#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
SCNN1D	6339	broad.mit.edu	37	1	1222331	1222331	+	Silent	SNP	C	C	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr1:1222331C>T	ENST00000338555.2	+	5	1747	c.603C>T	c.(601-603)agC>agT	p.S201S	SCNN1D_ENST00000400928.3_Silent_p.S201S|SCNN1D_ENST00000325425.8_Silent_p.S267S|SCNN1D_ENST00000379116.5_Silent_p.S365S			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	201					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	ACTCGGGCAGCCGGGTCAGAG	0.697																																						uc001adt.1																			0				lung(6)|skin(1)	7						c.(1093-1095)agC>agT		Homo sapiens sodium channel, nonvoltage-gated 1, delta (SCNN1D), transcript variant 1, mRNA.							25.0	31.0	29.0					1																	1222331		2188	4290	6478	SO:0001819	synonymous_variant	6339							g.chr1:1222331C>T	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.603C>T	1.37:g.1222331C>T						SCNN1D_uc001adu.1_Silent_p.S201S|SCNN1D_uc001adw.2_Silent_p.S267S|SCNN1D_uc001adv.2_Silent_p.S201S|SCNN1D_uc001adx.2_5'UTR	p.S365S	NM_001130413	NP_001123885				Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	7	1321	+	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)						A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Silent	SNP	ENST00000338555.2	37	c.1095C>T																																																																																					0.697	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
SYDE2	84144	broad.mit.edu	37	1	85656020	85656020	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr1:85656020C>A	ENST00000341460.5	-	2	1210	c.1161G>T	c.(1159-1161)ttG>ttT	p.L387F		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	387					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		CACCAAAACTCAAGGCACTTG	0.448																																						uc009wcm.3																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20						c.(1159-1161)ttG>ttT		Homo sapiens synapse defective 1, Rho GTPase, homolog 2 (C. elegans) (SYDE2), mRNA.							70.0	70.0	70.0					1																	85656020		2087	4217	6304	SO:0001583	missense	84144				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity	g.chr1:85656020C>A	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1161G>T	1.37:g.85656020C>A	ENSP00000340594:p.Leu387Phe					SYDE2_uc001dku.4_Missense_Mutation_p.L387F	p.L387F	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN		all cancers(265;0.0126)|Epithelial(280;0.0336)	1	1210	-			387					Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	c.1161G>T	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	C	5.557	0.287693	0.10513	.	.	ENSG00000097096	ENST00000341460	T	0.08102	3.13	6.05	2.97	0.34412	.	0.458962	0.18410	N	0.142067	T	0.06416	0.0165	M	0.65975	2.015	0.09310	N	1	P;D	0.53885	0.8;0.963	P;P	0.53809	0.467;0.735	T	0.24693	-1.0153	10	0.66056	D	0.02	.	2.3033	0.04168	0.1856:0.4568:0.1974:0.1602	.	387;387	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	F	387	ENSP00000340594:L387F	ENSP00000340594:L387F	L	-	3	2	SYDE2	85428608	0.002000	0.14202	0.270000	0.24601	0.047000	0.14425	0.704000	0.25661	0.387000	0.25024	-0.142000	0.14014	TTG		0.448	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
FLG	2312	broad.mit.edu	37	1	152281389	152281389	+	Silent	SNP	C	C	T	rs138652718	byFrequency	TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr1:152281389C>T	ENST00000368799.1	-	3	6008	c.5973G>A	c.(5971-5973)gcG>gcA	p.A1991A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1991	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGGGATGACGCAGCCTGTC	0.572									Ichthyosis				-|||	9	0.00179712	0.0053	0.0029	5008	,	,		29400	0.0		0.0	False		,,,				2504	0.0					uc001ezu.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(5971-5973)gcG>gcA		Homo sapiens filaggrin (FLG), mRNA.		C		29,4377	33.5+/-64.1	0,29,2174	584.0	465.0	505.0		5973	-7.1	0.0	1	dbSNP_134	505	0,8600		0,0,4300	no	coding-synonymous	FLG	NM_002016.1		0,29,6474	TT,TC,CC		0.0,0.6582,0.223		1991/4062	152281389	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152281389C>T	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5973G>A	1.37:g.152281389C>T							p.A1991A	NM_002016	NP_002007	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	6009	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		1991			Ser-rich.		Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	c.5973G>A	CCDS30860.1																																																																																				0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
KLHL20	27252	broad.mit.edu	37	1	173744944	173744944	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr1:173744944G>T	ENST00000209884.4	+	10	1737	c.1601G>T	c.(1600-1602)tGg>tTg	p.W534L	KLHL20_ENST00000546011.1_Missense_Mutation_p.W345L	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	534					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						ACCAACCAGTGGTCTCCAGTG	0.478																																					GBM(159;862 2695 6559 23041)	uc001gjc.3																			0				breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						c.(1600-1602)tGg>tTg		Homo sapiens kelch-like 20 (Drosophila) (KLHL20), mRNA.							111.0	110.0	110.0					1																	173744944		2203	4300	6503	SO:0001583	missense	27252				cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity	g.chr1:173744944G>T	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"""Kelch-like"", ""BTB/POZ domain containing"""	25056	protein-coding gene	gene with protein product			"""kelch-like 20 (Drosophila)"""			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.1601G>T	1.37:g.173744944G>T	ENSP00000209884:p.Trp534Leu					KLHL20_uc010pmr.2_Missense_Mutation_p.W345L|KLHL20_uc009wwf.3_Missense_Mutation_p.W516L	p.W534L	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN			9	1780	+			534					B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Missense_Mutation	SNP	ENST00000209884.4	37	c.1601G>T	CCDS1310.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.777944	0.90195	.	.	ENSG00000076321	ENST00000546011;ENST00000209884	D;D	0.96940	-4.18;-4.18	5.32	5.32	0.75619	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.99020	0.9665	H	0.98333	4.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99410	1.0930	10	0.87932	D	0	.	17.7813	0.88524	0.0:0.0:1.0:0.0	.	345;534	B4DUR0;Q9Y2M5	.;KLH20_HUMAN	L	345;534	ENSP00000443121:W345L;ENSP00000209884:W534L	ENSP00000209884:W534L	W	+	2	0	KLHL20	172011567	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.296000	0.96104	2.491000	0.84063	0.655000	0.94253	TGG		0.478	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458	
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						uc010qex.1																			0											c.(523-525)aAt>aGt		Homo sapiens hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2 (HSD17B7P2), non-coding RNA.																																						158160							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G						HSD17B7P2_uc001izq.3_Non-coding_Transcript|HSD17B7P2_uc001izo.1_Non-coding_Transcript|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S	p.N175S							4	599	+									Missense_Mutation	SNP	ENST00000494540.1	37	c.524A>G																																																																																					0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086	
PHLDA2	7262	broad.mit.edu	37	11	2950491	2950491	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:2950491C>T	ENST00000314222.4	-	1	194	c.104G>A	c.(103-105)cGc>cAc	p.R35H		NM_003311.3	NP_003302.1	Q53GA4	PHLA2_HUMAN	pleckstrin homology-like domain, family A, member 2	35	PH.				apoptotic process (GO:0006915)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|regulation of gene expression (GO:0010468)|regulation of glycogen metabolic process (GO:0070873)	cytoplasm (GO:0005737)|membrane (GO:0016020)				central_nervous_system(1)	1		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGCTCAGGCGGTCGGAGGT	0.667																																						uc021qci.1																			0				central_nervous_system(1)	1						c.(103-105)cGc>cAc		Homo sapiens pleckstrin homology-like domain, family A, member 2 (PHLDA2), mRNA.							20.0	22.0	22.0					11																	2950491		2195	4297	6492	SO:0001583	missense	7262				apoptosis	cytoplasm|membrane		g.chr11:2950491C>T	AF035444	CCDS7741.1	11p15.4	2013-01-10	2003-09-26	2003-10-01	ENSG00000181649	ENSG00000181649		"""Pleckstrin homology (PH) domain containing"""	12385	protein-coding gene	gene with protein product		602131	"""tumor suppressing subtransferable candidate 3"""	TSSC3		9328465, 9403053	Standard	NM_003311		Approved	IPL, BWR1C, HLDA2	uc001lxa.1	Q53GA4	OTTHUMG00000010926	ENST00000314222.4:c.104G>A	11.37:g.2950491C>T	ENSP00000319231:p.Arg35His					PHLDA2_uc001lxa.1_Missense_Mutation_p.R35H	p.R35H	NM_003311	NP_003302	Q53GA4	PHLA2_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)	0	104	-		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)	35			PH.		O00496	Missense_Mutation	SNP	ENST00000314222.4	37	c.104G>A	CCDS7741.1	.	.	.	.	.	.	.	.	.	.	C	35	5.447581	0.96205	.	.	ENSG00000181649	ENST00000314222	T	0.44083	0.93	3.51	3.51	0.40186	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.121887	0.53938	U	0.000053	T	0.50565	0.1623	L	0.57536	1.79	0.39290	D	0.964716	D	0.71674	0.998	P	0.51999	0.687	T	0.61098	-0.7131	10	0.56958	D	0.05	-11.4926	15.3955	0.74790	0.0:1.0:0.0:0.0	.	35	Q53GA4	PHLA2_HUMAN	H	35	ENSP00000319231:R35H	ENSP00000319231:R35H	R	-	2	0	PHLDA2	2907067	1.000000	0.71417	0.979000	0.43373	0.910000	0.53928	6.755000	0.74914	1.660000	0.50760	0.313000	0.20887	CGC		0.667	PHLDA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030116.1	NM_003311	
OR52J3	119679	broad.mit.edu	37	11	5068409	5068409	+	Silent	SNP	G	G	A	rs148600962		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:5068409G>A	ENST00000380370.1	+	1	654	c.654G>A	c.(652-654)tcG>tcA	p.S218S		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGGCATCTCGTATGTTTACA	0.448																																						uc010qyv.2																			0				NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36						c.(652-654)tcG>tcA		Homo sapiens olfactory receptor, family 52, subfamily J, member 3 (OR52J3), mRNA.		G		1,4401	2.1+/-5.4	0,1,2200	342.0	308.0	319.0		654	-1.8	0.0	11	dbSNP_134	319	0,8596		0,0,4298	no	coding-synonymous	OR52J3	NM_001001916.2		0,1,6498	AA,AG,GG		0.0,0.0227,0.0077		218/312	5068409	1,12997	2201	4298	6499	SO:0001819	synonymous_variant	119679				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:5068409G>A	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.654G>A	11.37:g.5068409G>A							p.S218S	NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)	0	654	+		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)	218					Q6IFE4	Silent	SNP	ENST00000380370.1	37	c.654G>A	CCDS31370.1																																																																																				0.448	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
OR5P2	120065	broad.mit.edu	37	11	7818191	7818191	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:7818191G>A	ENST00000329434.2	-	1	329	c.299C>T	c.(298-300)gCg>gTg	p.A100V	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAAGAAAGCCGCTGAACCAAG	0.483																																						uc001mfp.1																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22						c.(298-300)gCg>gTg		Homo sapiens olfactory receptor, family 5, subfamily P, member 2 (OR5P2), mRNA.							99.0	116.0	110.0					11																	7818191		2104	4292	6396	SO:0001583	missense	120065				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:7818191G>A	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.299C>T	11.37:g.7818191G>A	ENSP00000331823:p.Ala100Val						p.A100V	NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN		Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	0	299	-			100					Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	c.299C>T	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	G	1.595	-0.528102	0.04112	.	.	ENSG00000183303	ENST00000329434	T	0.00376	7.7	5.5	-3.17	0.05202	GPCR, rhodopsin-like superfamily (1);	0.679936	0.14063	N	0.343953	T	0.00109	0.0003	N	0.01289	-0.905	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.21690	-1.0238	10	0.41790	T	0.15	0.4364	6.3005	0.21109	0.4743:0.2502:0.2755:0.0	.	100	Q8WZ92	OR5P2_HUMAN	V	100	ENSP00000331823:A100V	ENSP00000331823:A100V	A	-	2	0	OR5P2	7774767	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.927000	0.03984	-0.349000	0.08274	0.555000	0.69702	GCG		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
OR5W2	390148	broad.mit.edu	37	11	55681318	55681318	+	Silent	SNP	C	C	T	rs547924373		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:55681318C>T	ENST00000344514.1	-	1	740	c.741G>A	c.(739-741)gcG>gcA	p.A247A		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A247A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AAATTGCAACCGCAGATAAGT	0.403																																					Melanoma(48;171 1190 15239 43886 49348)	uc010rir.2																			1	Substitution - coding silent(1)	p.A247A(2)	breast(1)	breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						c.(739-741)gcG>gcA		Homo sapiens olfactory receptor, family 5, subfamily W, member 2 (OR5W2), mRNA.							83.0	95.0	91.0					11																	55681318		2201	4296	6497	SO:0001819	synonymous_variant	390148				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55681318C>T	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.741G>A	11.37:g.55681318C>T							p.A247A	NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN			0	741	-			247						Silent	SNP	ENST00000344514.1	37	c.741G>A	CCDS31513.1																																																																																				0.403	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
OR5T2	219464	broad.mit.edu	37	11	55999905	55999905	+	Missense_Mutation	SNP	C	C	T	rs146086539		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:55999905C>T	ENST00000313264.4	-	1	832	c.757G>A	c.(757-759)Gtt>Att	p.V253I		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAGATCAGAACAATCAGGATA	0.448																																						uc010rjc.2																			0				endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41						c.(757-759)Gtt>Att		Homo sapiens olfactory receptor, family 5, subfamily T, member 2 (OR5T2), mRNA.							117.0	110.0	113.0					11																	55999905		2201	4296	6497	SO:0001583	missense	219464				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55999905C>T	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.757G>A	11.37:g.55999905C>T	ENSP00000323688:p.Val253Ile						p.V253I	NM_001004746	NP_001004746	Q8NGG2	OR5T2_HUMAN			0	757	-	Esophageal squamous(21;0.00448)		253					B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	c.757G>A	CCDS31523.1	.	.	.	.	.	.	.	.	.	.	C	4.751	0.139638	0.09083	.	.	ENSG00000181718	ENST00000313264	T	0.00014	9.22	5.07	-0.401	0.12407	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37857	U	0.001913	T	0.00039	0.0001	N	0.00966	-1.09	0.09310	N	1	B	0.21905	0.062	B	0.33960	0.173	T	0.42224	-0.9464	10	0.02654	T	1	.	5.9956	0.19491	0.1264:0.5661:0.0:0.3075	.	253	Q8NGG2	OR5T2_HUMAN	I	253	ENSP00000323688:V253I	ENSP00000323688:V253I	V	-	1	0	OR5T2	55756481	0.000000	0.05858	0.004000	0.12327	0.376000	0.30014	0.008000	0.13197	0.253000	0.21552	0.478000	0.44815	GTT		0.448	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
PDE2A	5138	broad.mit.edu	37	11	72293532	72293532	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:72293532A>G	ENST00000334456.5	-	21	2052	c.1807T>C	c.(1807-1809)Ttc>Ctc	p.F603L	PDE2A_ENST00000418754.2_Missense_Mutation_p.F488L|PDE2A_ENST00000540345.1_Missense_Mutation_p.F594L|PDE2A_ENST00000544570.1_Missense_Mutation_p.F596L|PDE2A_ENST00000444035.2_Missense_Mutation_p.F594L|PDE2A_ENST00000376450.3_Missense_Mutation_p.F347L|RP11-169D4.2_ENST00000545254.1_RNA	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	603					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	GTATAGGTGAAACTTGCAAAA	0.537																																						uc010rrc.2																			0				breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36						c.(1807-1809)Ttc>Ctc		Homo sapiens phosphodiesterase 2A, cGMP-stimulated (PDE2A), transcript variant 1, mRNA.	Sildenafil(DB00203)|Sulindac(DB00605)						102.0	83.0	89.0					11																	72293532		2200	4293	6493	SO:0001583	missense	5138				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding	g.chr11:72293532A>G	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.1807T>C	11.37:g.72293532A>G	ENSP00000334910:p.Phe603Leu					PDE2A_uc001oso.3_Missense_Mutation_p.F582L|PDE2A_uc010rra.2_Missense_Mutation_p.F596L|PDE2A_uc001osn.3_Missense_Mutation_p.F347L|PDE2A_uc010rrb.2_Missense_Mutation_p.F594L|PDE2A_uc010rrd.2_Missense_Mutation_p.F488L	p.F603L	NM_002599	NP_002590	O00408	PDE2A_HUMAN	BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		20	2053	-			603					B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Missense_Mutation	SNP	ENST00000334456.5	37	c.1807T>C	CCDS8216.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.363208	0.61513	.	.	ENSG00000186642	ENST00000334456;ENST00000376450;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345;ENST00000441209;ENST00000542223	T;T;T;T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94;-0.94;-0.94;-0.94	4.74	4.74	0.60224	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.64402	D	0.000003	T	0.67021	0.2849	L	0.57536	1.79	0.51012	D	0.999903	B;P;P;P;P;P	0.48162	0.096;0.849;0.849;0.906;0.754;0.775	B;B;B;B;B;B	0.37387	0.067;0.177;0.177;0.248;0.177;0.105	T	0.70142	-0.4953	10	0.45353	T	0.12	.	11.6556	0.51315	1.0:0.0:0.0:0.0	.	488;603;594;596;603;347	E9PEF1;O00408;E9PGI1;F6W5Z0;B2R646;Q6ZMR1	.;PDE2A_HUMAN;.;.;.;.	L	603;347;594;672;596;488;594;144;34	ENSP00000334910:F603L;ENSP00000365633:F347L;ENSP00000411657:F594L;ENSP00000442256:F596L;ENSP00000410310:F488L;ENSP00000446399:F594L;ENSP00000392457:F144L;ENSP00000440834:F34L	ENSP00000334910:F603L	F	-	1	0	PDE2A	71971180	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	8.127000	0.89593	1.784000	0.52394	0.460000	0.39030	TTC		0.537	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
OR8B4	283162	broad.mit.edu	37	11	124294255	124294255	+	Silent	SNP	G	G	A	rs146995996		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:124294255G>A	ENST00000356130.3	-	1	534	c.513C>T	c.(511-513)aaC>aaT	p.N171N		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GGTCAATGACGTTGGAATCAC	0.512													G|||	1	0.000199681	0.0	0.0	5008	,	,		21327	0.0		0.001	False		,,,				2504	0.0					uc010sak.2																			0				endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32						c.(511-513)aaC>aaT		Homo sapiens olfactory receptor, family 8, subfamily B, member 4 (OR8B4), mRNA.		G		3,4399	4.2+/-10.8	0,3,2198	96.0	65.0	75.0		513	-3.0	0.0	11	dbSNP_134	75	5,8593	3.7+/-12.6	0,5,4294	no	coding-synonymous	OR8B4	NM_001005196.1		0,8,6492	AA,AG,GG		0.0582,0.0682,0.0615		171/310	124294255	8,12992	2201	4299	6500	SO:0001819	synonymous_variant	283162				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:124294255G>A	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.513C>T	11.37:g.124294255G>A							p.N171N	NM_001005196	NP_001005196	Q96RC9	OR8B4_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)	0	513	-		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)	171					B2RNF8|Q6IFQ7	Silent	SNP	ENST00000356130.3	37	c.513C>T	CCDS31710.1																																																																																				0.512	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
SRPR	6734	broad.mit.edu	37	11	126134309	126134309	+	Nonsense_Mutation	SNP	C	C	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr11:126134309C>A	ENST00000332118.6	-	12	1805	c.1651G>T	c.(1651-1653)Gga>Tga	p.G551*	SRPR_ENST00000532259.1_Nonsense_Mutation_p.G523*	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	551					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		AAGGCTTCTCCTACAAACAGC	0.517																																						uc001qdh.3																			0				endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21						c.(1651-1653)Gga>Tga		Homo sapiens signal recognition particle receptor (docking protein) (SRPR), transcript variant 1, mRNA.							113.0	97.0	102.0					11																	126134309		2201	4299	6500	SO:0001587	stop_gained	6734				SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding	g.chr11:126134309C>A	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1651G>T	11.37:g.126134309C>A	ENSP00000328023:p.Gly551*					SRPR_uc010sbm.2_Nonsense_Mutation_p.G523*	p.G551*	NM_003139	NP_003130	P08240	SRPR_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)	11	1829	-	all_hematologic(175;0.145)		551					A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Nonsense_Mutation	SNP	ENST00000332118.6	37	c.1651G>T	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	C	39	7.499460	0.98322	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.5111	19.4521	0.94872	0.0:1.0:0.0:0.0	.	.	.	.	X	551;523	.	ENSP00000328023:G551X	G	-	1	0	SRPR	125639519	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.651000	0.83577	2.826000	0.97356	0.637000	0.83480	GGA		0.517	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
ZFC3H1	196441	broad.mit.edu	37	12	72057129	72057129	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr12:72057129G>A	ENST00000378743.3	-	1	620	c.262C>T	c.(262-264)Cgc>Tgc	p.R88C	THAP2_ENST00000547843.1_5'Flank|ZFC3H1_ENST00000552037.1_Missense_Mutation_p.R88C|ZFC3H1_ENST00000548100.1_Missense_Mutation_p.R88C|ZFC3H1_ENST00000549407.1_5'UTR|THAP2_ENST00000308086.2_5'UTR	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	88	Ser-rich.				RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TGCCGCGAGCGTGAGAAATTC	0.652											OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc001swo.2																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.(262-264)Cgc>Tgc		Homo sapiens zinc finger, C3H1-type containing (ZFC3H1), mRNA.							59.0	67.0	64.0					12																	72057129		1965	4150	6115	SO:0001583	missense	196441				RNA processing	intracellular	metal ion binding	g.chr12:72057129G>A	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.262C>T	12.37:g.72057129G>A	ENSP00000368017:p.Arg88Cys		OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1134	ZFC3H1_uc010sts.2_Missense_Mutation_p.R88C|ZFC3H1_uc001swp.3_Missense_Mutation_p.R88C|THAP2_uc001swq.3_5'Flank	p.R88C	NM_144982	NP_659419	O60293	ZC3H1_HUMAN			0	621	-			88			Ser-rich.		Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	c.262C>T	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.470943	0.63625	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	T	0.35421	1.31	4.09	4.09	0.47781	.	0.107907	0.38605	N	0.001639	T	0.40719	0.1128	N	0.14661	0.345	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;P	0.64595	0.927;0.927;0.551	T	0.48514	-0.9029	10	0.72032	D	0.01	.	15.0106	0.71547	0.0:0.0:1.0:0.0	.	88;88;88	G3V1X1;O60293-4;O60293	.;.;ZC3H1_HUMAN	C	88	ENSP00000368017:R88C	ENSP00000368017:R88C	R	-	1	0	ZFC3H1	70343396	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.762000	0.68809	2.276000	0.75962	0.455000	0.32223	CGC		0.652	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
NR1H4	9971	broad.mit.edu	37	12	100904745	100904745	+	Missense_Mutation	SNP	G	G	A	rs113431969		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr12:100904745G>A	ENST00000551379.1	+	2	327	c.299G>A	c.(298-300)cGt>cAt	p.R100H	NR1H4_ENST00000549996.1_Missense_Mutation_p.R90H|NR1H4_ENST00000188403.7_Missense_Mutation_p.R100H|NR1H4_ENST00000392986.3_Missense_Mutation_p.R90H|NR1H4_ENST00000548884.1_Missense_Mutation_p.R90H			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	100					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	GAACTCAGGCGTATGCCAGCT	0.522																																						uc001tht.2																			0				NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44						c.(298-300)cGt>cAt		Homo sapiens nuclear receptor subfamily 1, group H, member 4 (NR1H4), transcript variant 3, mRNA.							75.0	76.0	75.0					12																	100904745		2203	4300	6503	SO:0001583	missense	9971				bile acid metabolic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding	g.chr12:100904745G>A	U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"""Nuclear hormone receptors"""	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.299G>A	12.37:g.100904745G>A	ENSP00000447149:p.Arg100His					NR1H4_uc001thq.2_Missense_Mutation_p.R90H|NR1H4_uc001thp.2_Missense_Mutation_p.R90H|NR1H4_uc001thr.2_Missense_Mutation_p.R90H|NR1H4_uc010svk.2_Missense_Mutation_p.R90H|NR1H4_uc010svj.2_Non-coding_Transcript|NR1H4_uc001ths.2_Missense_Mutation_p.R100H	p.R100H	NM_001206993	NP_001193922	Q96RI1	NR1H4_HUMAN			1	327	+			100					A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Missense_Mutation	SNP	ENST00000551379.1	37	c.299G>A	CCDS55876.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.956705	0.53293	.	.	ENSG00000012504	ENST00000548884;ENST00000392986;ENST00000549996;ENST00000551379;ENST00000188403	D;D;D;D;D	0.93426	-3.0;-3.05;-3.22;-3.08;-3.02	5.9	5.0	0.66597	.	0.109563	0.64402	D	0.000007	D	0.91432	0.7296	L	0.29908	0.895	0.46260	D	0.998955	D;P;P;D;D	0.69078	0.997;0.841;0.943;0.972;0.978	P;P;P;P;B	0.53593	0.73;0.482;0.534;0.456;0.411	D	0.90222	0.4272	10	0.37606	T	0.19	.	11.2985	0.49292	0.068:0.1285:0.8035:0.0	.	90;100;100;90;90	F8VYG8;Q96RI1;Q96RI1-4;F1DAL1;B6ZGS9	.;NR1H4_HUMAN;.;.;.	H	90;90;90;100;100	ENSP00000448506:R90H;ENSP00000376712:R90H;ENSP00000448978:R90H;ENSP00000447149:R100H;ENSP00000188403:R100H	ENSP00000188403:R100H	R	+	2	0	NR1H4	99428876	1.000000	0.71417	0.993000	0.49108	0.333000	0.28666	4.775000	0.62346	1.477000	0.48234	0.650000	0.86243	CGT		0.522	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123	
GABRA5	2558	broad.mit.edu	37	15	27114460	27114460	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr15:27114460T>C	ENST00000335625.5	+	3	953	c.65T>C	c.(64-66)aTg>aCg	p.M22T	GABRA5_ENST00000400081.3_Missense_Mutation_p.M22T|GABRA5_ENST00000557449.1_3'UTR|GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000355395.5_Missense_Mutation_p.M22T	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	22					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	TGTATTTCCATGAACTTATCC	0.388																																						uc001zbd.2																			0				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49						c.(64-66)aTg>aCg		Homo sapiens gamma-aminobutyric acid (GABA) A receptor, alpha 5 (GABRA5), transcript variant 1, mRNA.	Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)						193.0	188.0	190.0					15																	27114460		1910	4135	6045	SO:0001583	missense	2558				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity	g.chr15:27114460T>C		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.65T>C	15.37:g.27114460T>C	ENSP00000335592:p.Met22Thr					GABRB3_uc001zbb.3_Intron|GABRA5_uc021sgi.1_Missense_Mutation_p.M22T	p.M22T	NM_000810	NP_001158509	P31644	GBRA5_HUMAN		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	2	597	+		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)	22					A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	c.65T>C	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.546279	0.45383	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000557484;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599	T;T;T;T;T;T	0.79749	-0.46;-0.46;-0.46;-1.01;-0.98;-1.3	5.82	5.82	0.92795	.	0.323684	0.35096	N	0.003459	T	0.63780	0.2540	N	0.08118	0	0.37034	D	0.896846	B	0.02656	0.0	B	0.01281	0.0	T	0.63765	-0.6563	10	0.32370	T	0.25	.	12.5835	0.56403	0.0:0.0:0.0:1.0	.	22	P31644	GBRA5_HUMAN	T	22	ENSP00000335592:M22T;ENSP00000347557:M22T;ENSP00000382953:M22T;ENSP00000451527:M22T;ENSP00000450806:M22T;ENSP00000450717:M22T	ENSP00000335592:M22T	M	+	2	0	GABRA5	24665553	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.380000	0.59581	2.216000	0.71823	0.533000	0.62120	ATG		0.388	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
LOC100288637	100288637	broad.mit.edu	37	15	30938316	30938316	+	lincRNA	SNP	G	G	A	rs112615235		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr15:30938316G>A	ENST00000602684.1	+	0	0																											TTCCTTGGCAGTGGATAAGTT	0.393																																						uc010azv.1																			0				endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8						c.e11-1		Homo sapiens Rho GTPase activating protein 11B (ARHGAP11B), mRNA.																																						89839				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr15:30938316G>A																													15.37:g.30938316G>A						ARHGAP11B_uc001zeu.3_Splice_Site|LOC100288637_uc001zev.3_5'Flank				Q3KRB8	RHGBB_HUMAN		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)	11		+		all_lung(180;2.71e-09)|Breast(32;0.00116)							Splice_Site	SNP	ENST00000602684.1	37	c.1127_splice																																																																																					0.393	RP11-932O9.10-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000467507.1		
CHSY1	22856	broad.mit.edu	37	15	101718018	101718018	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr15:101718018G>A	ENST00000254190.3	-	3	2459	c.1984C>T	c.(1984-1986)Cag>Tag	p.Q662*	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	662					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGGTCATACTGGCTGAAGATG	0.428																																						uc021sxt.1																			0				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24						c.(1984-1986)Cag>Tag		Homo sapiens chondroitin sulfate synthase 1 (CHSY1), mRNA.							71.0	76.0	74.0					15																	101718018		2203	4299	6502	SO:0001587	stop_gained	22856				chondroitin sulfate biosynthetic process	Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity	g.chr15:101718018G>A	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.1984C>T	15.37:g.101718018G>A	ENSP00000254190:p.Gln662*					CHSY1_uc010usd.2_Nonsense_Mutation_p.Q390*	p.Q662*	NM_014918	NP_055733	Q86X52	CHSS1_HUMAN	OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)		2	2460	-	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		662					Q6UX38|Q7LFU5|Q9Y2J5	Nonsense_Mutation	SNP	ENST00000254190.3	37	c.1984C>T	CCDS10390.1	.	.	.	.	.	.	.	.	.	.	G	42	9.533345	0.99198	.	.	ENSG00000131873	ENST00000254190;ENST00000543813	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-38.6355	19.8119	0.96549	0.0:0.0:1.0:0.0	.	.	.	.	X	662;390	.	ENSP00000254190:Q662X	Q	-	1	0	CHSY1	99535541	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.617000	0.98361	2.664000	0.90586	0.655000	0.94253	CAG		0.428	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
RLTPR	146206	broad.mit.edu	37	16	67683416	67683417	+	Frame_Shift_Ins	INS	-	-	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr16:67683416_67683417insT	ENST00000334583.6	+	20	2141_2142	c.1813_1814insT	c.(1813-1815)ctafs	p.L605fs	RLTPR_ENST00000545661.1_Frame_Shift_Ins_p.L569fs	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	605	Tropomodulin-like.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		ACTCCGGGCCCTAGCCACCAAT	0.629																																						uc002etn.3																			0				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18						c.(1813-1815)ctafs		Homo sapiens RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing (RLTPR), mRNA.																																				SO:0001589	frameshift_variant	146206							g.chr16:67683416_67683417insT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1814dupT	16.37:g.67683417_67683417dupT	ENSP00000334958:p.Leu605fs					RLTPR_uc010cel.1_Frame_Shift_Ins_p.L598fs|RLTPR_uc010vjr.2_Frame_Shift_Ins_p.L569fs	p.L605fs	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)	19	1933_1934	+		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)	605			Tropomodulin-like.		B8X2Z3	Frame_Shift_Ins	INS	ENST00000334583.6	37	c.1813_1814insT	CCDS45513.1																																																																																				0.629	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
DPEP1	1800	broad.mit.edu	37	16	89704306	89704306	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr16:89704306G>A	ENST00000393092.3	+	10	1283	c.992G>A	c.(991-993)aGg>aAg	p.R331K	DPEP1_ENST00000261615.4_Missense_Mutation_p.R331K|DPEP1_ENST00000421184.1_Missense_Mutation_p.R331K	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	331					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	CTGCTCAGGAGGAACTGGACG	0.627																																						uc010cin.3																			0				large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14						c.(991-993)aGg>aAg		Homo sapiens dipeptidase 1 (renal) (DPEP1), transcript variant 2, mRNA.	Cilastatin(DB01597)						78.0	84.0	82.0					16																	89704306		2187	4293	6480	SO:0001583	missense	1800				proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding	g.chr16:89704306G>A		CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.992G>A	16.37:g.89704306G>A	ENSP00000376807:p.Arg331Lys					DPEP1_uc002fnr.4_Missense_Mutation_p.R331K|DPEP1_uc002fns.4_Missense_Mutation_p.R331K	p.R331K	NM_001128141	NP_004404	P16444	DPEP1_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0258)	9	1195	+		all_lung(18;0.0054)|all_hematologic(23;0.094)	331					D3DX80|Q96AK2	Missense_Mutation	SNP	ENST00000393092.3	37	c.992G>A	CCDS10982.1	.	.	.	.	.	.	.	.	.	.	g	35	5.559731	0.96514	.	.	ENSG00000015413	ENST00000421184;ENST00000393092;ENST00000261615	T;T;T	0.26518	1.73;1.73;1.73	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.89214	3.015	0.51233	D	0.999916	P	0.42620	0.785	P	0.59595	0.86	T	0.62760	-0.6786	10	0.62326	D	0.03	-25.799	19.0565	0.93067	0.0:0.0:1.0:0.0	.	331	P16444	DPEP1_HUMAN	K	331	ENSP00000397313:R331K;ENSP00000376807:R331K;ENSP00000261615:R331K	ENSP00000261615:R331K	R	+	2	0	DPEP1	88231807	1.000000	0.71417	0.994000	0.49952	0.923000	0.55619	7.416000	0.80143	2.601000	0.87937	0.556000	0.70494	AGG		0.627	DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141	
FXR2	9513	broad.mit.edu	37	17	7495610	7495610	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr17:7495610G>A	ENST00000250113.7	-	16	2222	c.1888C>T	c.(1888-1890)Cgc>Tgc	p.R630C	FXR2_ENST00000573057.1_5'UTR|SOX15_ENST00000250055.2_5'Flank|MPDU1_ENST00000423172.2_Intron|SOX15_ENST00000570788.1_5'Flank|SOX15_ENST00000538513.2_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	630						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R630C(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		GGTTTAGTGCGTTCCAGGGGT	0.522																																						uc002gia.2																			1	Substitution - Missense(1)	p.R630C(2)	endometrium(1)	NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26						c.(1888-1890)Cgc>Tgc		Homo sapiens fragile X mental retardation, autosomal homolog 2 (FXR2), mRNA.							130.0	130.0	130.0					17																	7495610		1973	4173	6146	SO:0001583	missense	9513					cytosolic large ribosomal subunit	protein binding|RNA binding	g.chr17:7495610G>A	U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1888C>T	17.37:g.7495610G>A	ENSP00000250113:p.Arg630Cys					MPDU1_uc010vuc.1_Intron|SOX15_uc002ghy.1_5'Flank|SOX15_uc002ghz.1_5'Flank	p.R630C	NM_004860	NP_004851	P51116	FXR2_HUMAN		READ - Rectum adenocarcinoma(115;0.17)	15	2253	-			630					B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	37	c.1888C>T	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.483534	0.44147	.	.	ENSG00000129245	ENST00000250113	T	0.37411	1.2	4.89	4.89	0.63831	.	0.472069	0.23310	N	0.049569	T	0.18425	0.0442	N	0.08118	0	0.48511	D	0.999663	P	0.51537	0.946	B	0.34346	0.18	T	0.15464	-1.0436	10	0.72032	D	0.01	-23.3396	15.9292	0.79646	0.0:0.0:1.0:0.0	.	630	P51116	FXR2_HUMAN	C	630	ENSP00000250113:R630C	ENSP00000250113:R630C	R	-	1	0	FXR2	7436335	0.849000	0.29639	1.000000	0.80357	0.986000	0.74619	0.875000	0.28079	2.709000	0.92574	0.655000	0.94253	CGC		0.522	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
FKBP10	60681	broad.mit.edu	37	17	39975472	39975472	+	Silent	SNP	C	C	T	rs573865037		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr17:39975472C>T	ENST00000321562.4	+	5	842	c.738C>T	c.(736-738)atC>atT	p.I246I	FKBP10_ENST00000544340.1_5'Flank	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	246	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		GGACAGTGATCCCCCCACAGG	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		15171	0.0		0.0	False		,,,				2504	0.001					uc002hxv.2																			0				cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14						c.(736-738)atC>atT		Homo sapiens FK506 binding protein 10, 65 kDa (FKBP10), mRNA.							75.0	73.0	73.0					17																	39975472		2203	4300	6503	SO:0001819	synonymous_variant	60681				protein folding	endoplasmic reticulum lumen|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity	g.chr17:39975472C>T	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"""EF-hand domain containing"""	18169	protein-coding gene	gene with protein product		607063	"""FK506 binding protein 10 (65 kDa)"""			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.738C>T	17.37:g.39975472C>T						FKBP10_uc002hxw.1_5'UTR	p.I246I	NM_021939	NP_068758	Q96AY3	FKB10_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.148)	4	1063	+		Breast(137;0.00122)	246			PPIase FKBP-type 2.		Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Silent	SNP	ENST00000321562.4	37	c.738C>T	CCDS11409.1																																																																																				0.607	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939	
NPEPPS	9520	broad.mit.edu	37	17	45681356	45681356	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr17:45681356C>T	ENST00000322157.4	+	16	2053	c.1816C>T	c.(1816-1818)Cgt>Tgt	p.R606C	RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000530173.1_Missense_Mutation_p.R602C|NPEPPS_ENST00000544660.1_Missense_Mutation_p.R526C	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	606					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						ACCAGGCATTCGTGACCTTTC	0.433																																						uc002ilr.4																			0				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						c.(1816-1818)Cgt>Tgt		Homo sapiens aminopeptidase puromycin sensitive (NPEPPS), mRNA.							115.0	108.0	110.0					17																	45681356		1926	4126	6052	SO:0001583	missense	9520				proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding	g.chr17:45681356C>T	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1816C>T	17.37:g.45681356C>T	ENSP00000320324:p.Arg606Cys					NPEPPS_uc010wkt.2_Missense_Mutation_p.R602C|NPEPPS_uc010wku.2_Missense_Mutation_p.R570C|NPEPPS_uc010wkv.2_Missense_Mutation_p.R160C|NPEPPS_uc002ils.1_Missense_Mutation_p.R39C	p.R606C	NM_006310	NP_006301	P55786	PSA_HUMAN			15	2039	+			606					B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	c.1816C>T	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.346633	0.82022	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660	T;T;T	0.05513	3.43;3.43;3.43	5.73	4.73	0.59995	.	0.049822	0.85682	D	0.000000	T	0.16342	0.0393	L	0.52573	1.65	0.80722	D	1	D;D;D	0.67145	0.996;0.978;0.996	P;P;P	0.58970	0.849;0.773;0.849	T	0.00069	-1.2137	10	0.72032	D	0.01	.	14.8616	0.70387	0.257:0.743:0.0:0.0	.	602;289;606	E9PLK3;B7Z1H4;P55786	.;.;PSA_HUMAN	C	602;606;593;526	ENSP00000433287:R602C;ENSP00000320324:R606C;ENSP00000442461:R526C	ENSP00000320324:R606C	R	+	1	0	NPEPPS	43036355	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.454000	0.35178	2.716000	0.92895	0.561000	0.74099	CGT		0.433	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
DSG1	1828	broad.mit.edu	37	18	28934664	28934664	+	Silent	SNP	C	C	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr18:28934664C>T	ENST00000257192.4	+	15	2717	c.2505C>T	c.(2503-2505)gtC>gtT	p.V835V	DSG1_ENST00000462981.2_Silent_p.V194V|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	835					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			ATGGTAATGTCACTGTGACCG	0.512																																						uc002kwp.3																			0				NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76						c.(2503-2505)gtC>gtT		Homo sapiens desmoglein 1 (DSG1), mRNA.							229.0	191.0	204.0					18																	28934664		2203	4300	6503	SO:0001819	synonymous_variant	1828				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding	g.chr18:28934664C>T	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.2505C>T	18.37:g.28934664C>T						DSG1_uc010xbp.2_Silent_p.V194V	p.V835V	NM_001942	NP_001933	Q02413	DSG1_HUMAN	OV - Ovarian serous cystadenocarcinoma(10;0.00559)		14	2717	+			835					B7Z845	Silent	SNP	ENST00000257192.4	37	c.2505C>T	CCDS11896.1																																																																																				0.512	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
SLC14A2	8170	broad.mit.edu	37	18	43212315	43212315	+	Splice_Site	SNP	G	G	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr18:43212315G>T	ENST00000255226.6	+	5	1338	c.522G>T	c.(520-522)agG>agT	p.R174S	SLC14A2_ENST00000586448.1_Splice_Site_p.R174S	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	174					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCACCGCCAGGTCTGCCATTG	0.512																																						uc002lbe.3																			0				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						c.e5-1		Homo sapiens solute carrier family 14 (urea transporter), member 2 (SLC14A2), transcript variant 1, mRNA.							199.0	170.0	180.0					18																	43212315		2203	4300	6503	SO:0001630	splice_region_variant	8170					apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity	g.chr18:43212315G>T	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.522-1G>T	18.37:g.43212315G>T						SLC14A2_uc002lbb.3_Splice_Site_p.R174_splice|SLC14A2_uc010dnj.3_Splice_Site_p.R174_splice	p.R174_splice	NM_007163	NP_009094	Q15849	UT2_HUMAN			5	1338	+			174					A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	c.522_splice	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.079486	0.55753	.	.	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.51071	0.72;0.72	4.65	3.78	0.43462	.	0.000000	0.85682	D	0.000000	T	0.66157	0.2761	M	0.80183	2.485	0.52099	D	0.999947	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67577	-0.5635	9	.	.	.	.	8.9438	0.35747	0.2365:0.0:0.7635:0.0	.	174;174	Q15849;E7EPU1	UT2_HUMAN;.	S	174	ENSP00000255226:R174S;ENSP00000320689:R174S	.	R	+	3	2	SLC14A2	41466313	1.000000	0.71417	0.947000	0.38551	0.655000	0.38815	3.860000	0.55995	1.312000	0.45043	0.563000	0.77884	AGG		0.512	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		Missense_Mutation
MC4R	4160	broad.mit.edu	37	18	58038973	58038973	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr18:58038973T>A	ENST00000299766.3	-	1	1028	c.610A>T	c.(610-612)Atg>Ttg	p.M204L		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	204					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				AGAGCCAGCATGGTGAAGAAC	0.498																																						uc002lie.1																			0				endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17						c.(610-612)Atg>Ttg		Homo sapiens melanocortin 4 receptor (MC4R), mRNA.							84.0	77.0	79.0					18																	58038973		2203	4300	6503	SO:0001583	missense	4160				feeding behavior|G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of bone resorption|positive regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|ubiquitin protein ligase binding	g.chr18:58038973T>A	AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"""GPCR / Class A : Melanocortin receptors"""	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.610A>T	18.37:g.58038973T>A	ENSP00000299766:p.Met204Leu						p.M204L	NM_005912	NP_005903	P32245	MC4R_HUMAN			0	1029	-		Colorectal(73;0.0946)	204					B2RAC3|Q16317|Q3MIJ6	Missense_Mutation	SNP	ENST00000299766.3	37	c.610A>T	CCDS11976.1	.	.	.	.	.	.	.	.	.	.	T	16.78	3.218678	0.58560	.	.	ENSG00000166603	ENST00000299766	T	0.35789	1.29	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.66439	2.03	0.58432	D	0.999999	B	0.14012	0.009	B	0.20384	0.029	T	0.28776	-1.0033	10	0.66056	D	0.02	.	14.1876	0.65617	0.0:0.0:0.0:1.0	.	204	P32245	MC4R_HUMAN	L	204	ENSP00000299766:M204L	ENSP00000299766:M204L	M	-	1	0	MC4R	56189953	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.238000	0.73509	0.533000	0.62120	ATG		0.498	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912	
RBFA	79863	broad.mit.edu	37	18	77796687	77796687	+	Missense_Mutation	SNP	A	A	C			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr18:77796687A>C	ENST00000306735.5	+	2	316	c.178A>C	c.(178-180)Agt>Cgt	p.S60R	TXNL4A_ENST00000589926.1_5'Flank|TXNL4A_ENST00000592957.1_5'Flank|TXNL4A_ENST00000585474.1_5'Flank|RBFA_ENST00000586847.1_3'UTR|RBFA_ENST00000262197.7_Missense_Mutation_p.S60R|RP11-795F19.5_ENST00000569722.1_Intron	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	60					rRNA processing (GO:0006364)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						TTGGTATGAAAGTCCTTCCTT	0.378																																						uc002lns.3																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						c.(178-180)Agt>Cgt		Homo sapiens ribosome binding factor A (putative) (RBFA), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.							122.0	118.0	120.0					18																	77796687		2203	4300	6503	SO:0001583	missense	79863				rRNA processing	mitochondrion		g.chr18:77796687A>C	BC014195	CCDS12021.1, CCDS54194.1	18q23	2010-10-21	2010-10-21	2010-10-21	ENSG00000101546	ENSG00000101546			26120	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 22"""	C18orf22		12477932	Standard	NM_024805		Approved	FLJ21172, HsT169	uc002lns.3	Q8N0V3	OTTHUMG00000132923	ENST00000306735.5:c.178A>C	18.37:g.77796687A>C	ENSP00000305696:p.Ser60Arg					TXNL4A_uc010drg.3_5'Flank|RBFA_uc010drh.3_Missense_Mutation_p.S60R|RBFA_uc010dri.2_Intron	p.S60R	NM_024805	NP_079081	Q8N0V3	RBFA_HUMAN			1	328	+			60					Q6PF07|Q8WZ65|Q9H776	Missense_Mutation	SNP	ENST00000306735.5	37	c.178A>C	CCDS12021.1	.	.	.	.	.	.	.	.	.	.	A	10.13	1.265483	0.23136	.	.	ENSG00000101546	ENST00000262197;ENST00000306735	T;T	0.42900	0.96;0.96	4.04	-1.28	0.09318	.	0.487586	0.18851	N	0.129383	T	0.26955	0.0660	L	0.27053	0.805	0.27903	N	0.938902	P;P	0.40875	0.731;0.694	B;B	0.41088	0.347;0.244	T	0.17776	-1.0358	10	0.45353	T	0.12	-10.6472	7.8775	0.29603	0.6811:0.0:0.3189:0.0	.	60;60	Q8N0V3-2;Q8N0V3	.;RBFA_HUMAN	R	60	ENSP00000262197:S60R;ENSP00000305696:S60R	ENSP00000262197:S60R	S	+	1	0	RBFA	75897675	1.000000	0.71417	0.905000	0.35620	0.652000	0.38707	0.809000	0.27168	-0.171000	0.10797	-0.232000	0.12228	AGT		0.378	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805	
MAP1S	55201	broad.mit.edu	37	19	17844106	17844106	+	Nonsense_Mutation	SNP	G	G	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr19:17844106G>T	ENST00000324096.4	+	6	3044	c.2893G>T	c.(2893-2895)Gag>Tag	p.E965*	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Nonsense_Mutation_p.E939*	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	965	Necessary for association with actin. {ECO:0000250}.|Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.E965*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCTGGTGGATGAGGAGTTCTT	0.697																																						uc002nhe.1																			1	Substitution - Nonsense(1)	p.E965*(2)	endometrium(1)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						c.(2893-2895)Gag>Tag		Homo sapiens microtubule-associated protein 1S (MAP1S), mRNA.							34.0	28.0	30.0					19																	17844106		2195	4297	6492	SO:0001587	stop_gained	55201				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding	g.chr19:17844106G>T	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2893G>T	19.37:g.17844106G>T	ENSP00000325313:p.Glu965*					MAP1S_uc010xpv.1_Nonsense_Mutation_p.E939*	p.E965*	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN			5	2902	+			965			Necessary for association with actin (By similarity).|Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.		B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Nonsense_Mutation	SNP	ENST00000324096.4	37	c.2893G>T	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213012	0.79352	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	.	.	.	4.63	-9.26	0.00662	.	0.544163	0.15133	N	0.278749	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-1.8866	7.0315	0.24970	0.3149:0.4271:0.258:0.0	.	.	.	.	X	965;939	.	ENSP00000325313:E965X	E	+	1	0	MAP1S	17705106	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.073000	0.11468	-2.421000	0.00563	-1.058000	0.02302	GAG		0.697	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
ZNF98	148198	broad.mit.edu	37	19	22574462	22574462	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr19:22574462T>A	ENST00000357774.5	-	4	1696	c.1575A>T	c.(1573-1575)aaA>aaT	p.K525N		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	525					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TGTTAAAGGCTTTGCCGCATT	0.388																																						uc002nqt.2																			0				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37						c.(1573-1575)aaA>aaT		Homo sapiens zinc finger protein 98 (ZNF98), mRNA.							69.0	58.0	62.0					19																	22574462		2170	4271	6441	SO:0001583	missense	148198				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:22574462T>A		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1575A>T	19.37:g.22574462T>A	ENSP00000350418:p.Lys525Asn						p.K525N	NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN			3	1697	-		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)	525						Missense_Mutation	SNP	ENST00000357774.5	37	c.1575A>T	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	12.00	1.807531	0.31961	.	.	ENSG00000197360	ENST00000357774	T	0.27890	1.64	1.39	1.39	0.22231	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46288	0.1385	M	0.79011	2.435	0.21020	N	0.999804	P	0.51653	0.947	P	0.56648	0.803	T	0.25082	-1.0142	9	0.59425	D	0.04	.	7.6384	0.28280	0.0:0.0:0.0:1.0	.	525	A6NK75	ZNF98_HUMAN	N	525	ENSP00000350418:K525N	ENSP00000350418:K525N	K	-	3	2	ZNF98	22366302	0.084000	0.21492	0.211000	0.23655	0.367000	0.29736	0.238000	0.18004	0.627000	0.30340	0.240000	0.17902	AAA		0.388	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
CD37	951	broad.mit.edu	37	19	49840274	49840274	+	Missense_Mutation	SNP	G	G	A	rs375511347		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr19:49840274G>A	ENST00000323906.4	+	3	392	c.251G>A	c.(250-252)cGc>cAc	p.R84H	CD37_ENST00000598095.1_Missense_Mutation_p.R16H|CTC-301O7.4_ENST00000358234.4_lincRNA|CD37_ENST00000535669.2_Missense_Mutation_p.R84H|CD37_ENST00000596426.1_3'UTR|CD37_ENST00000426897.2_Missense_Mutation_p.R16H	NM_001774.2	NP_001765.1	P11049	CD37_HUMAN	CD37 molecule	84					defense response to protozoan (GO:0042832)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|positive regulation of immunoglobulin production (GO:0002639)|regulation of defense response to virus (GO:0050688)|regulation of humoral immune response (GO:0002920)	extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	11		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)		AAGGAGCTCCGCTGCCTCCTG	0.622																																						uc002pnd.3																			0				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	11						c.(250-252)cGc>cAc		Homo sapiens CD37 molecule (CD37), transcript variant 1, mRNA.		G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	65.0	60.0	61.0		47,251	3.5	1.0	19		61	0,8600		0,0,4300	no	missense,missense	CD37	NM_001040031.1,NM_001774.2	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	16/214,84/282	49840274	1,13005	2203	4300	6503	SO:0001583	missense	951					integral to membrane		g.chr19:49840274G>A		CCDS12760.1, CCDS46139.1	19p13-q13.4	2013-02-14	2006-03-28			ENSG00000104894		"""CD molecules"", ""Tetraspanins"""	1666	protein-coding gene	gene with protein product		151523	"""CD37 antigen"""			8436422	Standard	XM_005259435		Approved	TSPAN26	uc002pnd.3	P11049		ENST00000323906.4:c.251G>A	19.37:g.49840274G>A	ENSP00000325708:p.Arg84His					AK097351_uc002pnb.1_Intron|CD37_uc002pnc.3_Non-coding_Transcript|CD37_uc010yam.1_Missense_Mutation_p.R84H|CD37_uc010yan.1_Missense_Mutation_p.R16H|CD37_uc002pnf.3_Missense_Mutation_p.R56H|CD37_uc002pne.3_Missense_Mutation_p.R16H	p.R84H	NM_001774	NP_001035120	P11049	CD37_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)	2	372	+		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)	84					B4DVC1|Q3KPF9	Missense_Mutation	SNP	ENST00000323906.4	37	c.251G>A	CCDS12760.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959755	0.74016	2.27E-4	0.0	ENSG00000104894	ENST00000391859;ENST00000323906;ENST00000426897;ENST00000535669	T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37	4.55	3.49	0.39957	Tetraspanin, conserved site (1);	0.289185	0.25456	N	0.030552	D	0.87625	0.6224	M	0.74881	2.28	0.45194	D	0.998208	D;D;D;D	0.89917	1.0;0.998;0.998;0.998	D;D;D;D	0.83275	0.996;0.916;0.916;0.916	D	0.86637	0.1889	10	0.46703	T	0.11	.	10.8912	0.46996	0.0:0.1913:0.8087:0.0	.	16;84;84;84	B4DVC1;B7ZAN3;B4DW15;P11049	.;.;.;CD37_HUMAN	H	84;84;16;84	ENSP00000375732:R84H;ENSP00000325708:R84H;ENSP00000413151:R16H;ENSP00000441037:R84H	ENSP00000325708:R84H	R	+	2	0	CD37	54532086	0.190000	0.23276	0.994000	0.49952	0.757000	0.42996	1.021000	0.30040	1.049000	0.40321	0.467000	0.42956	CGC		0.622	CD37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465532.1		
GPR17	2840	broad.mit.edu	37	2	128408380	128408380	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr2:128408380G>T	ENST00000272644.3	+	3	229	c.155G>T	c.(154-156)gGc>gTc	p.G52V	LIMS2_ENST00000410038.1_5'Flank|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000324938.5_Intron|LIMS2_ENST00000409808.2_Intron|LIMS2_ENST00000409254.1_5'Flank|GPR17_ENST00000486700.1_3'UTR|LIMS2_ENST00000355119.4_Intron|GPR17_ENST00000393018.3_Missense_Mutation_p.G52V|GPR17_ENST00000544369.1_Missense_Mutation_p.G52V|LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000410011.1_Intron	NM_001161416.1|NM_001161417.1|NM_005291.2	NP_001154888.1|NP_001154889.1|NP_005282.1	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	52					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		gagcaatgtggccaggagacg	0.547											OREG0014966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc010yzn.2																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19						c.(154-156)gGc>gTc		Homo sapiens G protein-coupled receptor 17 (GPR17), transcript variant 1, mRNA.							93.0	93.0	93.0					2																	128408380		2203	4300	6503	SO:0001583	missense	2840					integral to plasma membrane	chemokine receptor activity|purinergic nucleotide receptor activity, G-protein coupled	g.chr2:128408380G>T		CCDS2148.1	2q21	2014-01-30			ENSG00000144230	ENSG00000144230		"""GPCR / Class A : Orphans"""	4471	protein-coding gene	gene with protein product		603071				8558062	Standard	NM_001161415		Approved		uc002tpc.3	Q13304	OTTHUMG00000131533	ENST00000272644.3:c.155G>T	2.37:g.128408380G>T	ENSP00000272644:p.Gly52Val		OREG0014966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1564	LIMS2_uc002tow.3_5'Flank|LIMS2_uc002tox.3_Intron|LIMS2_uc010fmb.3_Intron|LIMS2_uc002toy.3_Intron|LIMS2_uc002tpa.3_Intron|LIMS2_uc002toz.3_Intron|LIMS2_uc010yzm.2_Intron|LIMS2_uc002tpb.3_Intron|GPR17_uc002tpc.3_Missense_Mutation_p.G52V|GPR17_uc010yzo.2_Missense_Mutation_p.G24V|GPR17_uc002tpd.3_Missense_Mutation_p.G24V	p.G52V	NM_001161415	NP_001154889	Q13304	GPR17_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0677)	3	766	+	Colorectal(110;0.1)	Ovarian(717;0.15)	52					A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Missense_Mutation	SNP	ENST00000272644.3	37	c.155G>T	CCDS2148.1	.	.	.	.	.	.	.	.	.	.	g	8.191	0.795973	0.16327	.	.	ENSG00000144230	ENST00000544369;ENST00000339805;ENST00000272644;ENST00000423019;ENST00000393018	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.17	5.17	0.71159	.	0.202934	0.42294	D	0.000737	T	0.16257	0.0391	N	0.08118	0	0.58432	D	0.999996	P	0.35272	0.493	B	0.23275	0.045	T	0.13764	-1.0497	10	0.16896	T	0.51	.	13.9479	0.64096	0.0:0.0:0.8481:0.1519	.	52	Q13304	GPR17_HUMAN	V	52;24;52;52;52	ENSP00000442982:G52V;ENSP00000272644:G52V;ENSP00000387970:G52V;ENSP00000376741:G52V	ENSP00000272644:G52V	G	+	2	0	GPR17	128124850	1.000000	0.71417	0.996000	0.52242	0.786000	0.44442	1.873000	0.39558	2.573000	0.86826	0.655000	0.94253	GGC		0.547	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1		
AMER3	205147	broad.mit.edu	37	2	131521709	131521709	+	Silent	SNP	C	C	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr2:131521709C>T	ENST00000423981.1	+	2	2174	c.2064C>T	c.(2062-2064)aaC>aaT	p.N688N	AMER3_ENST00000321420.4_Silent_p.N688N	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	688					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										TCAGCTCAAACGAACAGCCCC	0.652																																						uc021voy.1																			0				breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(43)|ovary(2)|pancreas(4)|prostate(3)|skin(8)	73						c.(2062-2064)aaC>aaT		Homo sapiens family with sequence similarity 123C (FAM123C), transcript variant 1, mRNA.							21.0	23.0	22.0					2																	131521709		2201	4299	6500	SO:0001819	synonymous_variant	205147							g.chr2:131521709C>T	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.2064C>T	2.37:g.131521709C>T						FAM123C_uc002trw.2_Silent_p.N688N|FAM123C_uc010fmv.2_Silent_p.N688N|FAM123C_uc010fms.1_Silent_p.N688N|FAM123C_uc010fmt.1_Silent_p.N688N|FAM123C_uc010fmu.1_Silent_p.N688N	p.N688N	NM_152698	NP_689911	Q8N944	F123C_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.13)	0	2064	+	Colorectal(110;0.1)		688					B7ZLH6	Silent	SNP	ENST00000423981.1	37	c.2064C>T	CCDS2164.1																																																																																				0.652	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
CST7	8530	broad.mit.edu	37	20	24930092	24930092	+	5'UTR	SNP	C	C	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr20:24930092C>A	ENST00000480798.1	+	0	227				CST7_ENST00000376835.2_Missense_Mutation_p.A6E	NM_003650.3	NP_003641.3	O76096	CYTF_HUMAN	cystatin F (leukocystatin)						immune response (GO:0006955)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)			large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	5						CCTGAGAAGGCACTGCACGGC	0.672																																						uc002wtx.2																			0				large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	5								Homo sapiens cystatin F (leukocystatin) (CST7), mRNA.							74.0	64.0	67.0					20																	24930092		2203	4299	6502	SO:0001623	5_prime_UTR_variant	8530				immune response	cytoplasm|extracellular region	cysteine-type endopeptidase inhibitor activity	g.chr20:24930092C>A	AF036342	CCDS13165.1, CCDS13165.2	20p11.21	2008-04-15			ENSG00000077984	ENSG00000077984			2479	protein-coding gene	gene with protein product		603253				9733783, 9632704	Standard	NM_003650		Approved		uc002wtx.2	O76096	OTTHUMG00000032108	ENST00000480798.1:c.-50C>A	20.37:g.24930092C>A								NM_003650	NP_003641	O76096	CYTF_HUMAN			0		+								Q6FH95|Q7Z4J8|Q9UED4	Missense_Mutation	SNP	ENST00000480798.1	37		CCDS13165.2	.	.	.	.	.	.	.	.	.	.	C	5.802	0.332214	0.10956	.	.	ENSG00000077984	ENST00000376835	T	0.10573	2.86	1.18	-2.35	0.06684	.	.	.	.	.	T	0.08714	0.0216	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33979	-0.9847	6	0.87932	D	0	.	0.3298	0.00316	0.2467:0.299:0.2456:0.2087	.	.	.	.	E	6	ENSP00000366031:A6E	ENSP00000366031:A6E	A	+	2	0	CST7	24878092	0.018000	0.18449	0.000000	0.03702	0.042000	0.13812	0.000000	0.12993	-1.087000	0.03081	0.407000	0.27541	GCA		0.672	CST7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078381.2	NM_003650	
BPIFB3	359710	broad.mit.edu	37	20	31656654	31656654	+	Missense_Mutation	SNP	C	C	T	rs199722228		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr20:31656654C>T	ENST00000375494.3	+	10	1024	c.1024C>T	c.(1024-1026)Cgg>Tgg	p.R342W		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	342					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										ACTGTTCCTGCGGGTGAGGGA	0.577																																						uc002wym.1																			0											c.(1024-1026)Cgg>Tgg		Homo sapiens BPI fold containing family B, member 3 (BPIFB3), mRNA.							104.0	76.0	85.0					20																	31656654		2203	4300	6503	SO:0001583	missense	359710				innate immune response	cytoplasm|extracellular region	lipid binding|protein binding	g.chr20:31656654C>T	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1024C>T	20.37:g.31656654C>T	ENSP00000364643:p.Arg342Trp						p.R342W	NM_182658	NP_872599	P59826	LPLC3_HUMAN			9	1024	+			342					Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	c.1024C>T	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042148	0.35989	.	.	ENSG00000186190	ENST00000375494	T	0.09073	3.02	4.24	-0.563	0.11778	.	0.000000	0.46145	D	0.000308	T	0.18593	0.0446	M	0.75264	2.295	0.32997	D	0.525717	D	0.76494	0.999	D	0.63033	0.91	T	0.14200	-1.0481	10	0.72032	D	0.01	-22.3231	5.2012	0.15264	0.5059:0.3903:0.0:0.1037	.	342	P59826	BPIB3_HUMAN	W	342	ENSP00000364643:R342W	ENSP00000364643:R342W	R	+	1	2	BPIFB3	31120315	1.000000	0.71417	0.858000	0.33744	0.155000	0.21991	0.647000	0.24812	0.131000	0.18576	0.585000	0.79938	CGG		0.577	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
PHF20	51230	broad.mit.edu	37	20	34487354	34487354	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr20:34487354G>T	ENST00000374012.3	+	10	1474	c.1345G>T	c.(1345-1347)Gac>Tac	p.D449Y	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	449					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					TGTCGACCTAGACCATAAGTT	0.348																																						uc002xek.1																			0				breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.(1345-1347)Gac>Tac		Homo sapiens PHD finger protein 20 (PHF20), mRNA.							62.0	60.0	61.0					20																	34487354		2203	4300	6503	SO:0001583	missense	51230				regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding	g.chr20:34487354G>T	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1345G>T	20.37:g.34487354G>T	ENSP00000363124:p.Asp449Tyr					PHF20_uc002xei.1_Missense_Mutation_p.D449Y|PHF20_uc010gfo.1_Missense_Mutation_p.D449Y|PHF20_uc002xej.1_Missense_Mutation_p.D333Y	p.D449Y	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN			9	1456	+	Breast(12;0.00631)|all_lung(11;0.0145)		449					A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	c.1345G>T	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812196	0.70797	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.66995	0.5;-0.24;-0.24	5.93	2.85	0.33270	.	0.092333	0.64402	D	0.000001	T	0.67933	0.2946	M	0.62723	1.935	0.80722	D	1	P;D	0.61697	0.454;0.99	B;P	0.50659	0.17;0.647	T	0.67662	-0.5613	10	0.87932	D	0	.	8.5129	0.33229	0.1439:0.1256:0.7305:0.0	.	449;449	Q9BVI0;Q66K49	PHF20_HUMAN;.	Y	449	ENSP00000363124:D449Y;ENSP00000341900:D449Y;ENSP00000363112:D449Y	ENSP00000341900:D449Y	D	+	1	0	PHF20	33950768	1.000000	0.71417	0.991000	0.47740	0.977000	0.68977	6.167000	0.71902	0.366000	0.24427	0.591000	0.81541	GAC		0.348	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	
TMPRSS3	64699	broad.mit.edu	37	21	43803180	43803180	+	Silent	SNP	C	C	T	rs369903582		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr21:43803180C>T	ENST00000291532.3	-	8	1699	c.744G>A	c.(742-744)acG>acA	p.T248T	TMPRSS3_ENST00000398405.1_Silent_p.T246T|TMPRSS3_ENST00000380399.1_Silent_p.T332T|TMPRSS3_ENST00000398397.3_Silent_p.T248T|TMPRSS3_ENST00000433957.2_Silent_p.T248T|TMPRSS3_ENST00000474596.1_5'UTR	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	248	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TCCACAGGGGCGTGATGACAG	0.602																																						uc002zbb.2																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						c.(742-744)acG>acA		Homo sapiens transmembrane protease, serine 3 (TMPRSS3), transcript variant A, mRNA.		C	,	0,4406		0,0,2203	77.0	65.0	69.0		744,744	-11.0	0.0	21		69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMPRSS3	NM_024022.2,NM_032405.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	248/455,248/345	43803180	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64699				cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity	g.chr21:43803180C>T	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.744G>A	21.37:g.43803180C>T						TMPRSS3_uc002zay.2_5'UTR|TMPRSS3_uc002zaz.2_Silent_p.T121T|TMPRSS3_uc002zba.2_Silent_p.T121T|TMPRSS3_uc002zbc.2_Silent_p.T248T|TMPRSS3_uc002zbd.3_Silent_p.T248T	p.T248T	NM_024022	NP_076927	P57727	TMPS3_HUMAN			7	945	-			248			Peptidase S1.		D3DSJ6|Q5USC7|Q6ZMC3	Silent	SNP	ENST00000291532.3	37	c.744G>A	CCDS13686.1																																																																																				0.602	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
GGT5	2687	broad.mit.edu	37	22	24622188	24622188	+	Missense_Mutation	SNP	C	C	T	rs149456868	byFrequency	TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr22:24622188C>T	ENST00000327365.4	-	8	1501	c.1085G>A	c.(1084-1086)cGc>cAc	p.R362H	GGT5_ENST00000418439.2_Missense_Mutation_p.R285H|GGT5_ENST00000263112.7_Missense_Mutation_p.R330H|GGT5_ENST00000398292.3_Missense_Mutation_p.R362H	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	362					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GATCTGTTGGCGGATGAGCTG	0.692													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12269	0.0		0.0	False		,,,				2504	0.0					uc002zzp.4																			0		p.R362C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						c.(1084-1086)cGc>cAc		Homo sapiens gamma-glutamyltransferase 5 (GGT5), transcript variant 1, mRNA.		C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	31.0	36.0	34.0		1085,989,1085	3.5	0.9	22	dbSNP_134	34	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	29,29,29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	362/588,330/555,362/587	24622188	1,13003	2203	4299	6502	SO:0001583	missense	2687				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity	g.chr22:24622188C>T	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.1085G>A	22.37:g.24622188C>T	ENSP00000330080:p.Arg362His					GGT5_uc002zzo.4_Missense_Mutation_p.R362H|GGT5_uc002zzr.4_Missense_Mutation_p.R330H|GGT5_uc002zzq.4_Missense_Mutation_p.R330H|GGT5_uc011ajm.2_Missense_Mutation_p.R285H|GGT5_uc011ajn.1_Non-coding_Transcript	p.R362H	NM_001099781	NP_001093251	P36269	GGT5_HUMAN			7	1502	-			362					Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	37	c.1085G>A	CCDS13825.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	15.56	2.870233	0.51588	0.0	1.16E-4	ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292;ENST00000418439	T;T;T;T	0.08807	3.05;3.05;3.05;3.05	4.51	3.48	0.39840	.	0.057958	0.64402	D	0.000002	T	0.25195	0.0612	M	0.91663	3.23	0.47905	D	0.999547	D;D;D;D;D	0.89917	1.0;0.99;1.0;0.997;1.0	D;P;D;P;D	0.83275	0.993;0.764;0.996;0.881;0.996	T	0.12734	-1.0536	10	0.87932	D	0	-30.0248	9.9128	0.41417	0.0:0.8971:0.0:0.1029	.	285;330;362;362;362	E7EUG3;P36269-2;Q53XM9;Q6GMP0;P36269	.;.;.;.;GGT5_HUMAN	H	362;330;277;362;285	ENSP00000330080:R362H;ENSP00000263112:R330H;ENSP00000381340:R362H;ENSP00000392146:R285H	ENSP00000263112:R330H	R	-	2	0	GGT5	22952188	0.012000	0.17670	0.919000	0.36401	0.077000	0.17291	0.885000	0.28227	2.262000	0.75019	0.485000	0.47835	CGC		0.692	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
TMEM144	55314	broad.mit.edu	37	4	159136389	159136389	+	Silent	SNP	C	C	G	rs149733307		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr4:159136389C>G	ENST00000296529.6	+	4	676	c.156C>G	c.(154-156)gcC>gcG	p.A52A	TMEM144_ENST00000514558.1_Silent_p.A52A	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	52						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		GGTTGGTTGCCTTGGTTGTCA	0.383																																						uc003ipx.3																			0				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19						c.(154-156)gcC>gcG		Homo sapiens transmembrane protein 144 (TMEM144), mRNA.							242.0	216.0	224.0					4																	159136389		2203	4300	6503	SO:0001819	synonymous_variant	55314					integral to membrane		g.chr4:159136389C>G	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.156C>G	4.37:g.159136389C>G						TMEM144_uc010iqi.3_Non-coding_Transcript	p.A52A	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN		COAD - Colon adenocarcinoma(41;0.0539)	3	676	+	all_hematologic(180;0.24)	Renal(120;0.0854)	52					D3DP24|Q49A05|Q9NUT3	Silent	SNP	ENST00000296529.6	37	c.156C>G	CCDS3799.1																																																																																				0.383	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342	
PIK3R1	5295	broad.mit.edu	37	5	67591246	67591246	+	Splice_Site	SNP	A	A	G			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr5:67591246A>G	ENST00000521381.1	+	14	2361		c.e14-1		PIK3R1_ENST00000521657.1_Splice_Site|PIK3R1_ENST00000274335.5_Splice_Site|PIK3R1_ENST00000320694.8_Splice_Site|PIK3R1_ENST00000396611.1_Splice_Site|PIK3R1_ENST00000523872.1_Splice_Site|PIK3R1_ENST00000336483.5_Splice_Site	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.?(10)|p.Y580fs*1(1)|p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	ACTGTTTTTCAGGTGGTTGAC	0.363			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												uc003jva.3				Rec	yes		5	5q13.1	5295	"""Mis, F, O"""	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""			"""E, O"""			"""gliobastoma, ovarian, colorectal"""		12	Unknown(10)|Whole gene deletion(1)|Deletion - Frameshift(1)	p.?(10)|p.Y580fs*1(1)|p.0?(1)	endometrium(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178						c.e14-2		Homo sapiens phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1), transcript variant 1, mRNA.	Isoproterenol(DB01064)						150.0	148.0	149.0					5																	67591246		2203	4300	6503	SO:0001630	splice_region_variant	5295				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	g.chr5:67591246A>G	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1746-1A>G	5.37:g.67591246A>G		TCGA GBM(4;<1E-08)				PIK3R1_uc003jvc.3_Splice_Site_p.M282_splice|PIK3R1_uc003jvd.3_Splice_Site_p.M312_splice|PIK3R1_uc003jve.3_Splice_Site_p.M261_splice|PIK3R1_uc021xzn.1_Splice_Site_p.M219_splice|PIK3R1_uc011crb.2_Splice_Site_p.M252_splice	p.M582_splice	NM_181523	NP_852664	P27986	P85A_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	14	2326	+		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)	582					B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Splice_Site	SNP	ENST00000521381.1	37	c.1746_splice	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060385	0.76074	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000523872	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6086	0.68498	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PIK3R1	67627002	1.000000	0.71417	0.981000	0.43875	0.926000	0.56050	9.105000	0.94246	2.036000	0.60181	0.377000	0.23210	.		0.363	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	Intron
FSTL4	23105	broad.mit.edu	37	5	132535036	132535036	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr5:132535036G>T	ENST00000265342.7	-	16	2529	c.2280C>A	c.(2278-2280)gaC>gaA	p.D760E	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	760						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGAACAGCAGGTCCGGCTCCG	0.582																																						uc003kyn.1																			0				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23						c.(2278-2280)gaC>gaA		Homo sapiens follistatin-like 4 (FSTL4), mRNA.							59.0	58.0	58.0					5																	132535036		2203	4300	6503	SO:0001583	missense	23105					extracellular region	calcium ion binding	g.chr5:132535036G>T	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2280C>A	5.37:g.132535036G>T	ENSP00000265342:p.Asp760Glu					FSTL4_uc003kym.1_Missense_Mutation_p.D409E	p.D760E	NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		15	2498	-		all_cancers(142;0.244)	760					Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	37	c.2280C>A	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.474726	0.26511	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.52526	0.66	4.76	0.788	0.18601	WD40/YVTN repeat-like-containing domain (1);	0.360815	0.30859	N	0.008732	T	0.42471	0.1204	M	0.79011	2.435	0.32636	N	0.521348	B;P	0.43352	0.376;0.804	B;B	0.39840	0.108;0.311	T	0.54344	-0.8308	10	0.72032	D	0.01	-5.2742	4.0794	0.09919	0.3767:0.1789:0.4444:0.0	.	760;409	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	E	760;591	ENSP00000265342:D760E	ENSP00000265342:D760E	D	-	3	2	FSTL4	132562935	0.579000	0.26725	0.537000	0.28052	0.368000	0.29767	0.584000	0.23864	0.405000	0.25532	0.585000	0.79938	GAC		0.582	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
ARHGAP26	23092	broad.mit.edu	37	5	142281566	142281566	+	Missense_Mutation	SNP	G	G	A	rs148543665		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr5:142281566G>A	ENST00000274498.4	+	7	1042	c.664G>A	c.(664-666)Ggg>Agg	p.G222R	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.G222R	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	222					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.G222W(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAGGATTTCGGGGACTTCAA	0.448																																						uc011dbj.2																			1	Substitution - Missense(1)	p.G222W(2)	lung(1)	autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25						c.(664-666)Ggg>Agg		Homo sapiens Rho GTPase activating protein 26 (ARHGAP26), transcript variant 1, mRNA.		G	ARG/GLY,ARG/GLY	0,4406		0,0,2203	159.0	137.0	145.0		664,664	-1.9	0.1	5	dbSNP_134	145	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ARHGAP26	NM_001135608.1,NM_015071.4	125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	222/760,222/815	142281566	1,13005	2203	4300	6503	SO:0001583	missense	23092				actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding	g.chr5:142281566G>A	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"""Rho GTPase activating proteins"""	17073	protein-coding gene	gene with protein product	"""GTPase regulator associated with the focal adhesion kinase pp125"""	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.664G>A	5.37:g.142281566G>A	ENSP00000274498:p.Gly222Arg					ARHGAP26_uc003lmt.3_Missense_Mutation_p.G222R|ARHGAP26_uc003lmw.3_Missense_Mutation_p.G222R	p.G222R	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		6	699	+		all_hematologic(541;0.0416)	222					O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	c.664G>A	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702815	0.48307	0.0	1.16E-4	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.04083	3.71;3.71	5.79	-1.85	0.07784	.	0.376367	0.34603	N	0.003830	T	0.02267	0.0070	N	0.01576	-0.805	0.31060	N	0.714266	P;B	0.51147	0.942;0.001	P;B	0.48627	0.584;0.003	T	0.45190	-0.9278	10	0.16420	T	0.52	.	11.9348	0.52868	0.8099:0.0:0.1901:0.0	.	222;222	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	R	222	ENSP00000274498:G222R;ENSP00000367243:G222R	ENSP00000274498:G222R	G	+	1	0	ARHGAP26	142261750	1.000000	0.71417	0.112000	0.21494	0.989000	0.77384	1.999000	0.40806	-0.224000	0.09928	0.563000	0.77884	GGG		0.448	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	
SNX14	57231	broad.mit.edu	37	6	86253476	86253476	+	Nonsense_Mutation	SNP	C	C	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr6:86253476C>A	ENST00000314673.3	-	13	1287	c.1111G>T	c.(1111-1113)Gaa>Taa	p.E371*	SNX14_ENST00000346348.3_Nonsense_Mutation_p.E327*|SNX14_ENST00000369627.2_Nonsense_Mutation_p.E371*|SNX14_ENST00000513865.1_Nonsense_Mutation_p.E371*|SNX14_ENST00000505648.1_Nonsense_Mutation_p.E319*|SNX14_ENST00000508980.1_5'UTR	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	371	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TCATTAAATTCCTCTAACAAA	0.279																																						uc003pkr.3																			0				NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22						c.(1111-1113)Gaa>Taa		Homo sapiens sorting nexin 14 (SNX14), transcript variant 1, mRNA.							26.0	27.0	27.0					6																	86253476		2195	4278	6473	SO:0001587	stop_gained	57231				cell communication|protein transport	integral to membrane	phosphatidylinositol binding|signal transducer activity	g.chr6:86253476C>A	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"""Sorting nexins"""	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.1111G>T	6.37:g.86253476C>A	ENSP00000313121:p.Glu371*					SNX14_uc003pkp.3_Nonsense_Mutation_p.E234*|SNX14_uc003pkq.3_5'UTR|SNX14_uc011dzg.2_Nonsense_Mutation_p.E319*|SNX14_uc003pks.3_Nonsense_Mutation_p.E327*|SNX14_uc003pkt.3_Nonsense_Mutation_p.E371*	p.E371*	NM_153816	NP_722523	Q9Y5W7	SNX14_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0423)	12	1304	-		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)	371			RGS.		B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Nonsense_Mutation	SNP	ENST00000314673.3	37	c.1111G>T	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	C	41	9.027495	0.99040	.	.	ENSG00000135317	ENST00000346348;ENST00000314673;ENST00000513865;ENST00000505648;ENST00000369627;ENST00000515216	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-17.8318	15.5364	0.76007	0.0:0.8617:0.1383:0.0	.	.	.	.	X	327;371;371;319;371;298	.	ENSP00000313121:E371X	E	-	1	0	SNX14	86310195	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.492000	0.66893	2.602000	0.87976	0.467000	0.42956	GAA		0.279	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816	
EGFR	1956	broad.mit.edu	37	7	55221821	55221822	+	Missense_Mutation	DNP	GC	GC	AA	rs149840192		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr7:55221821_55221822GC>AA	ENST00000275493.2	+	7	1042_1043	c.865_866GC>AA	c.(865-867)GCc>AAc	p.A289N	EGFR_ENST00000442591.1_Missense_Mutation_p.A289N|EGFR_ENST00000344576.2_Missense_Mutation_p.A289N|EGFR_ENST00000420316.2_Missense_Mutation_p.A289N|EGFR_ENST00000455089.1_Missense_Mutation_p.A244N|EGFR_ENST00000454757.2_Missense_Mutation_p.A236N|EGFR_ENST00000342916.3_Missense_Mutation_p.A289N	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	289			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.A289V(20)|p.A289T(3)|p.A289D(3)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CAGCTTTGGTGCCACCTGCGTG	0.589		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.3		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""A, O, Mis"""	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	"""glioma, NSCLC"""		26	Substitution - Missense(26)	p.A289V(40)|p.A289T(6)|p.A289D(6)|p.V30_R297>G(5)	central_nervous_system(26)	NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110						c.(865-867)gcc>AAc		Homo sapiens epidermal growth factor receptor (EGFR), transcript variant 1, mRNA.	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)																																			SO:0001583	missense	1956	Lung Cancer, Familial Clustering of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55221821_55221822GC>AA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	Exception_encountered	7.37:g.55221821_55221822delinsAA	ENSP00000275493:p.Ala289Asn	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc003tqh.3_Missense_Mutation_p.A289N|EGFR_uc003tqi.3_Missense_Mutation_p.A289N|EGFR_uc003tqj.3_Missense_Mutation_p.A289N|EGFR_uc022adm.1_Missense_Mutation_p.A289N|EGFR_uc010kzg.2_Missense_Mutation_p.A244N|EGFR_uc022adn.1_Missense_Mutation_p.A244N|EGFR_uc011kco.2_Missense_Mutation_p.A236N|EGFR_uc011kcp.1_5'Flank|EGFR_uc011kcq.1_5'Flank	p.A289N	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		6	1111_1112	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		289					O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	DNP	ENST00000275493.2	37	c.865_866GC>AA	CCDS5514.1																																																																																				0.589	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
EGFR	1956	broad.mit.edu	37	7	55233037	55233037	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr7:55233037C>G	ENST00000275493.2	+	15	1964	c.1787C>G	c.(1786-1788)cCg>cGg	p.P596R	EGFR_ENST00000442591.1_Missense_Mutation_p.P596R|EGFR_ENST00000344576.2_Missense_Mutation_p.P596R|EGFR_ENST00000455089.1_Missense_Mutation_p.P551R|EGFR_ENST00000454757.2_Missense_Mutation_p.P543R|EGFR_ENST00000342916.3_Missense_Mutation_p.P596R	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	596					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.P596L(4)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AAGACCTGCCCGGCAGGAGTC	0.567		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.3		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""A, O, Mis"""	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	"""glioma, NSCLC"""		4	Substitution - Missense(4)	p.P596L(7)	large_intestine(2)|central_nervous_system(2)	NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110						c.(1786-1788)cCg>cGg		Homo sapiens epidermal growth factor receptor (EGFR), transcript variant 1, mRNA.	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						93.0	81.0	85.0					7																	55233037		2203	4300	6503	SO:0001583	missense	1956	Lung Cancer, Familial Clustering of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55233037C>G		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1787C>G	7.37:g.55233037C>G	ENSP00000275493:p.Pro596Arg	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc003tqi.3_Missense_Mutation_p.P596R|EGFR_uc003tqj.3_Missense_Mutation_p.P596R|EGFR_uc022adm.1_Missense_Mutation_p.P596R|EGFR_uc010kzg.2_Missense_Mutation_p.P551R|EGFR_uc022adn.1_Missense_Mutation_p.P551R|EGFR_uc011kco.2_Missense_Mutation_p.P543R|EGFR_uc011kcp.1_Intron|EGFR_uc011kcq.1_Non-coding_Transcript|EGFR_uc003tqn.3_Non-coding_Transcript	p.P596R	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		14	2033	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		596					O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	c.1787C>G	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.833608	0.91036	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	5.87	5.87	0.94306	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.84479	0.5481	M	0.84948	2.725	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.998;0.998;0.998	D	0.86044	0.1521	10	0.87932	D	0	.	18.7698	0.91887	0.0:1.0:0.0:0.0	.	551;596;596;596	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	R	551;596;466;596;596;596;543;390	ENSP00000415559:P551R;ENSP00000342376:P596R;ENSP00000345973:P596R;ENSP00000275493:P596R;ENSP00000410031:P596R;ENSP00000395243:P543R	ENSP00000275493:P596R	P	+	2	0	EGFR	55200531	1.000000	0.71417	0.967000	0.41034	0.752000	0.42762	7.738000	0.84966	2.785000	0.95823	0.655000	0.94253	CCG		0.567	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
PCLO	27445	broad.mit.edu	37	7	82784471	82784471	+	Missense_Mutation	SNP	A	A	G	rs199515717		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr7:82784471A>G	ENST00000333891.9	-	2	1823	c.1486T>C	c.(1486-1488)Tca>Cca	p.S496P	PCLO_ENST00000423517.2_Missense_Mutation_p.S496P	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.S496P(6)|p.?(3)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GGCTTTGCTGAGCCAGGCTGT	0.607																																						uc003uhx.2																			9	Substitution - Missense(6)|Unknown(3)	p.S496P(9)|p.?(3)	kidney(6)|prostate(3)	breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						c.(1486-1488)Tca>Cca		Homo sapiens piccolo (presynaptic cytomatrix protein) (PCLO), transcript variant 1, mRNA.		A	PRO/SER,PRO/SER	0,3888		0,0,1944	89.0	98.0	95.0		1486,1486	-0.1	0.0	7		95	1,8267		0,1,4133	no	missense,missense	PCLO	NM_014510.2,NM_033026.5	74,74	0,1,6077	GG,GA,AA		0.0121,0.0,0.0082	benign,benign	496/4936,496/5143	82784471	1,12155	1944	4134	6078	SO:0001583	missense	27445				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity	g.chr7:82784471A>G	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1486T>C	7.37:g.82784471A>G	ENSP00000334319:p.Ser496Pro					PCLO_uc003uhv.2_Missense_Mutation_p.S496P	p.S496P	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN			1	1775	-			442			10 X 10 AA tandem approximate repeats of P-A-K-P-Q-P-Q-Q-P-X.|Gln-rich.|Pro-rich.			Missense_Mutation	SNP	ENST00000333891.9	37	c.1486T>C	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	0.210	-1.037056	0.02013	0.0	1.21E-4	ENSG00000186472	ENST00000333891;ENST00000423517	T;T	0.15372	2.43;2.44	4.64	-0.0778	0.13717	.	.	.	.	.	T	0.04679	0.0127	N	0.00538	-1.39	0.22066	N	0.999381	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37009	-0.9724	9	0.87932	D	0	.	7.1447	0.25577	0.2775:0.116:0.6065:0.0	.	496;496	Q9Y6V0-5;Q9Y6V0-6	.;.	P	496	ENSP00000334319:S496P;ENSP00000388393:S496P	ENSP00000334319:S496P	S	-	1	0	PCLO	82622407	0.659000	0.27411	0.005000	0.12908	0.207000	0.24258	2.928000	0.48908	0.094000	0.17404	-0.379000	0.06801	TCA		0.607	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
BPGM	669	broad.mit.edu	37	7	134346723	134346723	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr7:134346723C>T	ENST00000393132.2	+	3	953	c.464C>T	c.(463-465)tCg>tTg	p.S155L	BPGM_ENST00000418040.1_Missense_Mutation_p.S155L|BPGM_ENST00000344924.3_Missense_Mutation_p.S155L	NM_199186.2	NP_954655.1	P07738	PMGE_HUMAN	2,3-bisphosphoglycerate mutase	155					carbohydrate metabolic process (GO:0005975)|erythrocyte development (GO:0048821)|glycolytic process (GO:0006096)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			breast(1)|endometrium(1)|lung(2)|stomach(1)	5						CTGCCACGGTCGGAAAGCTTA	0.473																																						uc003vrv.3																			0				breast(1)|endometrium(1)|lung(2)|stomach(1)	5						c.(463-465)tCg>tTg		Homo sapiens 2,3-bisphosphoglycerate mutase (BPGM), transcript variant 2, mRNA.							81.0	71.0	74.0					7																	134346723		2203	4300	6503	SO:0001583	missense	669				glycolysis|respiratory gaseous exchange		2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity|phosphoglycerate mutase activity	g.chr7:134346723C>T	BC017050	CCDS5833.1	7q33	2012-10-02			ENSG00000172331	ENSG00000172331	5.4.2.4		1093	protein-coding gene	gene with protein product		613896					Standard	NM_199186		Approved		uc003vrw.3	P07738	OTTHUMG00000155380	ENST00000393132.2:c.464C>T	7.37:g.134346723C>T	ENSP00000376840:p.Ser155Leu					BPGM_uc003vrw.3_Missense_Mutation_p.S155L	p.S155L	NM_199186	NP_954655	P07738	PMGE_HUMAN			2	1005	+			155					A4D1N9	Missense_Mutation	SNP	ENST00000393132.2	37	c.464C>T	CCDS5833.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.549768	0.27652	.	.	ENSG00000172331	ENST00000344924;ENST00000418040;ENST00000393132	T;T;T	0.72282	-0.64;-0.64;-0.64	6.02	4.2	0.49525	Histidine phosphatase superfamily, clade-1 (2);	0.306858	0.41396	D	0.000900	T	0.68677	0.3027	M	0.73962	2.25	0.09310	N	0.999992	D	0.54207	0.965	B	0.36766	0.232	T	0.65615	-0.6125	10	0.62326	D	0.03	-7.9073	16.9575	0.86263	0.0:0.7593:0.2407:0.0	.	155	P07738	PMGE_HUMAN	L	155	ENSP00000342032:S155L;ENSP00000399838:S155L;ENSP00000376840:S155L	ENSP00000342032:S155L	S	+	2	0	BPGM	133997263	0.049000	0.20398	0.301000	0.25044	0.183000	0.23260	3.261000	0.51530	0.862000	0.35528	-0.156000	0.13503	TCG		0.473	BPGM-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339763.1	NM_001724	
PRSS3P2	154754	broad.mit.edu	37	7	142482229	142482229	+	RNA	SNP	T	T	A			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr7:142482229T>A	ENST00000603901.1	+	0	609					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.P203P(1)									CTGGTGGCCCTGTGGTCTGCA	0.493																																						uc011ksq.2																			1	Substitution - coding silent(1)	p.P203P(1)	prostate(1)								c.(607-609)ccT>ccA		Homo sapiens protease, serine, 3 pseudogene (TRY6), non-coding RNA.																																						154754							g.chr7:142482229T>A			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482229T>A						TCRBV2S1_uc003vzp.2_Intron|TCRBV3S1_uc011ksh.2_Intron|TCRBV3S1_uc003vzw.2_Intron|TCRBV3S1_uc011ksi.2_Intron|TCRBV3S1_uc010loj.2_Intron|TCRBV3S1_uc003wag.2_Intron|BV6S4-BJ2S2_uc003wan.1_Intron	p.P203P							4	692	+									Silent	SNP	ENST00000603901.1	37	c.609T>A																																																																																					0.493	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296	
SLC34A3	142680	broad.mit.edu	37	9	140128961	140128961	+	Missense_Mutation	SNP	C	C	T	rs138798032		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chr9:140128961C>T	ENST00000538474.1	+	11	1411	c.1187C>T	c.(1186-1188)aCg>aTg	p.T396M	SLC34A3_ENST00000361134.2_Missense_Mutation_p.T396M	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	396					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		AGCGTCTTCACGGCGGCCGTC	0.721																																						uc022bqf.1																			0				kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						c.(1186-1188)aCg>aTg		Homo sapiens solute carrier family 34 (sodium phosphate), member 3 (SLC34A3), transcript variant 1, mRNA.		C	MET/THR,MET/THR,MET/THR	1,4255		0,1,2127	14.0	18.0	17.0		1187,1187,1187	3.5	0.8	9	dbSNP_134	17	1,8359		0,1,4179	yes	missense,missense,missense	SLC34A3	NM_001177316.1,NM_001177317.1,NM_080877.2	81,81,81	0,2,6306	TT,TC,CC		0.012,0.0235,0.0159	probably-damaging,probably-damaging,probably-damaging	396/600,396/600,396/600	140128961	2,12614	2128	4180	6308	SO:0001583	missense	142680				cellular phosphate ion homeostasis	apical plasma membrane|integral to membrane	sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity	g.chr9:140128961C>T	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"""Solute carriers"""	20305	protein-coding gene	gene with protein product		609826	"""solute carrier family 34 (sodium phosphate), member 3"""			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.1187C>T	9.37:g.140128961C>T	ENSP00000442397:p.Thr396Met					SLC34A3_uc011met.2_Missense_Mutation_p.T396M|SLC34A3_uc004cmf.1_Missense_Mutation_p.T396M	p.T396M	NM_001177316	NP_543153	Q8N130	NPT2C_HUMAN	STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)	10	1408	+	all_cancers(76;0.0926)		396					A2BFA1	Missense_Mutation	SNP	ENST00000538474.1	37	c.1187C>T	CCDS7038.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.416718	0.62511	2.35E-4	1.2E-4	ENSG00000198569	ENST00000538474;ENST00000361134	D;D	0.88509	-2.39;-2.39	3.51	3.51	0.40186	.	0.000000	0.53938	D	0.000052	D	0.83317	0.5228	L	0.48260	1.515	0.43824	D	0.996398	P	0.42973	0.796	B	0.35813	0.211	D	0.85389	0.1124	10	0.56958	D	0.05	-10.6698	12.8845	0.58036	0.0:1.0:0.0:0.0	.	396	Q8N130	NPT2C_HUMAN	M	396	ENSP00000442397:T396M;ENSP00000355353:T396M	ENSP00000355353:T396M	T	+	2	0	SLC34A3	139248782	0.998000	0.40836	0.769000	0.31535	0.802000	0.45316	4.273000	0.58914	1.948000	0.56530	0.448000	0.29417	ACG		0.721	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877	
DMD	1756	broad.mit.edu	37	X	32663088	32663088	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chrX:32663088G>C	ENST00000357033.4	-	10	1348	c.1142C>G	c.(1141-1143)aCt>aGt	p.T381S	DMD_ENST00000288447.4_Missense_Mutation_p.T373S|DMD_ENST00000378677.2_Missense_Mutation_p.T377S	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	381					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TACCTCATGAGTATGAAACTG	0.353																																						uc004dda.1																			0				NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77						c.(1141-1143)aCt>aGt		Homo sapiens dystrophin (DMD), transcript variant Dp427m, mRNA.							202.0	170.0	181.0					X																	32663088		2202	4300	6502	SO:0001583	missense	1756				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding	g.chrX:32663088G>C	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.1142C>G	X.37:g.32663088G>C	ENSP00000354923:p.Thr381Ser					DMD_uc004dcz.2_Missense_Mutation_p.T258S|DMD_uc004dcy.1_Missense_Mutation_p.T377S|DMD_uc004ddb.1_Missense_Mutation_p.T373S|DMD_uc010ngo.1_Intron|DMD_uc004ddf.3_Missense_Mutation_p.T373S|DMD_uc010ngp.1_Intron|DMD_uc010ngq.1_Intron|DMD_uc010ngr.1_Missense_Mutation_p.T92S	p.T381S	NM_004006	NP_004001	P11532	DMD_HUMAN			9	1386	-		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)	381					E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	c.1142C>G	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.401917	0.42613	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	T;T;T	0.50001	0.76;0.76;0.76	5.52	5.52	0.82312	.	0.191622	0.24256	U	0.040138	T	0.48660	0.1512	M	0.64170	1.965	0.80722	D	1	B;P;B;B;B	0.40000	0.394;0.698;0.144;0.016;0.174	B;B;B;B;B	0.41946	0.223;0.371;0.066;0.102;0.109	T	0.48456	-0.9034	10	0.41790	T	0.15	.	12.1871	0.54245	0.0802:0.0:0.9198:0.0	.	377;373;373;381;377	B1AK23;Q4G0X0;P11532-4;P11532;E9PDN5	.;.;.;DMD_HUMAN;.	S	373;377;381;381;258;373	ENSP00000367948:T377S;ENSP00000354923:T381S;ENSP00000288447:T373S	ENSP00000288447:T373S	T	-	2	0	DMD	32573009	1.000000	0.71417	1.000000	0.80357	0.370000	0.29829	7.844000	0.86867	2.458000	0.83093	0.600000	0.82982	ACT		0.353	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
PCDH11X	27328	broad.mit.edu	37	X	91132696	91132696	+	Missense_Mutation	SNP	C	C	T	rs62621113		TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chrX:91132696C>T	ENST00000373094.1	+	2	2302	c.1457C>T	c.(1456-1458)aCg>aTg	p.T486M	PCDH11X_ENST00000361655.2_Missense_Mutation_p.T486M|PCDH11X_ENST00000298274.8_Missense_Mutation_p.T486M|PCDH11X_ENST00000395337.2_Missense_Mutation_p.T486M|PCDH11X_ENST00000373097.1_Missense_Mutation_p.T486M|PCDH11X_ENST00000504220.2_Missense_Mutation_p.T486M|PCDH11X_ENST00000406881.1_Missense_Mutation_p.T486M|PCDH11X_ENST00000373088.1_Missense_Mutation_p.T486M|PCDH11X_ENST00000361724.1_Missense_Mutation_p.T486M	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	486	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						ATCCAGTTGACGAAAGTAAGT	0.438																																					NSCLC(38;925 1092 2571 38200 45895)	uc004efk.2																			0				NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						c.(1456-1458)aCg>aTg		Homo sapiens protocadherin 11 X-linked (PCDH11X), transcript variant c, mRNA.							99.0	82.0	88.0					X																	91132696		2203	4300	6503	SO:0001583	missense	27328				homophilic cell adhesion	integral to plasma membrane	calcium ion binding	g.chrX:91132696C>T	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.1457C>T	X.37:g.91132696C>T	ENSP00000362186:p.Thr486Met					PCDH11X_uc004efl.2_Missense_Mutation_p.T486M|PCDH11X_uc010nmv.2_Missense_Mutation_p.T486M|PCDH11X_uc004efm.2_Missense_Mutation_p.T486M|PCDH11X_uc004efn.2_Missense_Mutation_p.T486M|PCDH11X_uc004efo.2_Missense_Mutation_p.T486M|PCDH11X_uc004efh.2_Missense_Mutation_p.T486M|PCDH11X_uc004efj.1_Missense_Mutation_p.T486M	p.T486M	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN			1	2302	+			486			Cadherin 5.		A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	c.1457C>T	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	8.543	0.873758	0.17322	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71	5.38	5.38	0.77491	Cadherin (4);Cadherin-like (1);	0.049108	0.85682	D	0.000000	T	0.60379	0.2264	L	0.41906	1.305	0.51012	D	0.999908	D;D;D;D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.80764	0.975;0.967;0.99;0.99;0.99;0.994;0.958;0.958	T	0.57365	-0.7824	10	0.34782	T	0.22	.	17.0331	0.86466	0.0:1.0:0.0:0.0	rs62621113	486;486;486;486;486;486;486;486	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	M	486	ENSP00000378746:T486M;ENSP00000362186:T486M;ENSP00000362189:T486M;ENSP00000355040:T486M;ENSP00000362180:T486M;ENSP00000423762:T486M;ENSP00000355105:T486M;ENSP00000384758:T486M;ENSP00000298274:T486M	ENSP00000298274:T486M	T	+	2	0	PCDH11X	91019352	1.000000	0.71417	1.000000	0.80357	0.093000	0.18481	5.760000	0.68793	2.231000	0.72958	0.544000	0.68410	ACG		0.438	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
GPRASP2	114928	broad.mit.edu	37	X	101971308	101971308	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chrX:101971308A>G	ENST00000535209.1	+	4	2342	c.1511A>G	c.(1510-1512)cAt>cGt	p.H504R	GPRASP2_ENST00000332262.5_Missense_Mutation_p.H504R|GPRASP2_ENST00000543253.1_Missense_Mutation_p.H504R			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	504						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						GGTCTTTTTCATGGGGTTGGC	0.512																																						uc022cbh.1																			0											c.(1510-1512)cAt>cGt		Homo sapiens ARMCX5-GPRASP2 readthrough (ARMCX5-GPRASP2), mRNA.							78.0	72.0	74.0					X																	101971308		2203	4300	6503	SO:0001583	missense	114928					cytoplasm	protein binding	g.chrX:101971308A>G	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.1511A>G	X.37:g.101971308A>G	ENSP00000437394:p.His504Arg					ARMCX5-GPRASP2_uc022cay.1_Missense_Mutation_p.H504R|ARMCX5-GPRASP2_uc022cbe.1_Missense_Mutation_p.H504R|ARMCX5-GPRASP2_uc004ejl.3_Missense_Mutation_p.H504R|ARMCX5-GPRASP2_uc022cbf.1_Missense_Mutation_p.H504R|ARMCX5-GPRASP2_uc022cbg.1_Missense_Mutation_p.H504R|ARMCX5-GPRASP2_uc004ejm.3_Missense_Mutation_p.H504R|ARMCX5-GPRASP2_uc004ejk.3_Missense_Mutation_p.H504R	p.H504R	NM_001199818	NP_001186747	Q96D09	GASP2_HUMAN			0	1511	+			504					D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	c.1511A>G	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.440239	0.01098	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.06294	3.32;3.32;3.32	4.44	-0.588	0.11687	.	0.431614	0.19977	N	0.101846	T	0.04998	0.0134	L	0.54323	1.7	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44205	-0.9343	10	0.14252	T	0.57	.	3.8201	0.08832	0.4811:0.1942:0.3247:0.0	.	504	Q96D09	GASP2_HUMAN	R	504	ENSP00000437872:H504R;ENSP00000437394:H504R;ENSP00000339057:H504R	ENSP00000339057:H504R	H	+	2	0	GPRASP2	101857964	0.985000	0.35326	0.001000	0.08648	0.006000	0.05464	0.816000	0.27267	-0.211000	0.10124	-0.377000	0.06932	CAT		0.512	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
PCDH11Y	83259	broad.mit.edu	37	Y	4968500	4968500	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0750-01A-01W-0348-08	TCGA-06-0750-10A-01W-0348-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc15ced3-5ed1-4f88-8789-09ec713bd613	26786497-ed7d-4242-93b7-6f0793c2c384	g.chrY:4968500A>G	ENST00000333703.4	+	5	3361	c.2848A>G	c.(2848-2850)Aag>Gag	p.K950E	PCDH11Y_ENST00000215473.6_Missense_Mutation_p.K961E|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.K961E	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	961					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TACTACTTTCAAGCCTGACAG	0.458																																						uc004fqo.3																			0				autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						c.(2881-2883)Aag>Gag		Homo sapiens protocadherin 11 Y-linked (PCDH11Y), transcript variant c, mRNA.																																				SO:0001583	missense	83259				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chrY:4968500A>G	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"""Cadherins / Protocadherins : Non-clustered"""	15813	protein-coding gene	gene with protein product		400022	"""protocadherin 22"""	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.2848A>G	Y.37:g.4968500A>G	ENSP00000330552:p.Lys950Glu					PCDH11Y_uc010nwg.1_Missense_Mutation_p.K950E|PCDH11Y_uc004fql.1_Missense_Mutation_p.K950E|PCDH11Y_uc004fqm.1_Missense_Mutation_p.K950E|PCDH11Y_uc004fqn.1_Missense_Mutation_p.K961E|PCDH11Y_uc004fqp.1_Missense_Mutation_p.K732E	p.K961E	NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN			1	3615	+			961					Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	37	c.2881A>G	CCDS14776.1																																																																																				0.458	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973	
