11_ENST00000248041.8_Missense_Mutation_p.R444H|CYP4F11_ENST00000326742.8_Silent_p.P422P|CYP4F11_ENST00000591841.1_Missense_Mutation_p.R119H	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						TTGGTCGAAACGGAAGGGGTC	0.587																																						uc002nbu.2																			0				ovary(1)	1						c.(1330-1332)CGT>CAT		cytochrome P450 family 4 subfamily F polypeptide		C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	135.0	135.0	135.0		1331,1331	2.9	0.8	19		135	0,8600		0,0,4300	no	missense,missense	CYP4F11	NM_001128932.1,NM_021187.3	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	444/525,444/525	16025181	1,13005	2203	4300	6503	SO:0001583	missense	57834				inflammatory response|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding	g.chr19:16025181C>T	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.1331G>A	19.37:g.16025181C>T	ENSP00000384588:p.Arg444His					CYP4F11_uc010eab.1_Silent_p.P422P|CYP4F11_uc002nbt.2_Missense_Mutation_p.R444H	p.R444H	NM_001128932	NP_001122404	Q9HBI6	CP4FB_HUMAN			12	1367	-			444						Missense_Mutation	SNP	ENST00000402119.4	37	c.1331G>A	CCDS12337.1	.	.	.	.	.	.	.	.	.	.	c	14.69	2.611014	0.46631	2.27E-4	0.0	ENSG00000171903	ENST00000402119;ENST00000248041	D;D	0.94000	-3.33;-3.33	2.93	2.93	0.34026	.	0.000000	0.64402	U	0.000003	D	0.96731	0.8933	M	0.90483	3.12	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.96926	0.9677	10	0.87932	D	0	.	11.6202	0.51113	0.0:1.0:0.0:0.0	.	444	Q9HBI6	CP4FB_HUMAN	H	444	ENSP00000384588:R444H;ENSP00000248041:R444H	ENSP00000248041:R444H	R	-	2	0	CYP4F11	15886181	1.000000	0.71417	0.763000	0.31416	0.009000	0.06853	6.462000	0.73526	1.621000	0.50320	0.462000	0.41574	CGT		0.587	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187	
HKR1	284459	broad.mit.edu	37	19	37853365	37853365	+	Missense_Mutation	SNP	G	G	A	rs112164866		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr19:37853365G>A	ENST00000324411.4	+	6	937	c.668G>A	c.(667-669)cGg>cAg	p.R223Q	HKR1_ENST00000544914.1_5'UTR|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000541583.2_Missense_Mutation_p.R162Q|HKR1_ENST00000392153.3_Missense_Mutation_p.R204Q|HKR1_ENST00000589392.1_Missense_Mutation_p.R205Q|HKR1_ENST00000591471.1_5'UTR	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	223					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGCCCTGAACGGAGGGCAGAT	0.468													G|||	1	0.000199681	0.0	0.0	5008	,	,		22190	0.001		0.0	False		,,,				2504	0.0					uc002ogb.2																			0				ovary(2)	2						c.(667-669)CGG>CAG		GLI-Kruppel family member HKR1							81.0	80.0	80.0					19																	37853365		2203	4300	6503	SO:0001583	missense	284459				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:37853365G>A	M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"""Zinc fingers, C2H2-type"", ""-"""	4928	protein-coding gene	gene with protein product	"""oncogene HKR1"""	165250	"""GLI-Kruppel family member HKR1"""			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.668G>A	19.37:g.37853365G>A	ENSP00000315505:p.Arg223Gln					HKR1_uc002ofx.2_5'UTR|HKR1_uc002ofy.2_5'UTR|HKR1_uc002oga.2_Missense_Mutation_p.R205Q|HKR1_uc010xto.1_Missense_Mutation_p.R205Q|HKR1_uc002ogc.2_Missense_Mutation_p.R204Q|HKR1_uc010xtp.1_Missense_Mutation_p.R162Q|HKR1_uc002ogd.2_Missense_Mutation_p.R162Q	p.R223Q	NM_181786	NP_861451	P10072	HKR1_HUMAN	COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)		6	937	+			223					A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	c.668G>A	CCDS12502.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.464154	0.01053	.	.	ENSG00000181666	ENST00000414402;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T	0.04862	3.67;3.61;3.54	2.71	-2.33	0.06724	.	.	.	.	.	T	0.01454	0.0047	N	0.00926	-1.1	0.19300	N	0.999976	B;B;B;B	0.14438	0.0;0.002;0.01;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.44817	-0.9303	9	0.11794	T	0.64	0.0023	0.836	0.01140	0.3429:0.1714:0.3168:0.1688	.	162;204;223;205	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	Q	162;204;259;223;162	ENSP00000375994:R204Q;ENSP00000315505:R223Q;ENSP00000438261:R162Q	ENSP00000315505:R223Q	R	+	2	0	HKR1	42545205	0.005000	0.15991	0.002000	0.10522	0.001000	0.01503	0.236000	0.17967	-0.651000	0.05415	-0.898000	0.02899	CGG		0.468	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786	
CRX	1406	broad.mit.edu	37	19	48342915	48342915	+	Silent	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr19:48342915G>A	ENST00000221996.7	+	4	797	c.591G>A	c.(589-591)ccG>ccA	p.P197P	CRX_ENST00000539067.1_Silent_p.P197P|TPRX2P_ENST00000535362.1_Intron	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	197					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P197P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		CCTACGCCCCGGCCTCCGCTT	0.672																																					Pancreas(57;461 1196 22201 40716 47188)	uc002phq.3																			1	Substitution - coding silent(1)	p.P197P(1)	central_nervous_system(1)	breast(1)|central_nervous_system(1)	2						c.(589-591)CCG>CCA		cone-rod homeobox protein							60.0	63.0	62.0					19																	48342915		2203	4300	6503	SO:0001819	synonymous_variant	1406				organ morphogenesis|response to stimulus|visual perception		leucine zipper domain binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr19:48342915G>A	AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"""Homeoboxes / PRD class"""	2383	protein-coding gene	gene with protein product	"""orthodenticle homeobox 3"""	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.591G>A	19.37:g.48342915G>A							p.P197P	NM_000554	NP_000545	O43186	CRX_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)	4	795	+		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)	197					Q0QD45	Silent	SNP	ENST00000221996.7	37	c.591G>A	CCDS12706.1																																																																																				0.672	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554	
TPO	7173	broad.mit.edu	37	2	1480946	1480946	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr2:1480946C>T	ENST00000345913.4	+	8	999	c.908C>T	c.(907-909)gCg>gTg	p.A303V	TPO_ENST00000329066.4_Missense_Mutation_p.A303V|TPO_ENST00000337415.3_Missense_Mutation_p.A303V|TPO_ENST00000349624.3_Intron|TPO_ENST00000346956.3_Missense_Mutation_p.A303V|TPO_ENST00000382201.3_Missense_Mutation_p.A303V|TPO_ENST00000497517.2_Intron|TPO_ENST00000382198.1_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	303					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GACCAAGGCGCGCTCTTTGGG	0.706																																						uc002qww.2																			0				ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20						c.(907-909)GCG>GTG		thyroid peroxidase isoform a	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)						15.0	16.0	16.0					2																	1480946		2199	4293	6492	SO:0001583	missense	7173				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity	g.chr2:1480946C>T		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.908C>T	2.37:g.1480946C>T	ENSP00000318820:p.Ala303Val					TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.A303V|TPO_uc002qwr.2_Missense_Mutation_p.A303V|TPO_uc002qwx.2_Missense_Mutation_p.A303V|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Missense_Mutation_p.A303V	p.A303V	NM_000547	NP_000538	P07202	PERT_HUMAN		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	8	999	+	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)	303			Extracellular (Potential).		P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	c.908C>T	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	1.297	-0.605978	0.03717	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000329066;ENST00000382201;ENST00000422464	T;T;T;T;T;T	0.66815	-0.19;-0.21;-0.17;-0.21;-0.13;-0.23	4.99	4.06	0.47325	.	0.762550	0.12718	N	0.444971	T	0.45677	0.1354	L	0.31752	0.955	0.09310	N	1	B;B;B	0.20550	0.018;0.046;0.032	B;B;B	0.19666	0.015;0.015;0.026	T	0.45234	-0.9275	10	0.02654	T	1	-22.1178	5.1674	0.15092	0.0:0.5797:0.2151:0.2051	.	303;303;303	P07202-4;P07202-2;P07202	.;.;PERT_HUMAN	V	303;303;303;303;303;232	ENSP00000337263:A303V;ENSP00000318820:A303V;ENSP00000263886:A303V;ENSP00000329869:A303V;ENSP00000371636:A303V;ENSP00000405788:A232V	ENSP00000329869:A303V	A	+	2	0	TPO	1459953	0.000000	0.05858	0.022000	0.16811	0.009000	0.06853	0.281000	0.18810	2.315000	0.78130	0.460000	0.39030	GCG		0.706	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
APOB	338	broad.mit.edu	37	2	21233706	21233706	+	Nonsense_Mutation	SNP	G	G	A	rs147863759		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr2:21233706G>A	ENST00000233242.1	-	26	6161	c.6034C>T	c.(6034-6036)Cga>Tga	p.R2012*		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2012					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCAGAGTTCGTCCAGTAAGC	0.428																																						uc002red.2																			0				ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	GRCh37	CM962634	APOB	M	rs147863759	c.(6034-6036)CGA>TGA		apolipoprotein B precursor	Atorvastatin(DB01076)	G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	178.0	162.0	168.0		6034	1.3	0.1	2	dbSNP_134	168	0,8600		0,0,4300	no	stop-gained	APOB	NM_000384.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2012/4564	21233706	1,13005	2203	4300	6503	SO:0001587	stop_gained	338				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity	g.chr2:21233706G>A	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.6034C>T	2.37:g.21233706G>A	ENSP00000233242:p.Arg2012*						p.R2012*	NM_000384	NP_000375	P04114	APOB_HUMAN			26	6162	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		2012					O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	37	c.6034C>T	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	42	9.516436	0.99193	2.27E-4	0.0	ENSG00000084674	ENST00000233242;ENST00000535079	.	.	.	5.46	1.32	0.21799	.	0.834050	0.10100	N	0.716077	.	.	.	.	.	.	0.09310	N	0.999991	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2696	0.49131	0.0:0.3156:0.517:0.1674	.	.	.	.	X	2012	.	ENSP00000233242:R2012X	R	-	1	2	APOB	21087211	0.002000	0.14202	0.114000	0.21550	0.189000	0.23516	0.733000	0.26087	0.621000	0.30232	0.555000	0.69702	CGA		0.428	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
THSD7B	80731	broad.mit.edu	37	2	137988734	137988734	+	Missense_Mutation	SNP	A	A	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr2:137988734A>C	ENST00000409968.1	+	8	2022	c.1844A>C	c.(1843-1845)cAg>cCg	p.Q615P	THSD7B_ENST00000272643.3_Missense_Mutation_p.Q615P|THSD7B_ENST00000413152.2_Missense_Mutation_p.Q584P|THSD7B_ENST00000543459.1_Intron			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	615	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		TCCTGTTCCCAGTCCTGTTCA	0.507																																						uc002tva.1																			0				ovary(4)|central_nervous_system(2)|pancreas(1)	7						c.(1750-1752)CAG>CCG		thrombospondin, type I, domain containing 7B							62.0	63.0	63.0					2																	137988734		1948	4143	6091	SO:0001583	missense	80731							g.chr2:137988734A>C			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.1844A>C	2.37:g.137988734A>C	ENSP00000387145:p.Gln615Pro					THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Missense_Mutation_p.Q474P	p.Q584P	NM_001080427	NP_001073896				BRCA - Breast invasive adenocarcinoma(221;0.19)	7	1751	+									Missense_Mutation	SNP	ENST00000409968.1	37	c.1751A>C		.	.	.	.	.	.	.	.	.	.	A	24.7	4.561727	0.86335	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.52983	0.64;0.64;0.64	5.89	5.89	0.94794	.	0.095332	0.64402	D	0.000001	T	0.57007	0.2024	L	0.57536	1.79	0.80722	D	1	D;B	0.56746	0.977;0.242	P;B	0.53313	0.723;0.209	T	0.53549	-0.8423	10	0.30078	T	0.28	.	16.3109	0.82869	1.0:0.0:0.0:0.0	.	615;584	Q9C0I4;C9JKN6	THS7B_HUMAN;.	P	615;615;584	ENSP00000387145:Q615P;ENSP00000272643:Q615P;ENSP00000413841:Q584P	ENSP00000272643:Q615P	Q	+	2	0	THSD7B	137705204	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.257000	0.74773	0.460000	0.39030	CAG		0.507	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	
R3HDML	140902	broad.mit.edu	37	20	42979302	42979302	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr20:42979302G>A	ENST00000217043.2	+	5	804	c.632G>A	c.(631-633)gGc>gAc	p.G211D	RP5-881L22.5_ENST00000438702.1_RNA|RP5-881L22.5_ENST00000430481.2_RNA	NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	211						extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			TCTTCCAGGGGCAACTGGATT	0.567																																						uc002xls.1																			0					0						c.(631-633)GGC>GAC		R3H domain containing-like precursor							74.0	67.0	70.0					20																	42979302		2203	4300	6503	SO:0001583	missense	140902					extracellular region	peptidase inhibitor activity	g.chr20:42979302G>A	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing-like"""				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.632G>A	20.37:g.42979302G>A	ENSP00000217043:p.Gly211Asp						p.G211D	NM_178491	NP_848586	Q9H3Y0	CRSPL_HUMAN	COAD - Colon adenocarcinoma(18;0.00189)		5	804	+		Myeloproliferative disorder(115;0.028)	211						Missense_Mutation	SNP	ENST00000217043.2	37	c.632G>A	CCDS13329.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781513	0.90282	.	.	ENSG00000101074	ENST00000217043	T	0.16196	2.36	4.93	4.93	0.64822	CAP domain (2);	0.058955	0.64402	D	0.000003	T	0.49695	0.1572	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	T	0.61083	-0.7134	10	0.87932	D	0	.	17.7569	0.88451	0.0:0.0:1.0:0.0	.	211	Q9H3Y0	CRSPL_HUMAN	D	211	ENSP00000217043:G211D	ENSP00000217043:G211D	G	+	2	0	R3HDML	42412716	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	8.952000	0.93031	2.290000	0.77057	0.561000	0.74099	GGC		0.567	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
MPPED1	758	broad.mit.edu	37	22	43831125	43831125	+	Silent	SNP	C	C	T	rs368415701		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr22:43831125C>T	ENST00000417669.2	+	3	840	c.396C>T	c.(394-396)aaC>aaT	p.N132N	MPPED1_ENST00000538182.1_Silent_p.N165N|MPPED1_ENST00000414469.2_Silent_p.N26N|MPPED1_ENST00000443721.1_Silent_p.N132N|MPPED1_ENST00000542779.1_Silent_p.N132N|MPPED1_ENST00000439548.1_Intron			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	132							hydrolase activity (GO:0016787)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				AGAAGTTCAACGAGTGGCTGG	0.682																																						uc011apv.1																			0					0						c.(394-396)AAC>AAT		metallophosphoesterase domain containing 1		C		1,3967		0,1,1983	38.0	45.0	43.0		396	0.3	1.0	22		43	0,8282		0,0,4141	no	coding-synonymous	MPPED1	NM_001044370.1		0,1,6124	TT,TC,CC		0.0,0.0252,0.0082		132/327	43831125	1,12249	1984	4141	6125	SO:0001819	synonymous_variant	758						hydrolase activity	g.chr22:43831125C>T	U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732			1306	protein-coding gene	gene with protein product		602112	"""chromosome 22 open reading frame 1"""	C22orf1		9266672, 10591208	Standard	NM_001044370		Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.396C>T	22.37:g.43831125C>T						MPPED1_uc011apw.1_Silent_p.N26N|MPPED1_uc011apx.1_Intron|MPPED1_uc011apy.1_Silent_p.N132N|MPPED1_uc011apz.1_Silent_p.N165N	p.N132N	NM_001044370	NP_001037835	O15442	MPPD1_HUMAN			3	619	+		all_neural(38;0.0244)|Ovarian(80;0.0694)	132					A8K159|B7Z2S9|Q8N361	Silent	SNP	ENST00000417669.2	37	c.396C>T	CCDS46723.1																																																																																				0.682	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370	
ITIH3	3699	broad.mit.edu	37	3	52828907	52828907	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr3:52828907C>T	ENST00000449956.2	+	1	94	c.88C>T	c.(88-90)Ctt>Ttt	p.L30F	ITIH3_ENST00000416872.2_Missense_Mutation_p.L30F	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	30	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CTTTCGGCTGCTTGGGGTGAG	0.587																																						uc003dfv.2																			0				ovary(2)|liver(1)	3						c.(88-90)CTT>TTT		inter-alpha (globulin) inhibitor H3							83.0	89.0	87.0					3																	52828907		2005	4184	6189	SO:0001583	missense	3699				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity	g.chr3:52828907C>T		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"""pre-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha-trypsin inhibitor heavy chain H3"""	146650	"""inter-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha (globulin) inhibitor H3"""			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.88C>T	3.37:g.52828907C>T	ENSP00000415769:p.Leu30Phe					ITIH3_uc011bek.1_Missense_Mutation_p.L30F	p.L30F	NM_002217	NP_002208	Q06033	ITIH3_HUMAN		BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)	1	124	+			30			VIT.		Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	c.88C>T	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	4.996	0.184924	0.09495	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	T;T	0.02812	4.15;4.81	4.89	3.09	0.35607	Vault protein inter-alpha-trypsin (1);Vault protein inter-alpha-trypsin, metazoa (1);	0.664814	0.14084	N	0.342497	T	0.03136	0.0092	L	0.36672	1.1	0.09310	N	1	P;B	0.36065	0.535;0.359	B;B	0.40506	0.331;0.107	T	0.45145	-0.9281	10	0.17832	T	0.49	-11.5716	6.7935	0.23713	0.0:0.727:0.1779:0.0951	.	30;30	E7ET33;Q06033	.;ITIH3_HUMAN	F	30;30;25;30;30	ENSP00000413922:L30F;ENSP00000415769:L30F	ENSP00000273291:L25F	L	+	1	0	ITIH3	52803947	0.009000	0.17119	0.019000	0.16419	0.107000	0.19398	0.908000	0.28545	0.768000	0.33290	0.591000	0.81541	CTT		0.587	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217	
DPPA4	55211	broad.mit.edu	37	3	109046840	109046840	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr3:109046840C>T	ENST00000335658.6	-	7	964	c.910G>A	c.(910-912)Gaa>Aaa	p.E304K	DPPA4_ENST00000478791.1_5'Flank	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	304					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						ATATTCTATTCCCATTGGAGG	0.373																																						uc003dxq.3																			0				upper_aerodigestive_tract(1)	1						c.(910-912)GAA>AAA		developmental pluripotency associated 4							205.0	216.0	212.0					3																	109046840		2203	4300	6503	SO:0001583	missense	55211					nucleus	protein binding	g.chr3:109046840C>T	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.910G>A	3.37:g.109046840C>T	ENSP00000335306:p.Glu304Lys					DPPA4_uc011bho.1_3'UTR	p.E304K	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN			7	965	-			304					A8K4M7|Q9H9N5|Q9NVI6	Missense_Mutation	SNP	ENST00000335658.6	37	c.910G>A	CCDS33814.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.458739	0.43634	.	.	ENSG00000121570	ENST00000335658	T	0.25250	1.81	3.62	2.74	0.32292	.	2.157960	0.03146	N	0.167321	T	0.18257	0.0438	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.19321	-1.0309	10	0.62326	D	0.03	.	7.2586	0.26191	0.0:0.8782:0.0:0.1218	.	304	Q7L190	DPPA4_HUMAN	K	304	ENSP00000335306:E304K	ENSP00000335306:E304K	E	-	1	0	DPPA4	110529530	0.137000	0.22531	0.007000	0.13788	0.815000	0.46073	0.718000	0.25866	1.087000	0.41251	0.467000	0.42956	GAA		0.373	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
BOD1L1	259282	broad.mit.edu	37	4	13605551	13605551	+	Silent	SNP	T	T	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr4:13605551T>C	ENST00000040738.5	-	10	3108	c.2973A>G	c.(2971-2973)agA>agG	p.R991R		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	991	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)										GTAACTTGGCTCTATGACTAG	0.403																																						uc003gmz.1																			0				ovary(5)|breast(1)	6						c.(2971-2973)AGA>AGG		biorientation of chromosomes in cell division							202.0	215.0	211.0					4																	13605551		2203	4300	6503	SO:0001819	synonymous_variant	259282						DNA binding	g.chr4:13605551T>C	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.2973A>G	4.37:g.13605551T>C						BOD1L_uc010idr.1_Silent_p.R328R	p.R991R	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN			10	3090	-			991			Lys-rich.		Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	37	c.2973A>G	CCDS3411.2																																																																																				0.403	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
NUP54	53371	broad.mit.edu	37	4	77069476	77069476	+	Missense_Mutation	SNP	T	T	G			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr4:77069476T>G	ENST00000264883.3	-	1	192	c.52A>C	c.(52-54)Acc>Ccc	p.T18P	NUP54_ENST00000515460.1_5'UTR|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000514987.1_Missense_Mutation_p.T18P	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	18	9 X 2 AA repeats of F-G.|Gly-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GGGGCCGCGGTGGCTGCAGCG	0.667																																						uc003hjs.2																			0				ovary(1)|lung(1)	2						c.(52-54)ACC>CCC		nucleoporin 54kDa							15.0	20.0	18.0					4																	77069476		2188	4292	6480	SO:0001583	missense	53371				carbohydrate metabolic process|glucose transport|mRNA transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleoplasm		g.chr4:77069476T>G	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.52A>C	4.37:g.77069476T>G	ENSP00000264883:p.Thr18Pro					NUP54_uc010ije.2_5'UTR|NUP54_uc011cbs.1_5'UTR|NUP54_uc011cbt.1_Missense_Mutation_p.T18P|NUP54_uc003hjt.2_5'UTR	p.T18P	NM_017426	NP_059122	Q7Z3B4	NUP54_HUMAN			1	180	-			18			Gly-rich.|9 X 2 AA repeats of F-G.		B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	c.52A>C	CCDS3576.1	.	.	.	.	.	.	.	.	.	.	T	15.78	2.933611	0.52866	.	.	ENSG00000138750	ENST00000264883;ENST00000514987;ENST00000514901	.	.	.	5.09	-4.14	0.03892	.	0.300619	0.34959	N	0.003557	T	0.36082	0.0954	L	0.36672	1.1	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.01390	-1.1367	9	0.54805	T	0.06	-0.6988	3.6412	0.08168	0.1036:0.1543:0.4663:0.2758	.	18;18	B4DT35;Q7Z3B4	.;NUP54_HUMAN	P	18	.	ENSP00000264883:T18P	T	-	1	0	NUP54	77288500	0.979000	0.34478	0.968000	0.41197	0.945000	0.59286	-0.110000	0.10824	-0.625000	0.05604	-0.644000	0.03951	ACC		0.667	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
GATB	5188	broad.mit.edu	37	4	152680061	152680061	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr4:152680061C>T	ENST00000515812.1	-	2	206	c.190G>A	c.(190-192)Gct>Act	p.A64T	PET112_ENST00000508611.1_Missense_Mutation_p.A64T|PET112_ENST00000512306.1_Missense_Mutation_p.A64T|PET112_ENST00000263985.6_Missense_Mutation_p.A64T																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						ACCACAGCAGCCCATTTGTGT	0.363																																						uc003iml.2																			0					0						c.(190-192)GCT>ACT		PET112-like precursor	L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)						114.0	116.0	115.0					4																	152680061		2203	4300	6503	SO:0001583	missense	5188					mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding	g.chr4:152680061C>T																												ENST00000515812.1:c.190G>A	4.37:g.152680061C>T	ENSP00000426859:p.Ala64Thr					PET112L_uc003imm.3_Missense_Mutation_p.A64T	p.A64T	NM_004564	NP_004555	O75879	GATB_HUMAN			2	202	-	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)	64						Missense_Mutation	SNP	ENST00000515812.1	37	c.190G>A		.	.	.	.	.	.	.	.	.	.	C	18.41	3.618796	0.66787	.	.	ENSG00000059691	ENST00000263985;ENST00000515812;ENST00000512306;ENST00000508611	T;T;T;T	0.44482	0.95;0.95;0.94;0.92	6.03	4.32	0.51571	.	0.359658	0.27159	N	0.020658	T	0.26376	0.0644	N	0.11201	0.11	0.30124	N	0.805451	B;B	0.11235	0.004;0.004	B;B	0.15052	0.012;0.007	T	0.19614	-1.0300	10	0.87932	D	0	-13.6482	12.7112	0.57089	0.0:0.8675:0.0:0.1325	.	64;64	D6RDU9;O75879	.;GATB_HUMAN	T	64	ENSP00000263985:A64T;ENSP00000426859:A64T;ENSP00000420831:A64T;ENSP00000421105:A64T	ENSP00000263985:A64T	A	-	1	0	PET112	152899511	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.932000	0.40143	0.884000	0.36064	0.557000	0.71058	GCT		0.363	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
EGR1	1958	broad.mit.edu	37	5	137803130	137803130	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr5:137803130C>T	ENST00000239938.4	+	2	1264	c.992C>T	c.(991-993)aCg>aTg	p.T331M		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	331					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|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 core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCCAGCAAGACGCCCCCCCAC	0.652																																						uc003ldb.1																			0				ovary(1)	1						c.(991-993)ACG>ATG		early growth response 1							88.0	97.0	94.0					5																	137803130		2203	4300	6503	SO:0001583	missense	1958				cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr5:137803130C>T	M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"""Zinc fingers, C2H2-type"""	3238	protein-coding gene	gene with protein product	"""nerve growth factor-induced protein A"", ""transcription factor ETR103"", ""zinc finger protein 225"", ""early growth response protein 1"""	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.992C>T	5.37:g.137803130C>T	ENSP00000239938:p.Thr331Met					EGR1_uc011cyu.1_Intron	p.T331M	NM_001964	NP_001955	P18146	EGR1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)		2	1262	+			331						Missense_Mutation	SNP	ENST00000239938.4	37	c.992C>T	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.129594	0.56721	.	.	ENSG00000120738	ENST00000239938	T	0.17054	2.3	4.47	4.47	0.54385	.	0.157375	0.56097	D	0.000031	T	0.49064	0.1535	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.60530	-0.7245	10	0.87932	D	0	-11.8128	16.309	0.82862	0.0:1.0:0.0:0.0	.	331	P18146	EGR1_HUMAN	M	331	ENSP00000239938:T331M	ENSP00000239938:T331M	T	+	2	0	EGR1	137831029	1.000000	0.71417	0.986000	0.45419	0.958000	0.62258	7.651000	0.83577	2.319000	0.78375	0.563000	0.77884	ACG		0.652	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964	
PCDHA3	56145	broad.mit.edu	37	5	140181750	140181750	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr5:140181750C>T	ENST00000522353.2	+	1	968	c.968C>T	c.(967-969)aCg>aTg	p.T323M	PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.T323M	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	323	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAGAAGCCACGGATAAAGGA	0.378																																						uc003lhf.2																			0				ovary(6)|skin(2)	8						c.(967-969)ACG>ATG		protocadherin alpha 3 isoform 1 precursor							157.0	157.0	157.0					5																	140181750		2203	4300	6503	SO:0001583	missense	56145				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding	g.chr5:140181750C>T	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.968C>T	5.37:g.140181750C>T	ENSP00000429808:p.Thr323Met					PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.T323M	p.T323M	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	968	+			323			Cadherin 3.|Extracellular (Potential).		O75286	Missense_Mutation	SNP	ENST00000522353.2	37	c.968C>T	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	c	9.213	1.031538	0.19590	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.54479	0.57;0.57	4.79	-1.56	0.08532	Cadherin (4);Cadherin-like (1);	0.955501	0.08504	U	0.936035	T	0.57519	0.2059	M	0.77486	2.375	0.09310	N	1	P;P	0.48016	0.904;0.869	B;P	0.49301	0.335;0.606	T	0.51957	-0.8639	10	0.45353	T	0.12	.	6.2541	0.20864	0.0:0.3278:0.2404:0.4318	.	323;323	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	M	323	ENSP00000429808:T323M;ENSP00000434086:T323M	ENSP00000429808:T323M	T	+	2	0	PCDHA3	140161934	0.000000	0.05858	0.033000	0.17914	0.985000	0.73830	-5.144000	0.00147	-0.305000	0.08831	0.467000	0.42956	ACG		0.378	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
ARAP3	64411	broad.mit.edu	37	5	141041300	141041300	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr5:141041300G>A	ENST00000239440.4	-	21	3135	c.3070C>T	c.(3070-3072)Ccg>Tcg	p.P1024S	ARAP3_ENST00000513878.1_Missense_Mutation_p.P686S|ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000508305.1_Missense_Mutation_p.P855S	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1024	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TTGACCCGCGGCAGGCAGCCA	0.572																																						uc003llm.2																			0				breast(5)|ovary(1)|large_intestine(1)	7						c.(3070-3072)CCG>TCG		ArfGAP with RhoGAP domain, ankyrin repeat and PH							82.0	89.0	87.0					5																	141041300		2203	4300	6503	SO:0001583	missense	64411				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding	g.chr5:141041300G>A	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3070C>T	5.37:g.141041300G>A	ENSP00000239440:p.Pro1024Ser					ARAP3_uc003lll.2_5'UTR|ARAP3_uc011dbe.1_Missense_Mutation_p.P686S|ARAP3_uc003lln.2_Missense_Mutation_p.P855S	p.P1024S	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN			21	3148	-			1024			Rho-GAP.		B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	c.3070C>T	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.804480	0.90623	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.27557	1.66;1.66;1.66	5.33	5.33	0.75918	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.66626	0.2808	M	0.92691	3.335	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.987;0.998;0.999	T	0.73827	-0.3860	10	0.59425	D	0.04	.	18.8077	0.92045	0.0:0.0:1.0:0.0	.	686;855;1024	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	S	855;1024;686	ENSP00000421826:P855S;ENSP00000239440:P1024S;ENSP00000421468:P686S	ENSP00000239440:P1024S	P	-	1	0	ARAP3	141021484	1.000000	0.71417	0.998000	0.56505	0.693000	0.40251	9.043000	0.93799	2.777000	0.95525	0.655000	0.94253	CCG		0.572	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
SH3RF2	153769	broad.mit.edu	37	5	145428731	145428731	+	Silent	SNP	C	C	T	rs561869294		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr5:145428731C>T	ENST00000511217.1	+	6	1297	c.1245C>T	c.(1243-1245)gaC>gaT	p.D415D	SH3RF2_ENST00000359120.4_Silent_p.D415D			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	415	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGTGCCAGGACGGCTGGCTCA	0.597											OREG0016895	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		17901	0.0		0.0	False		,,,				2504	0.001					uc003lnt.2																			0				ovary(1)|skin(1)	2						c.(1243-1245)GAC>GAT		SH3 domain containing ring finger 2							66.0	66.0	66.0					5																	145428731		2203	4300	6503	SO:0001819	synonymous_variant	153769						ligase activity|protein phosphatase 1 binding|zinc ion binding	g.chr5:145428731C>T	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.1245C>T	5.37:g.145428731C>T			OREG0016895	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1694	SH3RF2_uc011dbl.1_Silent_p.D415D|SH3RF2_uc011dbm.1_5'Flank|SH3RF2_uc003lnu.2_5'Flank	p.D415D	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		7	1483	+			415			SH3 3.		A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Silent	SNP	ENST00000511217.1	37	c.1245C>T	CCDS4280.1																																																																																				0.597	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
PRSS16	10279	broad.mit.edu	37	6	27216987	27216987	+	Missense_Mutation	SNP	G	G	A	rs145240806		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr6:27216987G>A	ENST00000230582.3	+	4	461	c.446G>A	c.(445-447)cGc>cAc	p.R149H	PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	149					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GCCCAGCTCCGCTTCTTGTCC	0.562													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18411	0.0		0.0	False		,,,				2504	0.0				NSCLC(178;1118 2105 17078 23587 44429)	uc003nja.2																			0				ovary(2)|central_nervous_system(2)|skin(1)	5						c.(445-447)CGC>CAC		protease, serine, 16 precursor		G	HIS/ARG	0,4406		0,0,2203	85.0	85.0	85.0		446	3.2	1.0	6	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRSS16	NM_005865.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	149/515	27216987	1,13005	2203	4300	6503	SO:0001583	missense	10279				protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity	g.chr6:27216987G>A	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.446G>A	6.37:g.27216987G>A	ENSP00000230582:p.Arg149His					PRSS16_uc011dkt.1_Intron|PRSS16_uc003njb.2_Intron|PRSS16_uc010jqq.1_Missense_Mutation_p.R39H|PRSS16_uc010jqr.1_Missense_Mutation_p.R39H|PRSS16_uc003njc.1_RNA|PRSS16_uc003njd.2_5'Flank	p.R149H	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN			4	458	+			149					O75416	Missense_Mutation	SNP	ENST00000230582.3	37	c.446G>A	CCDS4623.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	16.07	3.019626	0.54576	0.0	1.16E-4	ENSG00000112812	ENST00000230582;ENST00000343467;ENST00000348953	T	0.17691	2.26	4.04	3.15	0.36227	.	0.459428	0.21587	N	0.072144	T	0.06508	0.0167	L	0.53617	1.68	0.40525	D	0.980879	B;B;P	0.40431	0.068;0.031;0.717	B;B;B	0.31614	0.033;0.012;0.133	T	0.14811	-1.0459	10	0.45353	T	0.12	-20.5965	10.1014	0.42507	0.1023:0.0:0.8977:0.0	.	40;149;149	Q7Z5N6;C9JI59;Q9NQE7	.;.;TSSP_HUMAN	H	149	ENSP00000230582:R149H	ENSP00000230582:R149H	R	+	2	0	PRSS16	27324966	0.892000	0.30473	1.000000	0.80357	0.879000	0.50718	1.984000	0.40658	1.015000	0.39444	0.557000	0.71058	CGC		0.562	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
HIST1H2BO	8348	broad.mit.edu	37	6	27861564	27861564	+	Silent	SNP	C	C	T			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr6:27861564C>T	ENST00000303806.4	+	1	362	c.324C>T	c.(322-324)gcC>gcT	p.A108A	HIST1H2AM_ENST00000359611.2_5'Flank|HIST1H3J_ENST00000479986.1_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank	NM_003527.4	NP_003518.2	P23527	H2B1O_HUMAN	histone cluster 1, H2bo	108					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)										GGGAGCTGGCCAAGCACGCCG	0.637																																						uc003nkc.1																			0					0						c.(322-324)GCC>GCT		histone cluster 1, H2bo							46.0	50.0	48.0					6																	27861564		2203	4299	6502	SO:0001819	synonymous_variant	8348				nucleosome assembly	nucleosome|nucleus	DNA binding	g.chr6:27861564C>T	X57138	CCDS4640.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196331			"""Histones / Replication-dependent"""	4758	protein-coding gene	gene with protein product		602808	"""H2B histone family, member N"", ""histone 1, H2bo"""	H2BFN		1768865, 12408966	Standard	NM_003527		Approved	H2B/n, H2B.2	uc003nkc.1	P23527	OTTHUMG00000014493	ENST00000303806.4:c.324C>T	6.37:g.27861564C>T						HIST1H3J_uc003nka.2_5'Flank|HIST1H2AM_uc003nkb.1_5'Flank	p.A108A	NM_003527	NP_003518	P23527	H2B1O_HUMAN			1	362	+			108					Q3KPI7|Q8TCV6	Silent	SNP	ENST00000303806.4	37	c.324C>T	CCDS4640.1																																																																																				0.637	HIST1H2BO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040161.1	NM_003527	
OR2J3	442186	broad.mit.edu	37	6	29080293	29080293	+	Missense_Mutation	SNP	T	T	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr6:29080293T>C	ENST00000377169.1	+	1	626	c.626T>C	c.(625-627)tTt>tCt	p.F209S		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F209C(1)		endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						AGCTCCATATTTGTTCTCATA	0.448																																						uc011dll.1																			1	Substitution - Missense(1)		lung(1)		0						c.(625-627)TTT>TCT		olfactory receptor, family 2, subfamily J,							103.0	114.0	110.0					6																	29080293		1319	2590	3909	SO:0001583	missense	442186				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr6:29080293T>C		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.626T>C	6.37:g.29080293T>C	ENSP00000366374:p.Phe209Ser						p.F209S	NM_001005216	NP_001005216	O76001	OR2J3_HUMAN			1	626	+			209			Helical; Name=5; (Potential).		B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	c.626T>C	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	11.17	1.559105	0.27827	.	.	ENSG00000204701	ENST00000377169	T	0.00048	8.82	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00144	0.0004	L	0.52266	1.64	0.09310	N	1	D	0.67145	0.996	D	0.68621	0.959	T	0.32587	-0.9901	9	0.87932	D	0	.	10.804	0.46507	0.0:0.0:0.0:1.0	.	209	O76001	OR2J3_HUMAN	S	209	ENSP00000366374:F209S	ENSP00000366374:F209S	F	+	2	0	OR2J3	29188272	0.000000	0.05858	0.560000	0.28344	0.500000	0.33767	0.205000	0.17356	1.268000	0.44264	0.358000	0.22013	TTT		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
ZBTB12	221527	broad.mit.edu	37	6	31868436	31868436	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr6:31868436G>A	ENST00000375527.2	-	2	822	c.647C>T	c.(646-648)gCc>gTc	p.A216V	C2_ENST00000452323.2_5'Flank|EHMT2_ENST00000375530.4_5'Flank|C2_ENST00000469372.1_Intron|EHMT2_ENST00000375537.4_5'Flank	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						CACCTCCAGGGCCGACTCCAC	0.627																																						uc003nyd.1																			0					0						c.(646-648)GCC>GTC		zinc finger and BTB domain containing 12							81.0	71.0	74.0					6																	31868436		2065	4091	6156	SO:0001583	missense	221527				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr6:31868436G>A	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19066	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 46"""	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.647C>T	6.37:g.31868436G>A	ENSP00000364677:p.Ala216Val					EHMT2_uc003nxz.1_5'Flank|EHMT2_uc003nya.1_5'Flank|EHMT2_uc003nyb.1_5'Flank|C2_uc003nyc.2_Intron|C2_uc011doo.1_Intron|C2_uc011dop.1_5'Flank	p.A216V	NM_181842	NP_862825	Q9Y330	ZBT12_HUMAN			2	823	-			216					B0UY00|Q5JQ98	Missense_Mutation	SNP	ENST00000375527.2	37	c.647C>T	CCDS4727.1	.	.	.	.	.	.	.	.	.	.	G	2.527	-0.309487	0.05458	.	.	ENSG00000204366	ENST00000375527	T	0.13420	2.59	4.3	4.3	0.51218	.	0.636195	0.15036	U	0.284161	T	0.02649	0.0080	N	0.14661	0.345	0.09310	N	1	B	0.30914	0.3	B	0.23275	0.045	T	0.37934	-0.9684	10	0.30854	T	0.27	.	11.5987	0.50990	0.0:0.181:0.819:0.0	.	216	Q9Y330	ZBT12_HUMAN	V	216	ENSP00000364677:A216V	ENSP00000364677:A216V	A	-	2	0	ZBTB12	31976415	0.024000	0.19004	0.991000	0.47740	0.978000	0.69477	1.078000	0.30754	1.932000	0.55993	0.313000	0.20887	GCC		0.627	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842	
ZNF318	24149	broad.mit.edu	37	6	43325085	43325085	+	Nonsense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr6:43325085G>A	ENST00000361428.2	-	3	1044	c.967C>T	c.(967-969)Cga>Tga	p.R323*	ZNF318_ENST00000318149.3_Nonsense_Mutation_p.R323*	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	323					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TCTCGCTTTCGTCTGGCAAGA	0.522																																						uc003oux.2																			0				ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7						c.(967-969)CGA>TGA		zinc finger protein 318							195.0	165.0	175.0					6																	43325085		2203	4300	6503	SO:0001587	stop_gained	24149				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding	g.chr6:43325085G>A	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.967C>T	6.37:g.43325085G>A	ENSP00000354964:p.Arg323*					ZNF318_uc003ouw.2_RNA	p.R323*	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)		3	1045	-			323			Potential.		O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Nonsense_Mutation	SNP	ENST00000361428.2	37	c.967C>T	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	36	5.779407	0.96929	.	.	ENSG00000171467	ENST00000318149;ENST00000361428	.	.	.	5.64	1.12	0.20585	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3836	13.799	0.63188	0.0:0.0:0.2729:0.7271	.	.	.	.	X	323	.	ENSP00000323032:R323X	R	-	1	2	ZNF318	43433063	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.676000	0.25247	0.264000	0.21851	0.650000	0.86243	CGA		0.522	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
IMPG1	3617	broad.mit.edu	37	6	76782168	76782169	+	Frame_Shift_Ins	INS	-	-	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr6:76782168_76782169insA	ENST00000369950.3	-	1	226_227	c.37_38insT	c.(37-39)tggfs	p.W13fs	IMPG1_ENST00000369963.3_Frame_Shift_Ins_p.W13fs	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GAGAAAAATCCAAAAAACAAAA	0.287																																					Pancreas(37;839 1141 2599 26037)	uc003pik.1																			0				ovary(2)|skin(1)	3						c.(37-39)TGGfs		interphotoreceptor matrix proteoglycan 1																																				SO:0001589	frameshift_variant	3617				visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity	g.chr6:76782168_76782169insA	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.38dupT	6.37:g.76782174_76782174dupA	ENSP00000358966:p.Trp13fs						p.W13fs	NM_001563	NP_001554	Q17R60	IMPG1_HUMAN			1	167_168	-		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)	13						Frame_Shift_Ins	INS	ENST00000369950.3	37	c.37_38insT	CCDS4985.1																																																																																				0.287	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
TNPO3	23534	broad.mit.edu	37	7	128612562	128612562	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr7:128612562G>A	ENST00000265388.5	-	19	2491	c.2348C>T	c.(2347-2349)tCt>tTt	p.S783F	TNPO3_ENST00000482320.1_Missense_Mutation_p.S717F|RN7SL306P_ENST00000492941.2_RNA|TNPO3_ENST00000471166.1_Missense_Mutation_p.S817F|TNPO3_ENST00000393245.1_Missense_Mutation_p.S817F|TNPO3_ENST00000471234.1_Missense_Mutation_p.S719F			Q9Y5L0	TNPO3_HUMAN	transportin 3	783					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						CAGGGTAGTAGAGGCAATGGC	0.478																																					Pancreas(147;583 2585 39696 52331)	uc003vol.1																			0				ovary(2)|skin(2)|lung(1)	5						c.(2347-2349)TCT>TTT		transportin 3							110.0	94.0	99.0					7																	128612562		2203	4300	6503	SO:0001583	missense	23534				splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity	g.chr7:128612562G>A	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.2348C>T	7.37:g.128612562G>A	ENSP00000265388:p.Ser783Phe					TNPO3_uc010llx.1_Missense_Mutation_p.S194F|TNPO3_uc003vom.1_Missense_Mutation_p.S717F|TNPO3_uc010lly.1_Missense_Mutation_p.S817F|TNPO3_uc010llz.1_Missense_Mutation_p.S719F	p.S783F	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN			19	2722	-			783					A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	37	c.2348C>T	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.659951	0.67586	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471234;ENST00000471166	T;T;T;T;T	0.69306	-0.23;-0.23;-0.23;-0.39;-0.23	5.41	4.47	0.54385	Armadillo-type fold (1);	0.164261	0.52532	D	0.000069	T	0.49695	0.1572	N	0.08118	0	0.46631	D	0.999134	B;B;P;P	0.44195	0.031;0.246;0.828;0.736	B;B;B;B	0.43783	0.033;0.11;0.431;0.17	T	0.55095	-0.8194	10	0.42905	T	0.14	.	13.645	0.62277	0.0:0.1564:0.8436:0.0	.	719;817;783;783	C9IZM0;C9J7E5;Q9Y5L0-3;Q9Y5L0	.;.;.;TNPO3_HUMAN	F	817;783;717;719;817	ENSP00000376936:S817F;ENSP00000265388:S783F;ENSP00000420089:S717F;ENSP00000418646:S719F;ENSP00000418267:S817F	ENSP00000265388:S783F	S	-	2	0	TNPO3	128399798	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.734000	0.84928	2.686000	0.91538	0.655000	0.94253	TCT		0.478	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470	
PARP12	64761	broad.mit.edu	37	7	139746776	139746776	+	Silent	SNP	C	C	T	rs147556524		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr7:139746776C>T	ENST00000263549.3	-	5	1767	c.894G>A	c.(892-894)ccG>ccA	p.P298P		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	298	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.P298P(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					GCCATCGATACGGCAAATGGA	0.403																																						uc003vvl.1																			1	Substitution - coding silent(1)		endometrium(1)	ovary(3)	3						c.(892-894)CCG>CCA		poly ADP-ribose polymerase 12		C		0,4406		0,0,2203	147.0	128.0	134.0		894	-11.1	0.2	7	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PARP12	NM_022750.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		298/702	139746776	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64761					nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding	g.chr7:139746776C>T	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.894G>A	7.37:g.139746776C>T						PARP12_uc003vvk.1_Silent_p.P84P|PARP12_uc010lnf.1_RNA	p.P298P	NM_022750	NP_073587	Q9H0J9	PAR12_HUMAN			5	1768	-	Melanoma(164;0.0142)		298			WWE 1.		Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	c.894G>A	CCDS5857.1																																																																																				0.403	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
NOBOX	135935	broad.mit.edu	37	7	144097327	144097327	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr7:144097327G>A	ENST00000467773.1	-	5	922	c.923C>T	c.(922-924)aCg>aTg	p.T308M	NOBOX_ENST00000483238.1_Missense_Mutation_p.T308M|NOBOX_ENST00000223140.5_Missense_Mutation_p.T223M	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	308					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					CACCCCCACCGTCTGGGCAAT	0.552																																						uc011kue.1																			0				ovary(1)	1						c.(922-924)ACG>ATG		NOBOX oogenesis homeobox							76.0	72.0	73.0					7																	144097327		1892	4110	6002	SO:0001583	missense	135935				cell differentiation|oogenesis	nucleus	sequence-specific DNA binding	g.chr7:144097327G>A			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.923C>T	7.37:g.144097327G>A	ENSP00000419457:p.Thr308Met						p.T308M	NM_001080413	NP_001073882	O60393	NOBOX_HUMAN			5	923	-	Melanoma(164;0.14)		308			Homeobox.		A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	37	c.923C>T		.	.	.	.	.	.	.	.	.	.	G	3.653	-0.071046	0.07228	.	.	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140;ENST00000555556	D;D;D	0.96168	-3.93;-3.93;-3.93	5.79	0.922	0.19408	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.854934	0.10629	N	0.652396	D	0.88276	0.6393	N	0.17901	0.54	0.09310	N	1	B	0.26708	0.157	B	0.21546	0.035	T	0.77487	-0.2569	10	0.33141	T	0.24	-7.562	4.4501	0.11616	0.3937:0.0:0.4614:0.1449	.	308	O60393	NOBOX_HUMAN	M	308;308;223;97	ENSP00000419565:T308M;ENSP00000419457:T308M;ENSP00000223140:T223M	ENSP00000223140:T223M	T	-	2	0	NOBOX	143728260	0.335000	0.24748	0.045000	0.18777	0.169000	0.22640	1.129000	0.31381	-0.106000	0.12110	-0.840000	0.03056	ACG		0.552	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
ZNF282	8427	broad.mit.edu	37	7	148920939	148920940	+	Frame_Shift_Ins	INS	-	-	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr7:148920939_148920940insC	ENST00000262085.3	+	8	1321_1322	c.1216_1217insC	c.(1216-1218)gccfs	p.A406fs	ZNF282_ENST00000479907.1_Frame_Shift_Ins_p.A406fs	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	406					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		cccacccccggccccgccacag	0.703																																						uc003wfm.2																			0					0						c.(1216-1218)GCCfs		zinc finger protein 282																																				SO:0001589	frameshift_variant	8427				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr7:148920939_148920940insC	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"""Zinc fingers, C2H2-type"", ""-"""	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.1220dupC	7.37:g.148920943_148920943dupC	ENSP00000262085:p.Ala406fs					ZNF282_uc011kun.1_Frame_Shift_Ins_p.A406fs|ZNF282_uc003wfo.2_Intron	p.A406fs	NM_003575	NP_003566	Q9UDV7	ZN282_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)	8	1321_1322	+	Melanoma(164;0.15)		406					B4DRI5|O43691|Q6DKK0	Frame_Shift_Ins	INS	ENST00000262085.3	37	c.1216_1217insC	CCDS5895.1																																																																																				0.703	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575	
XKR4	114786	broad.mit.edu	37	8	56270319	56270319	+	Silent	SNP	A	A	G			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr8:56270319A>G	ENST00000327381.6	+	2	988	c.888A>G	c.(886-888)gtA>gtG	p.V296V		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	296						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GGAAAATGGTATATGAGTATG	0.438																																						uc003xsf.2																			0				pancreas(2)	2						c.(886-888)GTA>GTG		XK, Kell blood group complex subunit-related							184.0	167.0	172.0					8																	56270319		2203	4300	6503	SO:0001819	synonymous_variant	114786					integral to membrane		g.chr8:56270319A>G	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.888A>G	8.37:g.56270319A>G							p.V296V	NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	Epithelial(17;0.000117)|all cancers(17;0.000836)		2	920	+			296					Q96PZ8	Silent	SNP	ENST00000327381.6	37	c.888A>G	CCDS34893.1																																																																																				0.438	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898	
CPSF1	29894	broad.mit.edu	37	8	145624369	145624369	+	Silent	SNP	G	G	A	rs371053206		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr8:145624369G>A	ENST00000349769.3	-	16	1621	c.1527C>T	c.(1525-1527)aaC>aaT	p.N509N	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	509					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			ACAAAGCCCCGTTCTTCCCGT	0.677																																					NSCLC(133;1088 1848 27708 34777 35269)	uc003zcj.2																			0				skin(1)	1						c.(1525-1527)AAC>AAT		cleavage and polyadenylation specific factor 1,		G		0,4404		0,0,2202	19.0	20.0	20.0		1527	-9.2	0.1	8		20	1,8597		0,1,4298	no	coding-synonymous	CPSF1	NM_013291.2		0,1,6500	AA,AG,GG		0.0116,0.0,0.0077		509/1444	145624369	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	29894				mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding	g.chr8:145624369G>A	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1527C>T	8.37:g.145624369G>A							p.N509N	NM_013291	NP_037423	Q10570	CPSF1_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)		16	1602	-	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		509					Q96AF0	Silent	SNP	ENST00000349769.3	37	c.1527C>T	CCDS34966.1																																																																																				0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
ASS1	445	broad.mit.edu	37	9	133342180	133342180	+	Silent	SNP	C	C	T	rs377319610		TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chr9:133342180C>T	ENST00000372394.1	+	7	970	c.489C>T	c.(487-489)taC>taT	p.Y163Y	ASS1_ENST00000352480.5_Silent_p.Y163Y|ASS1_ENST00000493984.2_3'UTR|ASS1_ENST00000372393.3_Silent_p.Y163Y			P00966	ASSY_HUMAN	argininosuccinate synthase 1	163					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	TGATGGAGTACGCAAAGGTAT	0.612																																						uc004bzm.2																			0				ovary(1)	1						c.(487-489)TAC>TAT		argininosuccinate synthetase 1	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	C	,	2,4404	4.2+/-10.8	0,2,2201	105.0	84.0	91.0		489,489	-3.8	0.1	9		91	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ASS1	NM_000050.4,NM_054012.3	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	163/413,163/413	133342180	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	445				arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding	g.chr9:133342180C>T	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"""argininosuccinate synthetase"""	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.489C>T	9.37:g.133342180C>T						ASS1_uc004bzn.2_Silent_p.Y163Y|ASS1_uc010mza.2_Silent_p.Y239Y|ASS1_uc004bzo.2_Silent_p.Y144Y|ASS1_uc010mzb.2_Silent_p.Y201Y|ASS1_uc004bzp.2_Silent_p.Y163Y|ASS1_uc010mzc.2_Silent_p.Y163Y	p.Y163Y	NM_000050	NP_000041	P00966	ASSY_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;0.000514)	7	845	+			163					Q6LDL2|Q86UZ0|Q96GT4	Silent	SNP	ENST00000372394.1	37	c.489C>T	CCDS6933.1																																																																																				0.612	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	
AKAP17A	8227	broad.mit.edu	37	X	1712915	1712915	+	Missense_Mutation	SNP	T	T	C			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chrX:1712915T>C	ENST00000313871.3	+	2	756	c.560T>C	c.(559-561)gTg>gCg	p.V187A	AKAP17A_ENST00000381261.3_Missense_Mutation_p.V187A	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	187	RRM.				B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						ATCCGGAATGTGGACATCCCC	0.607																																						uc004cqa.2																			0					0						c.(559-561)GTG>GCG		DNA segment on chromosome X and Y (unique) 155							145.0	133.0	137.0					X																	1712915		2203	4296	6499	SO:0001583	missense	8227				B cell activation|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|signal transduction	nuclear speck|spliceosomal complex	nucleotide binding|protein binding|RNA binding	g.chrX:1712915T>C	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"""Pseudoautosomal regions / PAR1"", ""A-kinase anchor proteins"""	18783	protein-coding gene	gene with protein product		312095, 465000	"""chromosome X and Y open reading frame 3"", ""splicing factor, arginine/serine-rich 17A"""	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.560T>C	X.37:g.1712915T>C	ENSP00000324827:p.Val187Ala					SFRS17A_uc010ncx.1_Missense_Mutation_p.V187A|SFRS17A_uc004cqb.2_RNA|ASMT_uc004cqd.2_5'Flank	p.V187A	NM_005088	NP_005079	Q02040	AK17A_HUMAN			2	756	+		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)	187			RRM.		Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	37	c.560T>C	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	t	12.88	2.071307	0.36566	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.50277	0.75;0.75	2.34	2.34	0.29019	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.64402	U	0.000006	T	0.64360	0.2591	.	.	.	0.27106	N	0.962507	P;D	0.76494	0.928;0.999	P;D	0.79108	0.632;0.992	T	0.57242	-0.7845	9	0.87932	D	0	-28.7259	10.2743	0.43501	0.0:0.0:0.0:1.0	.	187;187	Q02040-3;Q02040	.;AK17A_HUMAN	A	187	ENSP00000324827:V187A;ENSP00000370660:V187A	ENSP00000324827:V187A	V	+	2	0	AKAP17A	1672915	1.000000	0.71417	0.020000	0.16555	0.210000	0.24377	5.773000	0.68898	0.795000	0.33922	0.084000	0.15446	GTG		0.607	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088	
ZIC3	7547	broad.mit.edu	37	X	136649606	136649606	+	Silent	SNP	G	G	A			TCGA-32-2615-01A-01D-1495-08	TCGA-32-2615-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	65e3c804-b1a3-4e21-9407-90a6edc4e290	13640737-743d-4d84-a399-f3dba0539e70	g.chrX:136649606G>A	ENST00000287538.5	+	1	1306	c.756G>A	c.(754-756)tcG>tcA	p.S252S	ZIC3_ENST00000370606.3_Silent_p.S252S	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	252					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					AGGAGCTGTCGTGCAAGTGGA	0.607																																						uc004fak.2																			0				ovary(2)|breast(1)	3						c.(754-756)TCG>TCA		zinc finger protein of the cerebellum 3							45.0	44.0	45.0					X																	136649606		2202	4298	6500	SO:0001819	synonymous_variant	7547				cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chrX:136649606G>A	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"""Zinc fingers, C2H2-type"""	12874	protein-coding gene	gene with protein product		300265	"""heterotaxy 1"", ""Zic family member 3 (odd-paired homolog, Drosophila)"""	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.756G>A	X.37:g.136649606G>A							p.S252S	NM_003413	NP_003404	O60481	ZIC3_HUMAN			1	1261	+	Acute lymphoblastic leukemia(192;0.000127)		252			C2H2-type 1; atypical.		B2CNW4|Q14DE5|Q5JY75	Silent	SNP	ENST00000287538.5	37	c.756G>A	CCDS14663.1																																																																																				0.607	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1		
