#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
CPSF3L	54973	broad.mit.edu	37	1	1249704	1249704	+	Silent	SNP	G	G	C			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr1:1249704G>C	ENST00000435064.1	-	8	826	c.744C>G	c.(742-744)ctC>ctG	p.L248L	CPSF3L_ENST00000421495.2_5'UTR|CPSF3L_ENST00000411962.1_Silent_p.L150L|CPSF3L_ENST00000450926.2_Silent_p.L226L|CPSF3L_ENST00000462432.1_5'UTR|CPSF3L_ENST00000545578.1_Silent_p.L219L|CPSF3L_ENST00000540437.1_Silent_p.L254L|CPSF3L_ENST00000419704.1_Silent_p.L147L	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	248					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	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;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GGAGGATGCAGAGCTCCTGGG	0.667																																						uc001aee.1																			0					0						c.(742-744)CTC>CTG		cleavage and polyadenylation specific factor							18.0	21.0	20.0					1																	1249704		2190	4284	6474	SO:0001819	synonymous_variant	54973					Golgi apparatus|nucleus	hydrolase activity	g.chr1:1249704G>C	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"""integrator complex subunit 11"""	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.744C>G	1.37:g.1249704G>C						CPSF3L_uc009vjy.1_RNA|CPSF3L_uc001aef.1_Silent_p.L254L|CPSF3L_uc009vjz.1_Silent_p.L226L|CPSF3L_uc010nyj.1_Silent_p.L219L|CPSF3L_uc001aeg.1_Silent_p.L124L|CPSF3L_uc001aeh.1_Silent_p.L147L|CPSF3L_uc001aei.1_Silent_p.L150L|CPSF3L_uc001aej.1_Silent_p.L75L|CPSF3L_uc001aek.1_5'UTR	p.L248L	NM_017871	NP_060341	Q5TA45	INT11_HUMAN		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)	8	802	-	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)	248					A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Silent	SNP	ENST00000435064.1	37	c.744C>G	CCDS21.1																																																																																				0.667	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871	
THEM5	284486	broad.mit.edu	37	1	151820732	151820732	+	Silent	SNP	G	G	A	rs372391484		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr1:151820732G>A	ENST00000368817.5	-	4	632	c.501C>T	c.(499-501)gaC>gaT	p.D167D	AL450992.2_ENST00000434182.1_RNA	NM_182578.3	NP_872384	Q8N1Q8	ACO15_HUMAN	thioesterase superfamily member 5	167					cardiolipin acyl-chain remodeling (GO:0035965)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)	mitochondrial matrix (GO:0005759)	palmitoyl-CoA hydrolase activity (GO:0016290)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AAAAGGTCTCGTCCATCATGG	0.587																																						uc009wnd.2																			0				ovary(1)|skin(1)	2						c.(499-501)GAC>GAT		thioesterase superfamily member 5		G		0,4406		0,0,2203	68.0	68.0	68.0		501	-5.0	0.8	1		68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	THEM5	NM_182578.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		167/248	151820732	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	284486						hydrolase activity	g.chr1:151820732G>A	AK095283	CCDS1005.1	1q21.3	2008-02-05			ENSG00000196407	ENSG00000196407			26755	protein-coding gene	gene with protein product		615653					Standard	NM_182578		Approved	FLJ37964	uc021oyw.1	Q8N1Q8	OTTHUMG00000013070	ENST00000368817.5:c.501C>T	1.37:g.151820732G>A							p.D167D	NM_182578	NP_872384	Q8N1Q8	THEM5_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.181)		4	633	-	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		167					Q5T1C3	Silent	SNP	ENST00000368817.5	37	c.501C>T	CCDS1005.1	.	.	.	.	.	.	.	.	.	.	G	8.625	0.892271	0.17613	0.0	1.16E-4	ENSG00000196407	ENST00000453881	.	.	.	5.42	-4.98	0.03019	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52830	-0.8523	4	.	.	.	-22.1731	12.2909	0.54817	0.5155:0.0:0.4845:0.0	.	.	.	.	M	114	.	.	T	-	2	0	THEM5	150087356	0.045000	0.20229	0.839000	0.33178	0.925000	0.55904	-1.741000	0.01837	-1.343000	0.02219	-1.578000	0.00866	ACG		0.587	THEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036678.2	NM_182578	
MUC2	4583	broad.mit.edu	37	11	1096432	1096432	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr11:1096432G>A	ENST00000441003.2	+	34	6484	c.6457G>A	c.(6457-6459)Gtg>Atg	p.V2153M	MUC2_ENST00000361558.6_Missense_Mutation_p.V291M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4515					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAGCCCCTCCGTGGACAACTT	0.607																																						uc001lsx.1																			0				lung(1)|breast(1)	2						c.(13543-13545)GTG>ATG		mucin 2 precursor	Pranlukast(DB01411)						100.0	112.0	108.0					11																	1096432		2163	4254	6417	SO:0001583	missense	4583					inner mucus layer|outer mucus layer	protein binding	g.chr11:1096432G>A	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6457G>A	11.37:g.1096432G>A	ENSP00000415183:p.Val2153Met						p.V4515M	NM_002457	NP_002448	Q02817	MUC2_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	37	13570	+		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)	4515			VWFD 4.		Q14878	Missense_Mutation	SNP	ENST00000441003.2	37	c.13543G>A		.	.	.	.	.	.	.	.	.	.	g	8.919	0.960501	0.18583	.	.	ENSG00000198788	ENST00000441003;ENST00000361558	T;T	0.59083	0.29;0.29	3.95	-0.68	0.11346	.	.	.	.	.	T	0.42245	0.1194	L	0.52364	1.645	0.09310	N	1	P	0.38767	0.646	B	0.32465	0.146	T	0.26155	-1.0111	9	0.44086	T	0.13	.	4.5767	0.12238	0.23:0.0:0.5111:0.2588	.	2153	E7EUV1	.	M	2153;291	ENSP00000415183:V2153M;ENSP00000354885:V291M	ENSP00000354885:V291M	V	+	1	0	MUC2	1086432	0.001000	0.12720	0.001000	0.08648	0.109000	0.19521	0.059000	0.14322	0.003000	0.14656	0.479000	0.44913	GTG		0.607	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PTPRJ	5795	broad.mit.edu	37	11	48145364	48145364	+	Silent	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr11:48145364G>A	ENST00000418331.2	+	5	1168	c.816G>A	c.(814-816)ccG>ccA	p.P272P	PTPRJ_ENST00000440289.2_Silent_p.P272P	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	272	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ACATCAACCCGTATCTTCTAC	0.473																																						uc001ngp.3																			0				breast(3)|kidney(3)|ovary(1)|skin(1)	8						c.(814-816)CCG>CCA		protein tyrosine phosphatase, receptor type, J							74.0	70.0	71.0					11																	48145364		2201	4298	6499	SO:0001819	synonymous_variant	5795				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity	g.chr11:48145364G>A	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.816G>A	11.37:g.48145364G>A						PTPRJ_uc001ngo.3_Silent_p.P272P	p.P272P	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN			5	1171	+			272			Extracellular (Potential).|Fibronectin type-III 2.|Fibronectin type-III 3.		Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	c.816G>A	CCDS7945.1																																																																																				0.473	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
SPDYC	387778	broad.mit.edu	37	11	64939756	64939756	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr11:64939756C>A	ENST00000377185.2	+	4	380	c.298C>A	c.(298-300)Cac>Aac	p.H100N	AP003068.18_ENST00000534819.1_RNA	NM_001008778.1	NP_001008778.1			speedy/RINGO cell cycle regulator family member C											breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)	16						CCAGCGCGCCCACCTGAAGCT	0.597																																						uc010rnz.1																			0					0						c.(298-300)CAC>AAC		speedy C							87.0	81.0	83.0					11																	64939756		2201	4297	6498	SO:0001583	missense	387778				cell cycle	nucleus	protein kinase binding	g.chr11:64939756C>A	AY820305	CCDS31606.1	11q13.1	2013-05-08	2013-05-08		ENSG00000204710	ENSG00000204710		"""Speedy homologs"""	32681	protein-coding gene	gene with protein product		614030	"""speedy homolog C (Xenopus laevis)"""			15611625	Standard	NM_001008778		Approved	Ringo2	uc010rnz.2	Q5MJ68	OTTHUMG00000165611	ENST00000377185.2:c.298C>A	11.37:g.64939756C>A	ENSP00000366390:p.His100Asn						p.H100N	NM_001008778	NP_001008778	Q5MJ68	SPDYC_HUMAN			4	298	+			100			Speedy/Ringo box; Required for CDK- binding (By similarity).			Missense_Mutation	SNP	ENST00000377185.2	37	c.298C>A	CCDS31606.1	.	.	.	.	.	.	.	.	.	.	C	2.844	-0.239789	0.05944	.	.	ENSG00000204710	ENST00000377185	.	.	.	4.66	-8.74	0.00838	.	1.156870	0.06768	N	0.782938	T	0.09818	0.0241	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34576	-0.9823	9	0.08381	T	0.77	.	8.8517	0.35203	0.1632:0.6385:0.1983:0.0	.	100	Q5MJ68	SPDYC_HUMAN	N	100	.	ENSP00000366390:H100N	H	+	1	0	SPDYC	64696332	0.004000	0.15560	0.002000	0.10522	0.825000	0.46686	-0.156000	0.10100	-1.605000	0.01593	-0.181000	0.13052	CAC		0.597	SPDYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385299.1	NM_001008778	
INTS4	92105	broad.mit.edu	37	11	77632412	77632412	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr11:77632412G>C	ENST00000534064.1	-	14	1772	c.1738C>G	c.(1738-1740)Ctt>Gtt	p.L580V	INTS4_ENST00000525931.1_5'Flank	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	580					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			AGATGAGAAAGACTGTCTCGG	0.403																																						uc001oys.2																			0				ovary(2)	2						c.(1738-1740)CTT>GTT		integrator complex subunit 4							111.0	97.0	102.0					11																	77632412		2200	4292	6492	SO:0001583	missense	92105				snRNA processing	integrator complex	protein binding	g.chr11:77632412G>C	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1738C>G	11.37:g.77632412G>C	ENSP00000434466:p.Leu580Val					INTS4_uc001oyt.2_RNA	p.L580V	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)		14	1766	-	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		580					Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	c.1738C>G	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.998698	0.54147	.	.	ENSG00000149262	ENST00000534064;ENST00000354849	T	0.70045	-0.45	4.61	4.61	0.57282	.	0.000000	0.64402	D	0.000001	T	0.78387	0.4275	L	0.54323	1.7	0.80722	D	1	D	0.63880	0.993	D	0.70016	0.967	T	0.80448	-0.1378	10	0.62326	D	0.03	-7.9805	17.6231	0.88087	0.0:0.0:1.0:0.0	.	580	Q96HW7	INT4_HUMAN	V	580;431	ENSP00000434466:L580V	ENSP00000346913:L431V	L	-	1	0	INTS4	77310060	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.018000	0.76406	2.379000	0.81126	0.585000	0.79938	CTT		0.403	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
PARP4	143	broad.mit.edu	37	13	25009059	25009059	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr13:25009059C>T	ENST00000381989.3	-	31	4325	c.4220G>A	c.(4219-4221)aGc>aAc	p.S1407N		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1407					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTGTGCAGAGCTTAATGAGCT	0.542																																						uc001upl.2																			0				ovary(3)|skin(1)	4						c.(4219-4221)AGC>AAC		poly (ADP-ribose) polymerase family, member 4							41.0	43.0	43.0					13																	25009059		2203	4300	6503	SO:0001583	missense	143				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity	g.chr13:25009059C>T	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.4220G>A	13.37:g.25009059C>T	ENSP00000371419:p.Ser1407Asn						p.S1407N	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)	31	4326	-		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)	1407					O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	c.4220G>A	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	c	0.562	-0.844990	0.02671	.	.	ENSG00000102699	ENST00000381989	T	0.01804	4.63	2.32	-3.34	0.04943	.	3.133270	0.01912	U	0.039934	T	0.01320	0.0043	N	0.19112	0.55	0.09310	N	1	B	0.15473	0.013	B	0.13407	0.009	T	0.46428	-0.9192	10	0.20046	T	0.44	5.0715	1.9372	0.03339	0.1794:0.2682:0.4138:0.1386	.	1407	Q9UKK3	PARP4_HUMAN	N	1407	ENSP00000371419:S1407N	ENSP00000371419:S1407N	S	-	2	0	PARP4	23907059	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.691000	0.05133	-1.201000	0.02659	-0.823000	0.03104	AGC		0.542	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
GABRB3	2562	broad.mit.edu	37	15	26792999	26792999	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr15:26792999C>T	ENST00000311550.5	-	9	1474	c.1363G>A	c.(1363-1365)Gtg>Atg	p.V455M	GABRB3_ENST00000545868.1_Missense_Mutation_p.V370M|GABRB3_ENST00000400188.3_Missense_Mutation_p.V384M|GABRB3_ENST00000299267.4_Missense_Mutation_p.V455M|GABRB3_ENST00000541819.2_Missense_Mutation_p.V511M	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	455					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|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)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.V455L(2)|p.V511L(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|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)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATGGAAACACGATCCTGGAC	0.398																																						uc001zaz.2																			3	Substitution - Missense(3)		lung(3)	upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5						c.(1363-1365)GTG>ATG		gamma-aminobutyric acid (GABA) A receptor, beta	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)						124.0	103.0	110.0					15																	26792999		2203	4300	6503	SO:0001583	missense	2562				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	g.chr15:26792999C>T		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1363G>A	15.37:g.26792999C>T	ENSP00000308725:p.Val455Met					GABRB3_uc010uae.1_Missense_Mutation_p.V370M|GABRB3_uc001zba.2_Missense_Mutation_p.V455M|GABRB3_uc001zbb.2_Missense_Mutation_p.V511M	p.V455M	NM_000814	NP_000805	P28472	GBRB3_HUMAN		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	9	1505	-		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)	455			Helical; (Probable).		B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	c.1363G>A	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.581253	0.46006	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93	6.03	6.03	0.97812	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.049791	0.85682	D	0.000000	T	0.82181	0.4981	L	0.40543	1.245	0.58432	D	0.999999	P;P;P	0.45672	0.864;0.584;0.497	B;B;B	0.40375	0.294;0.22;0.327	T	0.83129	-0.0114	10	0.52906	T	0.07	.	19.545	0.95291	0.0:1.0:0.0:0.0	.	511;455;455	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	M	455;511;455;384;370	ENSP00000308725:V455M;ENSP00000442408:V511M;ENSP00000299267:V455M;ENSP00000383049:V384M;ENSP00000439169:V370M	ENSP00000299267:V455M	V	-	1	0	GABRB3	24344092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.438000	0.59961	2.861000	0.98227	0.655000	0.94253	GTG		0.398	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
UNC13C	440279	broad.mit.edu	37	15	54305644	54305644	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr15:54305644C>T	ENST00000260323.11	+	1	544	c.544C>T	c.(544-546)Cga>Tga	p.R182*	UNC13C_ENST00000537900.1_Nonsense_Mutation_p.R182*|UNC13C_ENST00000545554.1_Nonsense_Mutation_p.R182*	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	182					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GGGAGCTTTACGAAAACTGAG	0.458																																						uc002ack.2																			0				ovary(5)|pancreas(2)	7						c.(544-546)CGA>TGA		unc-13 homolog C							108.0	106.0	107.0					15																	54305644		1912	4110	6022	SO:0001587	stop_gained	440279				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding	g.chr15:54305644C>T	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.544C>T	15.37:g.54305644C>T	ENSP00000260323:p.Arg182*						p.R182*	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN		GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)	1	544	+			182					Q0P613|Q8ND48|Q96NP3	Nonsense_Mutation	SNP	ENST00000260323.11	37	c.544C>T	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	37	6.175219	0.97348	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	.	.	.	4.98	1.86	0.25419	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.984	0.58581	0.4508:0.5492:0.0:0.0	.	.	.	.	X	182	.	ENSP00000260323:R182X	R	+	1	2	UNC13C	52092936	0.959000	0.32827	0.984000	0.44739	0.834000	0.47266	1.468000	0.35332	0.074000	0.16767	-0.274000	0.10170	CGA		0.458	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
IRF8	3394	broad.mit.edu	37	16	85952286	85952286	+	Missense_Mutation	SNP	G	G	A	rs202107230		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr16:85952286G>A	ENST00000268638.5	+	7	1287	c.865G>A	c.(865-867)Gtc>Atc	p.V289I	IRF8_ENST00000562492.1_Missense_Mutation_p.V85I	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	289					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				GGGCGTGTTCGTCAAGCGGCT	0.677																																						uc002fjh.2																			0				breast(2)|ovary(1)	3						c.(865-867)GTC>ATC		interferon regulatory factor 8							21.0	24.0	23.0					16																	85952286		2198	4297	6495	SO:0001583	missense	3394				interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity	g.chr16:85952286G>A	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.865G>A	16.37:g.85952286G>A	ENSP00000268638:p.Val289Ile					IRF8_uc010chp.2_Intron	p.V289I	NM_002163	NP_002154	Q02556	IRF8_HUMAN			7	922	+		Prostate(104;0.0771)	289					A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	c.865G>A	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	G	9.246	1.039493	0.19669	.	.	ENSG00000140968	ENST00000268638	D	0.93953	-3.32	5.1	2.74	0.32292	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.147655	0.64402	D	0.000016	T	0.80138	0.4568	N	0.05012	-0.13	0.35246	D	0.778226	B	0.11235	0.004	B	0.14023	0.01	T	0.72007	-0.4420	10	0.14252	T	0.57	-34.1676	4.3065	0.10949	0.4742:0.0:0.5258:0.0	.	289	Q02556	IRF8_HUMAN	I	289	ENSP00000268638:V289I	ENSP00000268638:V289I	V	+	1	0	IRF8	84509787	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.857000	0.69525	1.289000	0.44618	-0.142000	0.14014	GTC		0.677	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
MYH2	4620	broad.mit.edu	37	17	10429979	10429979	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr17:10429979G>C	ENST00000245503.5	-	30	4508	c.4124C>G	c.(4123-4125)gCc>gGc	p.A1375G	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.A1375G|MYH2_ENST00000532183.2_Intron|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1375					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CCTCCATTGGGCAACCTCGGT	0.567																																						uc010coi.2																			0				ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						c.(4123-4125)GCC>GGC		myosin heavy chain IIa							197.0	180.0	186.0					17																	10429979		2203	4300	6503	SO:0001583	missense	4620				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle	g.chr17:10429979G>C		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.4124C>G	17.37:g.10429979G>C	ENSP00000245503:p.Ala1375Gly					uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.A1375G|MYH2_uc010coj.2_Intron	p.A1375G	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN			30	4252	-			1375			Potential.		A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	c.4124C>G	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	G	33	5.202502	0.94997	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.79749	-1.3;-1.3	5.2	5.2	0.72013	Myosin tail (1);	0.000000	0.39020	U	0.001488	D	0.89570	0.6753	M	0.86740	2.835	0.80722	D	1	P	0.39071	0.658	P	0.52031	0.688	D	0.90284	0.4317	10	0.62326	D	0.03	.	18.9148	0.92501	0.0:0.0:1.0:0.0	.	1375	Q9UKX2	MYH2_HUMAN	G	1375	ENSP00000245503:A1375G;ENSP00000380367:A1375G	ENSP00000245503:A1375G	A	-	2	0	MYH2	10370704	1.000000	0.71417	0.998000	0.56505	0.883000	0.51084	9.657000	0.98554	2.703000	0.92315	0.655000	0.94253	GCC		0.567	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
NPTX1	4884	broad.mit.edu	37	17	78447110	78447110	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr17:78447110C>T	ENST00000306773.4	-	3	944	c.787G>A	c.(787-789)Gcc>Acc	p.A263T	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	263	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CCTGGCGTGGCGCTGGACTTG	0.587																																						uc002jyp.1																			0					0						c.(787-789)GCC>ACC		neuronal pentraxin I precursor							201.0	173.0	183.0					17																	78447110		2203	4300	6503	SO:0001583	missense	4884				central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding	g.chr17:78447110C>T	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.787G>A	17.37:g.78447110C>T	ENSP00000307549:p.Ala263Thr						p.A263T	NM_002522	NP_002513	Q15818	NPTX1_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)		3	945	-	all_neural(118;0.0538)		263			Pentaxin.		B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	37	c.787G>A	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.046740	0.55110	.	.	ENSG00000171246	ENST00000306773;ENST00000535681	T	0.06449	3.3	4.27	3.3	0.37823	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.06962	0.0177	L	0.48986	1.54	0.80722	D	1	P	0.49447	0.924	B	0.41374	0.355	T	0.44847	-0.9301	10	0.17369	T	0.5	-21.6173	11.8502	0.52407	0.0:0.9132:0.0:0.0868	.	263	Q15818	NPTX1_HUMAN	T	263;25	ENSP00000307549:A263T	ENSP00000307549:A263T	A	-	1	0	NPTX1	76061705	1.000000	0.71417	0.671000	0.29857	0.545000	0.35147	5.703000	0.68340	1.001000	0.39076	0.511000	0.50034	GCC		0.587	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1		
APC2	10297	broad.mit.edu	37	19	1465389	1465389	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr19:1465389C>T	ENST00000535453.1	+	14	3802	c.2089C>T	c.(2089-2091)Cat>Tat	p.H697Y	C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_Missense_Mutation_p.H697Y|APC2_ENST00000238483.4_Missense_Mutation_p.H423Y|CTB-25B13.12_ENST00000588225.1_RNA			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGCTGGCCCATCGGCCCGC	0.716																																						uc002lsr.1																			0				breast(3)|pancreas(1)	4						c.(2089-2091)CAT>TAT		adenomatosis polyposis coli 2							8.0	8.0	8.0					19																	1465389		2145	4215	6360	SO:0001583	missense	10297				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|Wnt receptor signaling pathway	actin filament|catenin complex|cytoplasmic microtubule|Golgi membrane|lamellipodium membrane|perinuclear region of cytoplasm	beta-catenin binding|microtubule binding	g.chr19:1465389C>T		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.2089C>T	19.37:g.1465389C>T	ENSP00000442954:p.His697Tyr					APC2_uc002lss.1_Missense_Mutation_p.H279Y|APC2_uc002lst.1_Missense_Mutation_p.H697Y|APC2_uc002lsu.1_Missense_Mutation_p.H696Y|C19orf25_uc010xgn.1_Intron	p.H697Y	NM_005883	NP_005874	O95996	APC2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	15	2297	+		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)	697					C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000535453.1	37	c.2089C>T	CCDS12068.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.813479	0.50527	.	.	ENSG00000115266	ENST00000233607;ENST00000238483;ENST00000535453	T;T;T	0.65732	-0.17;0.78;-0.17	4.65	4.65	0.58169	Armadillo-like helical (1);Armadillo-type fold (1);	0.053747	0.64402	D	0.000001	T	0.61388	0.2343	L	0.27053	0.805	0.80722	D	1	D;D	0.62365	0.991;0.985	P;P	0.56088	0.791;0.622	T	0.65393	-0.6179	10	0.72032	D	0.01	-31.4827	12.1958	0.54296	0.1713:0.8286:0.0:0.0	.	696;697	O95996-3;O95996	.;APC2_HUMAN	Y	697;423;697	ENSP00000233607:H697Y;ENSP00000238483:H423Y;ENSP00000442954:H697Y	ENSP00000233607:H697Y	H	+	1	0	APC2	1416389	0.981000	0.34729	0.994000	0.49952	0.540000	0.34992	2.596000	0.46205	2.405000	0.81733	0.462000	0.41574	CAT		0.716	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	
PLIN4	729359	broad.mit.edu	37	19	4512541	4512541	+	Silent	SNP	C	C	T	rs139885054	byFrequency	TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr19:4512541C>T	ENST00000301286.3	-	3	1388	c.1389G>A	c.(1387-1389)gcG>gcA	p.A463A		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	463	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGGCCACATTCGCAGCACCGG	0.577													C|||	13	0.00259585	0.0	0.0	5008	,	,		22486	0.0129		0.0	False		,,,				2504	0.0					uc002mar.1																			0					0						c.(1387-1389)GCG>GCA		plasma membrane associated protein, S3-12							117.0	124.0	122.0					19																	4512541		1974	4163	6137	SO:0001819	synonymous_variant	729359					lipid particle|plasma membrane		g.chr19:4512541C>T	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1389G>A	19.37:g.4512541C>T						PLIN4_uc010dub.1_5'Flank	p.A463A	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN			3	1389	-			463			27 X 33 AA approximate tandem repeat.|12.		A6NEI2	Silent	SNP	ENST00000301286.3	37	c.1389G>A	CCDS45927.1																																																																																				0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CD209	30835	broad.mit.edu	37	19	7810925	7810925	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr19:7810925G>A	ENST00000315599.7	-	4	249	c.227C>T	c.(226-228)gCg>gTg	p.A76V	CD209_ENST00000394161.5_Intron|CD209_ENST00000601951.1_Missense_Mutation_p.A52V|CD209_ENST00000601256.1_Missense_Mutation_p.A52V|CD209_ENST00000204801.8_Missense_Mutation_p.A32V|CD209_ENST00000593821.1_Missense_Mutation_p.A32V|CD209_ENST00000593660.1_Missense_Mutation_p.A52V|CD209_ENST00000394173.4_Missense_Mutation_p.A76V|CD209_ENST00000301357.8_Missense_Mutation_p.A32V|CD209_ENST00000354397.6_Missense_Mutation_p.A76V|CD209_ENST00000602261.1_Missense_Mutation_p.A76V|CD209_ENST00000315591.8_Missense_Mutation_p.A52V	NM_001144895.1|NM_001144897.1|NM_021155.3	NP_001138367.1|NP_001138369.1|NP_066978.1	Q9NNX6	CD209_HUMAN	CD209 molecule	76					antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|heterophilic cell-cell adhesion (GO:0007157)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of T cell proliferation (GO:0042129)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|virion binding (GO:0046790)			endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CTGGTAGATCGCGTCTTGCCT	0.507																																						uc002mht.2																			0				skin(1)	1						c.(226-228)GCG>GTG		CD209 molecule isoform 1							174.0	172.0	173.0					19																	7810925		2203	4300	6503	SO:0001583	missense	30835				cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding	g.chr19:7810925G>A	M98457	CCDS12186.1, CCDS45949.1, CCDS45950.1, CCDS45951.1, CCDS45952.1, CCDS59344.1, CCDS59345.1	19p13	2011-08-30	2006-03-28			ENSG00000090659		"""C-type lectin domain containing"", ""CD molecules"""	1641	protein-coding gene	gene with protein product		604672	"""CD209 antigen"""			1518869	Standard	NM_021155		Approved	DC-SIGN, CDSIGN, DC-SIGN1, CLEC4L	uc002mht.2	Q9NNX6		ENST00000315599.7:c.227C>T	19.37:g.7810925G>A	ENSP00000315477:p.Ala76Val					CD209_uc010xju.1_Missense_Mutation_p.A76V|CD209_uc010dvp.2_Missense_Mutation_p.A52V|CD209_uc002mhr.2_Missense_Mutation_p.A52V|CD209_uc002mhs.2_Missense_Mutation_p.A52V|CD209_uc002mhu.2_Missense_Mutation_p.A76V|CD209_uc010dvq.2_Missense_Mutation_p.A76V|CD209_uc002mhq.2_Missense_Mutation_p.A76V|CD209_uc002mhv.2_Missense_Mutation_p.A52V|CD209_uc002mhx.2_Missense_Mutation_p.A32V|CD209_uc002mhw.2_Missense_Mutation_p.A32V|CD209_uc010dvr.2_Intron	p.A76V	NM_021155	NP_066978	Q9NNX6	CD209_HUMAN			4	294	-			76			Extracellular (Probable).		A8KAM4|A8MVQ9|G5E9C4|Q2TB19|Q96QP7|Q96QP8|Q96QP9|Q96QQ0|Q96QQ1|Q96QQ2|Q96QQ3|Q96QQ4|Q96QQ5|Q96QQ6|Q96QQ7|Q96QQ8	Missense_Mutation	SNP	ENST00000315599.7	37	c.227C>T	CCDS12186.1	.	.	.	.	.	.	.	.	.	.	g	0.297	-0.976144	0.02215	.	.	ENSG00000090659	ENST00000315599;ENST00000354397;ENST00000315591;ENST00000204801;ENST00000394173;ENST00000301357;ENST00000540789	T;T;T;T;T;T	0.16897	4.08;4.46;4.11;4.1;2.31;4.12	0.734	-1.47	0.08772	.	.	.	.	.	T	0.18087	0.0434	N	0.22421	0.69	0.80722	D	1	B;B;B;D;B;B;B;B;B;B;B	0.63046	0.007;0.021;0.014;0.992;0.301;0.027;0.006;0.007;0.011;0.086;0.026	B;B;B;D;B;B;B;B;B;B;B	0.66716	0.002;0.013;0.008;0.946;0.146;0.008;0.008;0.002;0.008;0.011;0.009	T	0.32455	-0.9906	8	0.30078	T	0.28	.	.	.	.	.	76;76;52;32;32;52;76;76;52;52;76	B2R907;Q9NNX6-2;Q9NNX6-12;Q9NNX6-7;Q9NNX6-8;Q9NNX6-6;G5E9C4;Q9NNX6;Q9NNX6-11;Q9NNX6-10;Q9NNX6-5	.;.;.;.;.;.;.;CD209_HUMAN;.;.;.	V	76;76;52;32;76;32;60	ENSP00000315477:A76V;ENSP00000346373:A76V;ENSP00000315407:A52V;ENSP00000204801:A32V;ENSP00000377728:A76V;ENSP00000301357:A32V	ENSP00000204801:A32V	A	-	2	0	CD209	7716925	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.828000	0.04419	-1.812000	0.01227	-1.986000	0.00452	GCG		0.507	CD209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462241.1	NM_021155	
HNRNPL	3191	broad.mit.edu	37	19	39330868	39330868	+	Silent	SNP	T	T	G			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr19:39330868T>G	ENST00000221419.5	-	8	1467	c.1101A>C	c.(1099-1101)ccA>ccC	p.P367P	HNRNPL_ENST00000600873.1_Silent_p.P234P|AC104534.3_ENST00000594769.1_5'Flank	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	367	Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)	p.P367P(1)|p.P234P(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GGGGAGGGGGTGGGGGGTGCC	0.642																																						uc010xul.1																			2	Substitution - coding silent(2)		central_nervous_system(2)		0						c.(1099-1101)CCA>CCC		heterogeneous nuclear ribonucleoprotein L							7.0	9.0	8.0					19																	39330868		1496	3077	4573	SO:0001819	synonymous_variant	3191				nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding	g.chr19:39330868T>G	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1101A>C	19.37:g.39330868T>G						HNRNPL_uc010ege.1_Silent_p.P23P|HNRNPL_uc002ojj.1_Silent_p.P23P|HNRNPL_uc002ojo.1_5'Flank|HNRNPL_uc002ojk.2_Silent_p.P23P|HNRNPL_uc002ojl.2_Silent_p.P23P|HNRNPL_uc010xum.1_Silent_p.P234P|HNRNPL_uc002ojp.1_Silent_p.P23P|HNRNPL_uc010xun.1_Missense_Mutation_p.H75P	p.P367P	NM_001533	NP_001524	P14866	HNRPL_HUMAN	Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)		8	1112	-	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		367			Pro-rich.		A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	c.1101A>C	CCDS33015.1																																																																																				0.642	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		
FCGBP	8857	broad.mit.edu	37	19	40432968	40432968	+	Missense_Mutation	SNP	C	C	T	rs142198641	byFrequency	TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr19:40432968C>T	ENST00000221347.6	-	2	1308	c.1301G>A	c.(1300-1302)cGg>cAg	p.R434Q		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	434	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TTACTTACTCCGGCCGCAATC	0.587													C|||	2	0.000399361	0.0008	0.0	5008	,	,		18517	0.0		0.0	False		,,,				2504	0.001					uc002omp.3																			0				ovary(4)|skin(4)|central_nervous_system(1)	9						c.(1300-1302)CGG>CAG		Fc fragment of IgG binding protein precursor		C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	64.0	57.0	60.0		1301	-7.6	0.0	19	dbSNP_134	60	0,8600		0,0,4300	yes	missense	FCGBP	NM_003890.2	43	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	434/5406	40432968	3,13003	2203	4300	6503	SO:0001583	missense	8857					extracellular region	protein binding	g.chr19:40432968C>T	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.1301G>A	19.37:g.40432968C>T	ENSP00000221347:p.Arg434Gln						p.R434Q	NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		2	1309	-	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		434			IgGFc-binding.		O95784	Missense_Mutation	SNP	ENST00000221347.6	37	c.1301G>A	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	9.117	1.007911	0.19199	6.81E-4	0.0	ENSG00000090920	ENST00000221347	T	0.18657	2.2	3.85	-7.64	0.01286	.	1.787720	0.03887	N	0.278114	T	0.10723	0.0262	N	0.24115	0.695	0.09310	N	1	B	0.31077	0.307	B	0.21151	0.033	T	0.16482	-1.0401	10	0.11182	T	0.66	.	11.4707	0.50266	0.0:0.6149:0.106:0.2791	.	434	Q9Y6R7	FCGBP_HUMAN	Q	434	ENSP00000221347:R434Q	ENSP00000221347:R434Q	R	-	2	0	FCGBP	45124808	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.267000	0.02839	-1.694000	0.01425	-0.982000	0.02568	CGG		0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
NLRP5	126206	broad.mit.edu	37	19	56539808	56539808	+	Missense_Mutation	SNP	C	C	T	rs537471101		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr19:56539808C>T	ENST00000390649.3	+	7	2209	c.2209C>T	c.(2209-2211)Cgg>Tgg	p.R737W		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	737					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GCGGAAAATTCGGGTGGATGT	0.498													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19546	0.0		0.0	False		,,,				2504	0.0					uc002qmj.2																			0				ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7						c.(2209-2211)CGG>TGG		NACHT, LRR and PYD containing protein 5							151.0	151.0	151.0					19																	56539808		2010	4186	6196	SO:0001583	missense	126206					mitochondrion|nucleolus	ATP binding	g.chr19:56539808C>T	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2209C>T	19.37:g.56539808C>T	ENSP00000375063:p.Arg737Trp					NLRP5_uc002qmi.2_Missense_Mutation_p.R718W	p.R737W	NM_153447	NP_703148	P59047	NALP5_HUMAN		GBM - Glioblastoma multiforme(193;0.0326)	7	2209	+		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)	737			LRR 2.		A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	c.2209C>T	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.355347	0.41700	.	.	ENSG00000171487	ENST00000390649	D	0.89681	-2.55	3.26	2.19	0.27852	.	0.000000	0.33438	N	0.004906	D	0.92074	0.7488	M	0.72894	2.215	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83301	-0.0028	10	0.56958	D	0.05	.	7.7281	0.28771	0.2506:0.7494:0.0:0.0	.	737	P59047	NALP5_HUMAN	W	737	ENSP00000375063:R737W	ENSP00000375063:R737W	R	+	1	2	NLRP5	61231620	0.000000	0.05858	0.004000	0.12327	0.027000	0.11550	0.265000	0.18515	0.903000	0.36546	0.561000	0.74099	CGG		0.498	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
HNRNPLL	92906	broad.mit.edu	37	2	38812883	38812883	+	Frame_Shift_Del	DEL	C	C	-			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr2:38812883delC	ENST00000449105.3	-	3	788	c.449delG	c.(448-450)agcfs	p.S150fs	HNRNPLL_ENST00000378915.3_Frame_Shift_Del_p.S150fs|HNRNPLL_ENST00000358367.4_Frame_Shift_Del_p.S150fs|HNRNPLL_ENST00000608859.1_Frame_Shift_Del_p.S150fs|HNRNPLL_ENST00000409636.1_Frame_Shift_Del_p.S145fs|HNRNPLL_ENST00000410076.1_Frame_Shift_Del_p.S145fs|HNRNPLL_ENST00000409328.1_Frame_Shift_Del_p.S150fs			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	150	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										GATCCTTTTGCTTGTAGAATA	0.408																																						uc002rqw.2																			0				skin(1)	1						c.(448-450)AGCfs		heterogeneous nuclear ribonucleoprotein L-like							157.0	148.0	151.0					2																	38812883		2203	4300	6503	SO:0001589	frameshift_variant	92906				mRNA processing|positive regulation of RNA splicing	nucleus|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding	g.chr2:38812883delC	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"""RNA binding motif (RRM) containing"""	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.449delG	2.37:g.38812883delC	ENSP00000390625:p.Ser150fs					HNRPLL_uc002rqx.2_Frame_Shift_Del_p.S145fs	p.S150fs	NM_138394	NP_612403	Q8WVV9	HNRLL_HUMAN			3	859	-		all_hematologic(82;0.248)	150			RRM 1.		Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Frame_Shift_Del	DEL	ENST00000449105.3	37	c.449delG																																																																																					0.408	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394	
TRABD2A	129293	broad.mit.edu	37	2	85051124	85051124	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr2:85051124C>A	ENST00000409520.2	-	6	1329	c.1287G>T	c.(1285-1287)agG>agT	p.R429S	TRABD2A_ENST00000335459.5_Missense_Mutation_p.R380S|TRABD2A_ENST00000479944.1_5'UTR	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	429					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										GGAGTCGCGGCCTCCGCTGTG	0.652																																						uc010ysl.1																			0				ovary(1)	1						c.(1285-1287)AGG>AGT		hypothetical protein LOC129293 precursor							36.0	42.0	40.0					2																	85051124		2202	4300	6502	SO:0001583	missense	129293					integral to membrane		g.chr2:85051124C>A	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.1287G>T	2.37:g.85051124C>A	ENSP00000387075:p.Arg429Ser					C2orf89_uc002sou.3_Missense_Mutation_p.R380S	p.R429S	NM_001080824	NP_001074293	Q86V40	CB089_HUMAN			6	1376	-			429			Extracellular (Potential).		B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	37	c.1287G>T		.	.	.	.	.	.	.	.	.	.	c	12.16	1.854112	0.32791	.	.	ENSG00000186854	ENST00000335459;ENST00000409520	T;T	0.25085	1.82;1.85	3.65	1.7	0.24286	.	1.154120	0.06700	N	0.771240	T	0.11836	0.0288	.	.	.	0.09310	N	1	B;B	0.16603	0.018;0.013	B;B	0.16289	0.007;0.015	T	0.35151	-0.9800	9	0.09843	T	0.71	.	4.8788	0.13668	0.0:0.6544:0.22:0.1256	.	429;380	Q86V40;Q86V40-2	CB089_HUMAN;.	S	380;429	ENSP00000335004:R380S;ENSP00000387075:R429S	ENSP00000335004:R380S	R	-	3	2	C2orf89	84904635	0.018000	0.18449	0.001000	0.08648	0.182000	0.23217	0.700000	0.25601	0.288000	0.22398	0.444000	0.29173	AGG		0.652	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824	
TSHZ2	128553	broad.mit.edu	37	20	51870755	51870755	+	Missense_Mutation	SNP	C	C	T	rs141985599		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr20:51870755C>T	ENST00000371497.5	+	2	1645	c.758C>T	c.(757-759)aCg>aTg	p.T253M	TSHZ2_ENST00000603338.2_Missense_Mutation_p.T250M|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.T250M	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	253					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CTCAGACCCACGAGCTATTCA	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21048	0.0		0.0	False		,,,				2504	0.0					uc002xwo.2																			0				ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6						c.(757-759)ACG>ATG		teashirt zinc finger homeobox 2		C	MET/THR,MET/THR	2,4404	4.2+/-10.8	0,2,2201	65.0	51.0	55.0		749,758	4.6	0.9	20	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	81,81	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	probably-damaging,probably-damaging	250/1032,253/1035	51870755	3,13003	2203	4300	6503	SO:0001583	missense	128553				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr20:51870755C>T	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.758C>T	20.37:g.51870755C>T	ENSP00000360552:p.Thr253Met						p.T253M	NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	STAD - Stomach adenocarcinoma(23;0.1)		2	1714	+			253					B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	c.758C>T	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456697	0.63401	4.54E-4	1.16E-4	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.14516	2.5;2.5	5.5	4.56	0.56223	.	0.255407	0.45867	D	0.000334	T	0.10208	0.0250	N	0.08118	0	0.54753	D	0.999984	P	0.48016	0.904	P	0.44647	0.456	T	0.18618	-1.0331	10	0.72032	D	0.01	-1.229	14.6139	0.68534	0.0:0.9296:0.0:0.0704	.	253	Q9NRE2	TSH2_HUMAN	M	253;250	ENSP00000360552:T253M;ENSP00000333114:T250M	ENSP00000333114:T250M	T	+	2	0	TSHZ2	51304162	0.941000	0.31946	0.940000	0.37924	0.740000	0.42216	4.625000	0.61262	1.448000	0.47680	0.643000	0.83706	ACG		0.488	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
CASR	846	broad.mit.edu	37	3	121976021	121976021	+	Silent	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr3:121976021G>A	ENST00000490131.1	+	3	651	c.279G>A	c.(277-279)ctG>ctA	p.L93L	CASR_ENST00000498619.1_Silent_p.L93L|CASR_ENST00000296154.5_Silent_p.L93L	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	93					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	ACTTGACGCTGGGATACAGGA	0.448																																						uc003eev.3																			0				ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7						c.(277-279)CTG>CTA		calcium-sensing receptor precursor	Cinacalcet(DB01012)						123.0	123.0	123.0					3																	121976021		2203	4300	6503	SO:0001819	synonymous_variant	846				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity	g.chr3:121976021G>A	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.279G>A	3.37:g.121976021G>A						CASR_uc003eew.3_Silent_p.L93L	p.L93L	NM_000388	NP_000379	P41180	CASR_HUMAN		GBM - Glioblastoma multiforme(114;0.226)	3	651	+			93			Extracellular (Potential).		Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Silent	SNP	ENST00000490131.1	37	c.279G>A	CCDS3010.1																																																																																				0.448	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388	
RBM47	54502	broad.mit.edu	37	4	40440364	40440364	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr4:40440364C>T	ENST00000381793.2	-	3	943	c.547G>A	c.(547-549)Gtc>Atc	p.V183I	RBM47_ENST00000295971.7_Missense_Mutation_p.V183I|RBM47_ENST00000381795.6_Missense_Mutation_p.V183I|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000319592.4_Missense_Mutation_p.V183I|RBM47_ENST00000514014.1_Missense_Mutation_p.V145I			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	183	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CTGGCGTAGACGATCACGTCC	0.637																																						uc003gvc.2																			0				breast(3)	3						c.(547-549)GTC>ATC		RNA binding motif protein 47 isoform a							66.0	60.0	62.0					4																	40440364		2203	4299	6502	SO:0001583	missense	54502					nucleus	nucleotide binding|RNA binding	g.chr4:40440364C>T	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.547G>A	4.37:g.40440364C>T	ENSP00000371212:p.Val183Ile					RBM47_uc003gvd.2_Missense_Mutation_p.V183I|RBM47_uc003gve.2_RNA|RBM47_uc011bys.1_Missense_Mutation_p.V145I|RBM47_uc003gvg.1_Missense_Mutation_p.V183I	p.V183I	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN			4	1257	-			183			RRM 2.		A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	37	c.547G>A	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.906327	0.52333	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014;ENST00000515053;ENST00000513473	T;T;T;T;T;T;T	0.24908	2.41;2.41;2.41;2.41;2.41;2.41;1.83	5.8	5.8	0.92144	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.35219	0.0924	L	0.58810	1.83	0.80722	D	1	P;P	0.37141	0.584;0.54	B;B	0.41202	0.152;0.35	T	0.02743	-1.1116	10	0.40728	T	0.16	-41.0621	20.0591	0.97667	0.0:1.0:0.0:0.0	.	183;183	A0AV96-2;A0AV96	.;RBM47_HUMAN	I	183;183;183;183;145;183;183	ENSP00000320108:V183I;ENSP00000371212:V183I;ENSP00000371214:V183I;ENSP00000295971:V183I;ENSP00000423243:V145I;ENSP00000422564:V183I;ENSP00000421589:V183I	ENSP00000295971:V183I	V	-	1	0	RBM47	40135121	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	6.089000	0.71384	2.747000	0.94245	0.462000	0.41574	GTC		0.637	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
CSN1S1	1446	broad.mit.edu	37	4	70810660	70810660	+	Silent	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr4:70810660C>T	ENST00000246891.4	+	15	544	c.495C>T	c.(493-495)tcC>tcT	p.S165S	CSN1S1_ENST00000507772.1_Silent_p.S157S|CSN1S1_ENST00000507763.1_Silent_p.S156S|CSN1S1_ENST00000505782.1_Silent_p.S149S|CSN1S1_ENST00000444405.3_Silent_p.S156S	NM_001890.1	NP_001881.1	P47710	CASA1_HUMAN	casein alpha s1	165						extracellular region (GO:0005576)|extracellular space (GO:0005615)	transporter activity (GO:0005215)			lung(5)|prostate(1)|upper_aerodigestive_tract(1)	7						CACCGTTTTCCGACATCTCCA	0.423																																						uc003hep.1																			0					0						c.(493-495)TCC>TCT		casein alpha s1 isoform 1							270.0	256.0	260.0					4																	70810660		1921	4131	6052	SO:0001819	synonymous_variant	1446					extracellular region	protein binding|transporter activity	g.chr4:70810660C>T	X78416	CCDS47067.1, CCDS54769.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000126545	ENSG00000126545			2445	protein-coding gene	gene with protein product		115450	"""casein, alpha"""	CASA, CSN1		9050925, 7619062	Standard	NM_001890		Approved		uc003hep.1	P47710	OTTHUMG00000160843	ENST00000246891.4:c.495C>T	4.37:g.70810660C>T						CSN1S1_uc003heq.1_Silent_p.S156S|CSN1S1_uc003her.1_Silent_p.S157S	p.S165S	NM_001890	NP_001881	P47710	CASA1_HUMAN			15	544	+			165					A1A510|A1A511|E9PB60|Q4PNR5	Silent	SNP	ENST00000246891.4	37	c.495C>T	CCDS47067.1																																																																																				0.423	CSN1S1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362629.1		
FRAS1	80144	broad.mit.edu	37	4	79396642	79396642	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr4:79396642C>T	ENST00000264895.6	+	54	8173	c.7733C>T	c.(7732-7734)aCt>aTt	p.T2578I		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2578	Calx-beta 1.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GTGCAGAGGACTGGGAACCTG	0.542																																						uc003hlb.2																			0				large_intestine(5)	5						c.(7732-7734)ACT>ATT		Fraser syndrome 1							128.0	142.0	137.0					4																	79396642		2119	4231	6350	SO:0001583	missense	80144				cell communication	integral to membrane|plasma membrane	metal ion binding	g.chr4:79396642C>T	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7733C>T	4.37:g.79396642C>T	ENSP00000264895:p.Thr2578Ile						p.T2578I	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN			54	8173	+			2577			Calx-beta 1.|Extracellular (Potential).		A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	c.7733C>T	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320939	0.41096	.	.	ENSG00000138759	ENST00000264895	T	0.30981	1.51	5.44	3.71	0.42584	.	0.248292	0.39407	N	0.001363	T	0.29749	0.0743	M	0.71296	2.17	0.80722	D	1	B	0.30563	0.285	B	0.32762	0.152	T	0.04495	-1.0947	10	0.23302	T	0.38	.	6.6542	0.22979	0.0:0.565:0.2772:0.1578	.	2578	E9PHH6	.	I	2578	ENSP00000264895:T2578I	ENSP00000264895:T2578I	T	+	2	0	FRAS1	79615666	0.334000	0.24739	0.976000	0.42696	0.994000	0.84299	0.892000	0.28322	0.666000	0.31087	0.591000	0.81541	ACT		0.542	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SDHAP3	728609	broad.mit.edu	37	5	1593264	1593264	+	lincRNA	SNP	C	C	T	rs111700178		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr5:1593264C>T	ENST00000605200.1	+	0	0				SDHAP3_ENST00000436493.2_RNA																							AGGGCACATGCCTGACCAAAG	0.557																																						uc010itg.1																			0					0						c.(196-198)GCA>ACA		Homo sapiens cDNA clone IMAGE:40127561.																																						728609							g.chr5:1593264C>T																													5.37:g.1593264C>T						SDHAP3_uc011cme.1_RNA	p.A66T							2	273	-									Missense_Mutation	SNP	ENST00000605200.1	37	c.196G>A																																																																																					0.557	CTD-2012J19.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000469651.1		
FBN2	2201	broad.mit.edu	37	5	127800505	127800505	+	Silent	SNP	C	C	T	rs150087436	byFrequency	TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr5:127800505C>T	ENST00000508053.1	-	12	1712	c.738G>A	c.(736-738)gcG>gcA	p.A246A	FBN2_ENST00000262464.4_Silent_p.A246A|FBN2_ENST00000508989.1_Silent_p.A213A			P35556	FBN2_HUMAN	fibrillin 2	246	TB 1.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GATGGCCCCACGCCCGTCCAA	0.607													C|||	4	0.000798722	0.0008	0.0	5008	,	,		17648	0.0		0.003	False		,,,				2504	0.0					uc003kuu.2																			0				ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15						c.(736-738)GCG>GCA		fibrillin 2 precursor		C		1,4405	2.1+/-5.4	0,1,2202	90.0	83.0	86.0		738	-1.0	1.0	5	dbSNP_134	86	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous	FBN2	NM_001999.3		0,27,6476	TT,TC,CC		0.3023,0.0227,0.2076		246/2913	127800505	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	2201				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent	g.chr5:127800505C>T	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.738G>A	5.37:g.127800505C>T						FBN2_uc003kuv.2_Silent_p.A213A|FBN2_uc003kuw.3_Silent_p.A246A|FBN2_uc003kux.1_Silent_p.A246A	p.A246A	NM_001999	NP_001990	P35556	FBN2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)	6	1177	-		all_cancers(142;0.0216)|Prostate(80;0.0551)	246			TB 1.		B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	c.738G>A	CCDS34222.1																																																																																				0.607	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
ABLIM3	22885	broad.mit.edu	37	5	148637907	148637907	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr5:148637907G>C	ENST00000506113.1	+	23	2474	c.1992G>C	c.(1990-1992)gaG>gaC	p.E664D	ABLIM3_ENST00000356541.3_Intron|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000326685.7_Missense_Mutation_p.E569D|RP11-331K21.1_ENST00000512647.2_RNA|RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000517451.1_Missense_Mutation_p.E150D|ABLIM3_ENST00000309868.7_Missense_Mutation_p.E664D|ABLIM3_ENST00000508983.1_Missense_Mutation_p.E631D|AC012613.2_ENST00000523176.1_RNA			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	664	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCATCTCTGAGTTTGACCGGC	0.517																																						uc003lpy.2																			0				ovary(2)|skin(1)	3						c.(1990-1992)GAG>GAC		actin binding LIM protein family, member 3							62.0	59.0	60.0					5																	148637907		2203	4300	6503	SO:0001583	missense	22885				axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding	g.chr5:148637907G>C	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1992G>C	5.37:g.148637907G>C	ENSP00000425394:p.Glu664Asp					ABLIM3_uc003lpz.1_Missense_Mutation_p.E664D|ABLIM3_uc003lqa.1_Missense_Mutation_p.E561D|ABLIM3_uc003lqb.2_Intron|ABLIM3_uc003lqc.1_Missense_Mutation_p.E631D|ABLIM3_uc003lqd.1_Missense_Mutation_p.E569D|ABLIM3_uc003lqf.2_Intron|ABLIM3_uc003lqe.1_Missense_Mutation_p.E553D	p.E664D	NM_014945	NP_055760	O94929	ABLM3_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		24	2243	+			664			HP.		A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	c.1992G>C	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.985115	0.53934	.	.	ENSG00000173210	ENST00000326685;ENST00000309868;ENST00000506113;ENST00000508983;ENST00000517451;ENST00000536903	T;T;T;T;T	0.59224	0.28;0.34;0.34;0.36;0.63	5.86	3.77	0.43336	Villin headpiece (5);	0.052790	0.85682	D	0.000000	T	0.68118	0.2966	L	0.52266	1.64	0.80722	D	1	B;D;B	0.61697	0.013;0.99;0.07	B;D;B	0.72982	0.009;0.979;0.046	T	0.69628	-0.5094	10	0.54805	T	0.06	.	12.0851	0.53691	0.2061:0.0:0.7939:0.0	.	150;569;664	O94929-4;O94929-3;O94929	.;.;ABLM3_HUMAN	D	569;664;664;631;150;149	ENSP00000315841:E569D;ENSP00000310309:E664D;ENSP00000425394:E664D;ENSP00000420855:E631D;ENSP00000430150:E150D	ENSP00000310309:E664D	E	+	3	2	ABLIM3	148618100	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.250000	0.32850	1.497000	0.48584	0.542000	0.68232	GAG		0.517	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
LY6G6F	259215	broad.mit.edu	37	6	31675363	31675363	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr6:31675363C>A	ENST00000375832.4	+	2	203	c.181C>A	c.(181-183)Ctg>Atg	p.L61M	XXbac-BPG32J3.20_ENST00000461287.1_Intron|LY6G6F_ENST00000556581.1_Missense_Mutation_p.L61M|MEGT1_ENST00000503322.1_Missense_Mutation_p.L61M	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	61	Ig-like V-type.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						CTTCACCACCCTGGTAGCCCA	0.592																																						uc003nwa.1																			0				breast(1)|central_nervous_system(1)	2						c.(181-183)CTG>ATG		G6f protein precursor							45.0	42.0	43.0					6																	31675363		2203	4300	6503	SO:0001583	missense	259215					integral to membrane|plasma membrane		g.chr6:31675363C>A		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"""Immunoglobulin superfamily / V-set domain containing"""	13933	protein-coding gene	gene with protein product		611404	"""chromosome 6 open reading frame 21"""	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.181C>A	6.37:g.31675363C>A	ENSP00000364992:p.Leu61Met					BAT5_uc011dnz.1_Intron|LY6G6F_uc003nwb.1_Missense_Mutation_p.L61M	p.L61M	NM_001003693	NP_001003693	Q5SQ64	LY66F_HUMAN			2	181	+			61			Extracellular (Potential).|Ig-like V-type.		B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	c.181C>A	CCDS34403.1	.	.	.	.	.	.	.	.	.	.	C	6.453	0.451737	0.12223	.	.	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.67698	-0.28;-0.28;-0.28	5.17	-3.69	0.04450	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.481497	0.17197	N	0.183283	T	0.38453	0.1041	M	0.62723	1.935	0.09310	N	1	B;B	0.29481	0.245;0.245	B;B	0.35182	0.197;0.14	T	0.45279	-0.9272	10	0.54805	T	0.06	-1.1543	3.6032	0.08032	0.3569:0.2836:0.0:0.3596	.	61;61	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	M	61	ENSP00000452432:L61M;ENSP00000364992:L61M;ENSP00000421232:L61M	ENSP00000364992:L61M	L	+	1	2	XXbac-BPG32J3.19;LY6G6F	31783342	0.005000	0.15991	0.018000	0.16275	0.167000	0.22549	-0.258000	0.08733	-0.328000	0.08539	-0.218000	0.12543	CTG		0.592	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
TBX18	9096	broad.mit.edu	37	6	85446758	85446758	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr6:85446758G>A	ENST00000369663.5	-	8	1806	c.1469C>T	c.(1468-1470)tCg>tTg	p.S490L	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	490					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		GGACATTCCCGAAATCTGCAT	0.527																																						uc003pkl.1																			0				ovary(2)|pancreas(2)|lung(1)	5						c.(1468-1470)TCG>TTG		T-box 18							152.0	156.0	155.0					6																	85446758		2203	4300	6503	SO:0001583	missense	9096				multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr6:85446758G>A	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1469C>T	6.37:g.85446758G>A	ENSP00000358677:p.Ser490Leu					TBX18_uc010kbq.1_Intron	p.S490L	NM_001080508	NP_001073977	O95935	TBX18_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0267)	8	1469	-		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)	490					A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	37	c.1469C>T	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680807	0.47886	.	.	ENSG00000112837	ENST00000369663	D	0.87179	-2.22	5.48	5.48	0.80851	.	3.507440	0.00604	N	0.000384	T	0.75664	0.3880	N	0.24115	0.695	0.47276	D	0.99937	P	0.51537	0.946	B	0.41723	0.365	T	0.67488	-0.5658	10	0.12430	T	0.62	.	19.3305	0.94285	0.0:0.0:1.0:0.0	.	490	O95935	TBX18_HUMAN	L	490	ENSP00000358677:S490L	ENSP00000358677:S490L	S	-	2	0	TBX18	85503477	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	5.606000	0.67641	2.571000	0.86741	0.585000	0.79938	TCG		0.527	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
ASCC3	10973	broad.mit.edu	37	6	101037629	101037629	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr6:101037629C>T	ENST00000369162.2	-	36	5775	c.5431G>A	c.(5431-5433)Gaa>Aaa	p.E1811K		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1811					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GTTAGAGGTTCAATGCTGCGA	0.343																																						uc003pqk.2																			0				ovary(5)|skin(1)	6						c.(5431-5433)GAA>AAA		activating signal cointegrator 1 complex subunit							103.0	106.0	105.0					6																	101037629		2203	4300	6503	SO:0001583	missense	10973				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr6:101037629C>T	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.5431G>A	6.37:g.101037629C>T	ENSP00000358159:p.Glu1811Lys						p.E1811K	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)	36	5760	-		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)	1811					E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	c.5431G>A	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.793376	0.31685	.	.	ENSG00000112249	ENST00000369162	T	0.42513	0.97	5.22	5.22	0.72569	Sec63 domain (1);	0.053706	0.64402	D	0.000001	T	0.25044	0.0608	L	0.58810	1.83	0.80722	D	1	B	0.24618	0.107	B	0.22386	0.039	T	0.18681	-1.0329	10	0.09338	T	0.73	.	19.1375	0.93433	0.0:1.0:0.0:0.0	.	1811	Q8N3C0	HELC1_HUMAN	K	1811	ENSP00000358159:E1811K	ENSP00000358159:E1811K	E	-	1	0	ASCC3	101144350	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.228000	0.58619	2.607000	0.88179	0.585000	0.79938	GAA		0.343	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
PNLDC1	154197	broad.mit.edu	37	6	160240368	160240368	+	Missense_Mutation	SNP	G	G	A	rs138386704		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr6:160240368G>A	ENST00000610273.1	+	18	1654	c.1483G>A	c.(1483-1485)Gtc>Atc	p.V495I	PNLDC1_ENST00000392167.3_Missense_Mutation_p.V506I	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	495						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTCCCCAAACGTCAACTGCCT	0.617																																						uc003qsx.1																			0					0						c.(1483-1485)GTC>ATC		poly(A)-specific ribonuclease (PARN)-like domain		G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	88.0	66.0	74.0		1483	-7.8	0.8	6	dbSNP_134	74	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PNLDC1	NM_173516.1	29	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	benign	495/521	160240368	3,13003	2203	4300	6503	SO:0001583	missense	154197					integral to membrane|nucleus	nucleic acid binding	g.chr6:160240368G>A	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.1483G>A	6.37:g.160240368G>A	ENSP00000476448:p.Val495Ile					PNLDC1_uc003qsy.1_Missense_Mutation_p.V506I	p.V495I	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)	18	1654	+		Breast(66;0.00519)|Ovarian(120;0.123)	495			Helical; Anchor for type IV membrane protein; (Potential).		Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	c.1483G>A	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	G	9.716	1.158311	0.21454	4.54E-4	1.16E-4	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	5.86	-7.76	0.01232	.	0.904550	0.09461	N	0.799073	T	0.10551	0.0258	N	0.11560	0.145	0.21527	N	0.999654	B;B	0.18310	0.027;0.016	B;B	0.14578	0.011;0.005	T	0.18871	-1.0323	9	0.17369	T	0.5	.	20.2616	0.98447	0.1653:0.0:0.8347:0.0	.	506;495	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	I	495;506	.	ENSP00000275275:V495I	V	+	1	0	PNLDC1	160160358	0.000000	0.05858	0.847000	0.33407	0.016000	0.09150	-0.446000	0.06837	-1.600000	0.01603	-0.291000	0.09656	GTC		0.617	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516	
QKI	9444	broad.mit.edu	37	6	163956153	163956153	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr6:163956153C>G	ENST00000361752.3	+	4	1093	c.542C>G	c.(541-543)cCt>cGt	p.P181R	QKI_ENST00000424802.3_Missense_Mutation_p.P181R|QKI_ENST00000275262.7_Missense_Mutation_p.P181R|QKI_ENST00000392127.2_Missense_Mutation_p.P181R|QKI_ENST00000453779.2_Missense_Mutation_p.P181R|QKI_ENST00000361195.2_Missense_Mutation_p.P181R	NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	181					long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		TTATTGGTACCTGCAGTAAGT	0.333																																						uc003qui.2																			0				large_intestine(1)|ovary(1)	2						c.(541-543)CCT>CGT		quaking homolog, KH domain RNA binding isoform							101.0	108.0	106.0					6																	163956153		2203	4300	6503	SO:0001583	missense	9444				mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding	g.chr6:163956153C>G	AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531			21100	protein-coding gene	gene with protein product		609590	"""quaking homolog, KH domain RNA binding (mouse)"""			10535969	Standard	NM_006775		Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.542C>G	6.37:g.163956153C>G	ENSP00000355094:p.Pro181Arg					QKI_uc003que.2_Missense_Mutation_p.P181R|QKI_uc003quf.2_Missense_Mutation_p.P181R|QKI_uc003qug.2_Missense_Mutation_p.P181R|QKI_uc003quh.2_Missense_Mutation_p.P181R|QKI_uc003quj.2_Missense_Mutation_p.P181R	p.P181R	NM_006775	NP_006766	Q96PU8	QKI_HUMAN		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)	4	1093	+		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)	181					Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	Missense_Mutation	SNP	ENST00000361752.3	37	c.542C>G	CCDS5285.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631555	0.87660	.	.	ENSG00000112531	ENST00000453779;ENST00000275262;ENST00000392127;ENST00000361752;ENST00000361195;ENST00000424802;ENST00000537041;ENST00000544823	T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	5.56	5.56	0.83823	.	0.142736	0.64402	D	0.000004	T	0.41880	0.1178	M	0.77486	2.375	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.992;1.0;0.999;0.999;0.998	D;P;D;P;P;P	0.65684	0.93;0.636;0.937;0.906;0.906;0.897	T	0.37888	-0.9686	10	0.66056	D	0.02	-1.7164	19.533	0.95237	0.0:1.0:0.0:0.0	.	181;181;181;181;181;181	Q96PU8-3;Q96PU8;Q96PU8-5;Q96PU8-9;Q96PU8-6;Q96PU8-8	.;QKI_HUMAN;.;.;.;.	R	181;181;181;181;181;181;126;126	ENSP00000408775:P181R;ENSP00000275262:P181R;ENSP00000375973:P181R;ENSP00000355094:P181R;ENSP00000354867:P181R;ENSP00000408382:P181R;ENSP00000440991:P126R;ENSP00000440599:P126R	ENSP00000275262:P181R	P	+	2	0	QKI	163876143	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.423000	0.80229	2.604000	0.88044	0.591000	0.81541	CCT		0.333	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043016.2	NM_006775	
EGFR	1956	broad.mit.edu	37	7	55223531	55223533	+	In_Frame_Del	DEL	GTG	GTG	-			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr7:55223531_55223533delGTG	ENST00000275493.2	+	8	1075_1077	c.898_900delGTG	c.(898-900)gtgdel	p.V301del	EGFR_ENST00000442591.1_In_Frame_Del_p.V301del|EGFR_ENST00000455089.1_In_Frame_Del_p.V256del|EGFR_ENST00000454757.2_In_Frame_Del_p.V248del|EGFR_ENST00000420316.2_In_Frame_Del_p.V301del|EGFR_ENST00000342916.3_In_Frame_Del_p.V301del|EGFR_ENST00000344576.2_In_Frame_Del_p.V301del	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	301					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)			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)	AGGTAATTATGTGGTGACAGATC	0.601		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.2		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		0		p.V301V(1)		lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(898-900)GTGdel		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)																																			SO:0001651	inframe_deletion	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.chr7:55223531_55223533delGTG		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.898_900delGTG	7.37:g.55223534_55223536delGTG	ENSP00000275493:p.Val301del	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc003tqh.2_In_Frame_Del_p.V301del|EGFR_uc003tqi.2_In_Frame_Del_p.V301del|EGFR_uc003tqj.2_In_Frame_Del_p.V301del|EGFR_uc010kzg.1_In_Frame_Del_p.V256del|EGFR_uc011kco.1_In_Frame_Del_p.V248del|EGFR_uc011kcp.1_5'Flank|EGFR_uc011kcq.1_5'Flank	p.V301del	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)		8	1144_1146	+	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)		301			Extracellular (Potential).		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	In_Frame_Del	DEL	ENST00000275493.2	37	c.898_900delGTG	CCDS5514.1																																																																																				0.601	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
EGFR	1956	broad.mit.edu	37	7	55241677	55241677	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr7:55241677G>A	ENST00000275493.2	+	18	2302	c.2125G>A	c.(2125-2127)Gaa>Aaa	p.E709K	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.E664K|EGFR_ENST00000454757.2_Missense_Mutation_p.E656K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	709			E -> A (found in a lung cancer sample; more sensitive to gefitinib than wild- type). {ECO:0000269|PubMed:15623594, ECO:0000269|PubMed:16533793}.|E -> G (found in a lung cancer sample; constitutively activated kinase with higher levels of basal autophosphorylation; more sensitive to gefitinib than wild-type). {ECO:0000269|PubMed:15623594}.|E -> K (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.		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.E709K(16)|p.E709H(2)|p.E709fs*1(1)|p.E709Q(1)		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)	GATCTTGAAGGAAACTGAATT	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.2		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		20	Substitution - Missense(19)|Deletion - Frameshift(1)	p.E709K(17)|p.E709A(11)|p.E709G(7)|p.E709V(5)|p.E709_T710>D(5)|p.E709H(2)|p.E709_T710>G(1)|p.E709_T710>A(1)|p.E709fs*1(1)	lung(15)|upper_aerodigestive_tract(2)|prostate(2)|ovary(1)	lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(2125-2127)GAA>AAA		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						88.0	91.0	90.0					7																	55241677		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.chr7:55241677G>A		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.2125G>A	7.37:g.55241677G>A	ENSP00000275493:p.Glu709Lys	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc010kzg.1_Missense_Mutation_p.E664K|EGFR_uc011kco.1_Missense_Mutation_p.E656K	p.E709K	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)		18	2371	+	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)		709		E -> K (found in a lung cancer sample).|E -> A (found in a lung cancer sample).	Cytoplasmic (Potential).		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	c.2125G>A	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	34	5.304179	0.95601	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.61859	0.07;0.07;0.07	5.83	5.83	0.93111	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.65626	0.2709	M	0.71581	2.175	0.80722	D	1	P;P	0.49862	0.929;0.912	B;P	0.46172	0.283;0.506	T	0.70454	-0.4867	10	0.87932	D	0	.	18.672	0.91514	0.0:0.0:1.0:0.0	.	664;709	Q504U8;P00533	.;EGFR_HUMAN	K	664;579;709;656	ENSP00000415559:E664K;ENSP00000275493:E709K;ENSP00000395243:E656K	ENSP00000275493:E709K	E	+	1	0	EGFR	55209171	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	9.833000	0.99426	2.745000	0.94114	0.563000	0.77884	GAA		0.567	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
EGFR	1956	broad.mit.edu	37	7	55241708	55241708	+	Missense_Mutation	SNP	G	G	A	rs121913428		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr7:55241708G>A	ENST00000275493.2	+	18	2333	c.2156G>A	c.(2155-2157)gGc>gAc	p.G719D	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.G674D|EGFR_ENST00000454757.2_Missense_Mutation_p.G666D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	719	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> A (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.|G -> C (found in a lung cancer sample; dbSNP:rs28929495). {ECO:0000269|PubMed:15623594, ECO:0000269|PubMed:16533793}.|G -> D (found in a lung cancer sample). {ECO:0000269|PubMed:16533793}.|G -> S (found in a lung cancer sample; somatic mutation; strongly increased kinase activity; constitutively activated kinase with higher levels of basal autophosphorylation; more sensitive to gefitinib than wild-type). {ECO:0000269|PubMed:15118125, ECO:0000269|PubMed:15623594, ECO:0000269|PubMed:16533793}.		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.G719A(27)|p.G719D(4)|p.G719fs*29(1)		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)	AAAGTGCTGGGCTCCGGTGCG	0.582		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.2		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		32	Substitution - Missense(31)|Deletion - Frameshift(1)	p.G719S(61)|p.G719A(52)|p.G719C(31)|p.G719?(9)|p.G719D(6)|p.G719V(1)|p.G719fs*29(1)	lung(30)|oesophagus(1)|central_nervous_system(1)	lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(2155-2157)GGC>GAC		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						68.0	70.0	69.0					7																	55241708		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.chr7:55241708G>A		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.2156G>A	7.37:g.55241708G>A	ENSP00000275493:p.Gly719Asp	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc010kzg.1_Missense_Mutation_p.G674D|EGFR_uc011kco.1_Missense_Mutation_p.G666D	p.G719D	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)		18	2402	+	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)		719		G -> A (found in a lung cancer sample).|G -> D (found in a lung cancer sample).|G -> S (found in a lung cancer sample; somatic mutation; strongly increased kinase activity).	Cytoplasmic (Potential).|Protein kinase.|ATP.		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	c.2156G>A	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639359	0.67244	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.78364	-1.17;-1.17;-1.17	5.5	5.5	0.81552	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90469	0.7015	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	D	0.92165	0.5739	10	0.87932	D	0	.	17.9478	0.89044	0.0:0.0:1.0:0.0	.	674;719	Q504U8;P00533	.;EGFR_HUMAN	D	674;589;719;666	ENSP00000415559:G674D;ENSP00000275493:G719D;ENSP00000395243:G666D	ENSP00000275493:G719D	G	+	2	0	EGFR	55209202	1.000000	0.71417	0.996000	0.52242	0.044000	0.14063	9.772000	0.98984	2.562000	0.86427	0.563000	0.77884	GGC		0.582	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
MUC17	140453	broad.mit.edu	37	7	100678917	100678917	+	Missense_Mutation	SNP	C	C	T	rs71286278		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr7:100678917C>T	ENST00000306151.4	+	3	4284	c.4220C>T	c.(4219-4221)cCg>cTg	p.P1407L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1407	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCACCACGCCGGTAGTCAGT	0.512																																						uc003uxp.1																			0				ovary(14)|skin(8)|breast(3)|lung(2)	27						c.(4219-4221)CCG>CTG		mucin 17 precursor							274.0	279.0	278.0					7																	100678917		2203	4300	6503	SO:0001583	missense	140453					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity	g.chr7:100678917C>T	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.4220C>T	7.37:g.100678917C>T	ENSP00000302716:p.Pro1407Leu					MUC17_uc010lho.1_RNA	p.P1407L	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN			3	4273	+	Lung NSC(181;0.136)|all_lung(186;0.182)		1407			Extracellular (Potential).|59 X approximate tandem repeats.|21.|Ser-rich.		O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	c.4220C>T	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.556	-0.847423	0.02651	.	.	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.838	-1.68	0.08212	.	.	.	.	.	T	0.02610	0.0079	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46317	-0.9200	9	0.26408	T	0.33	.	4.2	0.10462	0.0:0.5117:0.0:0.4883	.	1407	Q685J3	MUC17_HUMAN	L	1407	ENSP00000302716:P1407L	ENSP00000302716:P1407L	P	+	2	0	MUC17	100465637	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.002000	0.13061	-0.630000	0.05567	-1.368000	0.01194	CCG		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
KCND2	3751	broad.mit.edu	37	7	120386073	120386073	+	Silent	SNP	G	G	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr7:120386073G>T	ENST00000331113.4	+	5	2672	c.1707G>T	c.(1705-1707)ctG>ctT	p.L569L	RP4-797C5.2_ENST00000450480.1_RNA	NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	569					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GAACACCTCTGTCTAACAGGT	0.443																																						uc003vjj.1																			0				ovary(2)|central_nervous_system(2)|skin(1)	5						c.(1705-1707)CTG>CTT		potassium voltage-gated channel, Shal-related							89.0	70.0	76.0					7																	120386073		2203	4300	6503	SO:0001819	synonymous_variant	3751				regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding	g.chr7:120386073G>T	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1707G>T	7.37:g.120386073G>T							p.L569L	NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN			5	2672	+	all_neural(327;0.117)		569			Cytoplasmic (Potential).		O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Silent	SNP	ENST00000331113.4	37	c.1707G>T	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	4.666	0.123843	0.08931	.	.	ENSG00000184408	ENST00000425288	.	.	.	6.06	-12.1	0.00011	.	.	.	.	.	T	0.59595	0.2205	.	.	.	0.53688	D	0.999978	.	.	.	.	.	.	T	0.74450	-0.3661	4	.	.	.	.	16.9632	0.86278	0.1149:0.2585:0.6267:0.0	.	.	.	.	F	155	.	.	C	+	2	0	KCND2	120173309	0.001000	0.12720	0.018000	0.16275	0.838000	0.47535	-1.521000	0.02239	-2.414000	0.00569	-2.042000	0.00416	TGT		0.443	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281	
CEP41	95681	broad.mit.edu	37	7	130038800	130038800	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr7:130038800C>T	ENST00000223208.5	-	11	1324	c.1054G>A	c.(1054-1056)Ggc>Agc	p.G352S	CEP41_ENST00000541543.1_Missense_Mutation_p.G264S|CEP41_ENST00000343969.5_Missense_Mutation_p.G280S	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	352					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											CTGGCGGGGCCGCCACCTGGC	0.562																																						uc003vpz.2																			0					0						c.(1054-1056)GGC>AGC		testis specific, 14							101.0	118.0	112.0					7																	130038800		2203	4300	6503	SO:0001583	missense	95681				G2/M transition of mitotic cell cycle	centrosome|cytosol		g.chr7:130038800C>T	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"""testis specific, 14"""	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.1054G>A	7.37:g.130038800C>T	ENSP00000223208:p.Gly352Ser					TSGA14_uc003vpy.2_Missense_Mutation_p.G114S|TSGA14_uc010lmf.2_Missense_Mutation_p.G149S|TSGA14_uc003vqa.2_Missense_Mutation_p.G280S|TSGA14_uc011kpg.1_Missense_Mutation_p.G264S	p.G352S	NM_018718	NP_061188	Q9BYV8	CEP41_HUMAN			11	1101	-	Melanoma(18;0.0435)		352					A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	c.1054G>A	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.808310	0.00606	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969	D;D;D	0.88741	-2.35;-2.09;-2.42	4.97	-3.29	0.05017	.	1.097150	0.06817	N	0.791398	T	0.76779	0.4035	L	0.36672	1.1	0.09310	N	1	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.08055	0.0;0.001;0.003	T	0.60762	-0.7199	10	0.07482	T	0.82	2.0E-4	1.9292	0.03323	0.1319:0.3602:0.1234:0.3845	.	264;280;352	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	S	352;264;280	ENSP00000223208:G352S;ENSP00000445888:G264S;ENSP00000342738:G280S	ENSP00000223208:G352S	G	-	1	0	TSGA14	129826036	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.329000	0.07935	-0.607000	0.05738	-0.150000	0.13652	GGC		0.562	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718	
RP1L1	94137	broad.mit.edu	37	8	10466088	10466088	+	Silent	SNP	A	A	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr8:10466088A>T	ENST00000382483.3	-	4	5743	c.5520T>A	c.(5518-5520)gcT>gcA	p.A1840A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1920					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCTCCCCTTCAGCCTCCGGGG	0.632																																						uc003wtc.2																			0				ovary(4)|breast(3)|central_nervous_system(1)	8						c.(5518-5520)GCT>GCA		retinitis pigmentosa 1-like 1							151.0	168.0	163.0					8																	10466088		1958	4131	6089	SO:0001819	synonymous_variant	94137				intracellular signal transduction			g.chr8:10466088A>T	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5520T>A	8.37:g.10466088A>T							p.A1840A	NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN		COAD - Colon adenocarcinoma(149;0.0811)	4	5749	-			1840					Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	c.5520T>A	CCDS43708.1																																																																																				0.632	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
KCNB2	9312	broad.mit.edu	37	8	73848725	73848725	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr8:73848725A>G	ENST00000523207.1	+	3	1723	c.1135A>G	c.(1135-1137)Atg>Gtg	p.M379V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	379					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CACCATCACCATGACCACTGT	0.448																																						uc003xzb.2																			0				skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7						c.(1135-1137)ATG>GTG		potassium voltage-gated channel, Shab-related							105.0	105.0	105.0					8																	73848725		2203	4300	6503	SO:0001583	missense	9312				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding	g.chr8:73848725A>G	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1135A>G	8.37:g.73848725A>G	ENSP00000430846:p.Met379Val						p.M379V	NM_004770	NP_004761	Q92953	KCNB2_HUMAN	Epithelial(68;0.105)		3	1723	+	Breast(64;0.137)		379					Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	c.1135A>G	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.336619	0.60963	.	.	ENSG00000182674	ENST00000523207	D	0.98807	-5.15	5.58	5.58	0.84498	Ion transport (1);	0.000000	0.56097	D	0.000035	D	0.98880	0.9621	M	0.70275	2.135	0.58432	D	0.999999	D	0.65815	0.995	D	0.68039	0.955	D	0.99860	1.1082	10	0.87932	D	0	.	15.7481	0.77962	1.0:0.0:0.0:0.0	.	379	Q92953	KCNB2_HUMAN	V	379	ENSP00000430846:M379V	ENSP00000430846:M379V	M	+	1	0	KCNB2	74011279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.121000	0.65114	0.533000	0.62120	ATG		0.448	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
PTPRD	5789	broad.mit.edu	37	9	8485910	8485910	+	Silent	SNP	C	C	T			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chr9:8485910C>T	ENST00000381196.4	-	25	3450	c.2907G>A	c.(2905-2907)gaG>gaA	p.E969E	PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000358503.5_Silent_p.E947E|PTPRD_ENST00000360074.4_Silent_p.E956E|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000356435.5_Silent_p.E969E|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000540109.1_Silent_p.E969E	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	969	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CAATAAGCTGCTCCATCGGGA	0.468										TSP Lung(15;0.13)																												uc003zkk.2																			0				lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22						c.(2905-2907)GAG>GAA		protein tyrosine phosphatase, receptor type, D							163.0	155.0	158.0					9																	8485910		2203	4300	6503	SO:0001819	synonymous_variant	5789				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr9:8485910C>T	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2907G>A	9.37:g.8485910C>T		TSP Lung(15;0.13)				PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Silent_p.E960E|PTPRD_uc003zkm.2_Silent_p.E956E|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	p.E969E	NM_002839	NP_002830	P23468	PTPRD_HUMAN		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)	27	3618	-		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)	969			Fibronectin type-III 7.|Extracellular (Potential).		B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	37	c.2907G>A	CCDS43786.1																																																																																				0.468	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
GPR143	4935	broad.mit.edu	37	X	9711677	9711677	+	Missense_Mutation	SNP	G	G	A	rs137852297		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chrX:9711677G>A	ENST00000467482.1	-	6	841	c.695C>T	c.(694-696)aCg>aTg	p.T232M	GPR143_ENST00000380929.2_Missense_Mutation_p.T252M			P51810	GP143_HUMAN	G protein-coupled receptor 143	232	Necessary for its G protein-activation ability and normal distribution of melanosomes.		T -> K (in OA1; abnormal distribution of melanosomes; Not delivered at the cell surface of melanocytic and non- melanocytic cells). {ECO:0000269|PubMed:9529334}.		calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)			endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				CTCGTTCTCCGTGTAAATGCC	0.383																																						uc004cst.1																			0				ovary(1)	1	GRCh37	CM981400	GPR143	M	rs137852297	c.(754-756)ACG>ATG		G protein-coupled receptor 143							154.0	131.0	139.0					X																	9711677		2203	4300	6503	SO:0001583	missense	4935				calcium-mediated signaling using intracellular calcium source|eye pigment biosynthetic process|melanosome organization|melanosome transport|phosphatidylinositol-mediated signaling|regulation of calcium-mediated signaling|visual perception	apical plasma membrane|Golgi apparatus|integral to membrane|lysosomal membrane|melanosome membrane|membrane fraction	dopamine binding|L-DOPA receptor activity|protein binding|tyrosine binding	g.chrX:9711677G>A	Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"""GPCR / Unclassified : 7TM orphan receptors"""	20145	protein-coding gene	gene with protein product	"""ocular albinism 1"""	300808	"""ocular albinism 1 (Nettleship-Falls)"""	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.695C>T	X.37:g.9711677G>A	ENSP00000417161:p.Thr232Met						p.T252M	NM_000273	NP_000264	P51810	GP143_HUMAN			6	755	-		Hepatocellular(5;0.000888)	232		T -> K (in OA1; abnormal distribution of melanosomes; Not delivered at the cell surface of melanocytic and non- melanocytic cells).	Cytoplasmic (Potential).|Necessary for its G protein-activation ability and normal distribution of melanosomes.		Q6NTI7	Missense_Mutation	SNP	ENST00000467482.1	37	c.755C>T	CCDS14134.2	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263348	0.80358	.	.	ENSG00000101850	ENST00000467482;ENST00000380929;ENST00000431126	D;D;D	0.99329	-5.75;-5.75;-5.75	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.99375	0.9780	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98948	1.0793	10	0.72032	D	0.01	-10.3298	16.3904	0.83533	0.0:0.0:1.0:0.0	.	232	P51810	GP143_HUMAN	M	232;252;148	ENSP00000417161:T232M;ENSP00000370316:T252M;ENSP00000406138:T148M	ENSP00000370316:T252M	T	-	2	0	GPR143	9671677	1.000000	0.71417	0.657000	0.29651	0.834000	0.47266	8.316000	0.89985	2.124000	0.65301	0.513000	0.50165	ACG		0.383	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055714.2	NM_000273	
WDR13	64743	broad.mit.edu	37	X	48463240	48463240	+	Silent	SNP	G	G	A	rs144018865		TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chrX:48463240G>A	ENST00000218056.5	+	9	1783	c.1278G>A	c.(1276-1278)acG>acA	p.T426T	WDR13_ENST00000376729.5_Silent_p.T426T	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	426						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						CGACAGTGACGGGCAGTGAGG	0.622																																						uc004dkh.1																			0				ovary(2)	2						c.(1276-1278)ACG>ACA		WD repeat domain 13 protein		G	,	1,3834		0,1,1631,571	51.0	39.0	43.0		1002,1278	-7.3	0.7	X	dbSNP_134	43	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous	WDR13	NM_001166426.1,NM_017883.4	,	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	,	334/394,426/486	48463240	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	64743					cytoplasm|nucleus		g.chrX:48463240G>A	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.1278G>A	X.37:g.48463240G>A						WDR13_uc004dki.1_Silent_p.T334T|WDR13_uc004dkj.1_Silent_p.T426T|WDR13_uc004dkk.1_Silent_p.T334T|WDR13_uc004dkl.3_Silent_p.T334T	p.T426T	NM_017883	NP_060353	Q9H1Z4	WDR13_HUMAN			10	1425	+			426			WD 4.		Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Silent	SNP	ENST00000218056.5	37	c.1278G>A	CCDS14302.1																																																																																				0.622	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
GRIPAP1	56850	broad.mit.edu	37	X	48847434	48847434	+	Silent	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chrX:48847434G>A	ENST00000376441.1	-	7	580	c.546C>T	c.(544-546)acC>acT	p.T182T	GRIPAP1_ENST00000376444.3_Silent_p.T137T|GRIPAP1_ENST00000376425.3_Silent_p.T182T|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376423.4_Silent_p.T129T	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	182						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						GGGCCAGGACGGTGGGGGCCG	0.607																																						uc004dly.1																			0				breast(2)|kidney(1)	3						c.(544-546)ACC>ACT		GRIP1 associated protein 1 isoform 1							45.0	45.0	45.0					X																	48847434		2202	4299	6501	SO:0001819	synonymous_variant	56850					early endosome		g.chrX:48847434G>A	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.546C>T	X.37:g.48847434G>A						GRIPAP1_uc004dlz.2_Silent_p.T72T|GRIPAP1_uc004dma.2_Silent_p.T129T	p.T182T	NM_020137	NP_064522	Q4V328	GRAP1_HUMAN			7	581	-			182					A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	37	c.546C>T	CCDS35248.1																																																																																				0.607	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
FMR1NB	158521	broad.mit.edu	37	X	147063166	147063166	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chrX:147063166G>A	ENST00000370467.3	+	1	318	c.244G>A	c.(244-246)Gtg>Atg	p.V82M		NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	82						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)				breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					CCTGCTGTTCGTGTGCTACTA	0.612																																						uc004fcm.2																			0				ovary(1)	1						c.(244-246)GTG>ATG		fragile X mental retardation 1 neighbor							142.0	132.0	136.0					X																	147063166		2203	4300	6503	SO:0001583	missense	158521					integral to membrane		g.chrX:147063166G>A		CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988			26372	protein-coding gene	gene with protein product	"""cancer/testis antigen 37"""					12601173	Standard	NM_152578		Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.244G>A	X.37:g.147063166G>A	ENSP00000359498:p.Val82Met						p.V82M	NM_152578	NP_689791	Q8N0W7	FMR1N_HUMAN			1	318	+	Acute lymphoblastic leukemia(192;6.56e-05)		82			Helical; (Potential).		D3DWT3	Missense_Mutation	SNP	ENST00000370467.3	37	c.244G>A	CCDS14683.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301653	0.23736	.	.	ENSG00000176988	ENST00000370467	T	0.48836	0.8	1.98	-1.05	0.10036	.	.	.	.	.	T	0.24736	0.0600	N	0.08118	0	0.09310	N	1	D	0.56968	0.978	P	0.45712	0.491	T	0.10941	-1.0608	9	0.37606	T	0.19	-2.0653	2.9924	0.05987	0.0:0.4005:0.2518:0.3477	.	82	Q8N0W7	FMR1N_HUMAN	M	82	ENSP00000359498:V82M	ENSP00000359498:V82M	V	+	1	0	FMR1NB	146870858	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.096000	0.03353	-0.436000	0.07254	-0.221000	0.12465	GTG		0.612	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058667.1	NM_152578	
SRPK3	26576	broad.mit.edu	37	X	153049494	153049494	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0650-01A-02D-1696-08	TCGA-06-0650-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	89af56db-b7f9-41d2-af62-c9b2ee7b540f	ed56d74a-781d-4408-9adc-9bfcfbe34585	g.chrX:153049494G>A	ENST00000370101.3	+	10	1019	c.973G>A	c.(973-975)Gcc>Acc	p.A325T	SRPK3_ENST00000370104.1_Missense_Mutation_p.A324T|SRPK3_ENST00000393786.3_Intron|SRPK3_ENST00000370100.1_Intron|SRPK3_ENST00000489426.1_Missense_Mutation_p.A392T|SRPK3_ENST00000370108.3_Intron	NM_001170760.1|NM_014370.3	NP_001164231.1|NP_055185.2	Q9UPE1	SRPK3_HUMAN	SRSF protein kinase 3	325	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|muscle tissue development (GO:0060537)|skeletal muscle tissue development (GO:0007519)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(2)|pancreas(2)|urinary_tract(1)	13	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCCGGGGGCGCCAGAGCAGG	0.697																																					Esophageal Squamous(167;766 3400 32156)	uc004fil.2																			0				pancreas(2)|lung(1)	3						c.(973-975)GCC>ACC		serine arginine rich protein-specific kinase 3							17.0	20.0	19.0					X																	153049494		2192	4289	6481	SO:0001583	missense	26576				cell differentiation|muscle organ development|muscle tissue development		ATP binding|protein serine/threonine kinase activity	g.chrX:153049494G>A	AF027406	CCDS35441.1, CCDS55537.1, CCDS55538.1	Xq28	2010-06-23	2010-06-23	2006-08-17	ENSG00000184343	ENSG00000184343			11402	protein-coding gene	gene with protein product			"""serine/threonine kinase 23"", ""SFRS protein kinase 3"""	STK23		16140986	Standard	NM_014370		Approved	MSSK1	uc004fil.3	Q9UPE1	OTTHUMG00000024207	ENST00000370101.3:c.973G>A	X.37:g.153049494G>A	ENSP00000359119:p.Ala325Thr					SRPK3_uc004fik.2_Missense_Mutation_p.A391T|SRPK3_uc010nul.2_Intron|SRPK3_uc004fin.2_Missense_Mutation_p.A324T|SRPK3_uc004fim.2_Intron	p.A325T	NM_014370	NP_055185	Q9UPE1	SRPK3_HUMAN			10	1005	+	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)		325			Protein kinase.		Q13583|Q4F970|Q562F5|Q9UM62	Missense_Mutation	SNP	ENST00000370101.3	37	c.973G>A	CCDS35441.1	.	.	.	.	.	.	.	.	.	.	G	4.071	0.010927	0.07912	.	.	ENSG00000184343	ENST00000489426;ENST00000370104;ENST00000370101	T;T;T	0.54675	0.56;0.57;0.57	4.52	-1.84	0.07809	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.263920	0.05604	N	0.576850	T	0.27027	0.0662	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.11941	-1.0567	10	0.13470	T	0.59	-9.5281	5.1664	0.15088	0.5196:0.1569:0.3235:0.0	.	324;325;392	Q9UPE1-4;Q9UPE1;E7ETV6	.;SRPK3_HUMAN;.	T	392;324;325	ENSP00000420058:A392T;ENSP00000359122:A324T;ENSP00000359119:A325T	ENSP00000359119:A325T	A	+	1	0	SRPK3	152702688	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.096000	0.11059	-0.927000	0.03766	-0.295000	0.09555	GCC		0.697	SRPK3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354501.1	NM_014370	
