#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
MS4A8	83661	broad.mit.edu	37	11	60470906	60470906	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr11:60470906C>T	ENST00000300226.2	+	3	478	c.275C>T	c.(274-276)aCg>aTg	p.T92M		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	92						integral component of membrane (GO:0016021)											ATCATGGCGACGGTTCTCGTA	0.552																																						uc001npv.2																			0					0						c.(274-276)ACG>ATG		membrane-spanning 4-domains, subfamily A, member							151.0	139.0	143.0					11																	60470906		2203	4300	6503	SO:0001583	missense	83661					integral to membrane	receptor activity	g.chr11:60470906C>T	AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"""membrane-spanning 4-domains, subfamily A, member 8B"""	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.275C>T	11.37:g.60470906C>T	ENSP00000300226:p.Thr92Met					MS4A8B_uc009yne.1_Missense_Mutation_p.T92M	p.T92M	NM_031457	NP_113645	Q9BY19	M4A8B_HUMAN			3	478	+			92			Helical; (Potential).		Q8TCA5	Missense_Mutation	SNP	ENST00000300226.2	37	c.275C>T	CCDS7990.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.36|11.36	1.615604|1.615604	0.28801|0.28801	.|.	.|.	ENSG00000166959|ENSG00000166959	ENST00000525458|ENST00000300226;ENST00000529752	.|T;T	.|0.02301	.|4.35;4.35	3.62|3.62	2.6|2.6	0.31112|0.31112	.|.	.|0.472817	.|0.19530	.|N	.|0.112065	T|T	0.03739|0.03739	0.0106|0.0106	L|L	0.41573|0.41573	1.285|1.285	0.09310|0.09310	N|N	1|1	.|D;D	.|0.69078	.|0.964;0.997	.|P;P	.|0.53102	.|0.557;0.718	T|T	0.45818|0.45818	-0.9235|-0.9235	5|10	.|0.31617	.|T	.|0.26	-14.2382|-14.2382	7.6502|7.6502	0.28344|0.28344	0.2522:0.7478:0.0:0.0|0.2522:0.7478:0.0:0.0	.|.	.|92;92	.|E9PQE1;Q9BY19	.|.;M4A8B_HUMAN	W|M	74|92	.|ENSP00000300226:T92M;ENSP00000436857:T92M	.|ENSP00000300226:T92M	R|T	+|+	1|2	2|0	MS4A8B|MS4A8B	60227482|60227482	0.001000|0.001000	0.12720|0.12720	0.011000|0.011000	0.14972|0.14972	0.004000|0.004000	0.04260|0.04260	0.804000|0.804000	0.27098|0.27098	1.745000|1.745000	0.51790|0.51790	0.491000|0.491000	0.48974|0.48974	CGG|ACG		0.552	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1		
PRB2	653247	broad.mit.edu	37	12	11546320	11546322	+	In_Frame_Del	DEL	TTG	TTG	-			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr12:11546320_11546322delTTG	ENST00000389362.4	-	3	725_727	c.690_692delCAA	c.(688-693)aacaag>aag	p.N230del	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	230	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACTTTGGGACTTGTTGTCTCCTT	0.601																																						uc010shk.1																			0					0						c.(688-693)AACAAG>AAG		proline-rich protein BstNI subfamily 2																																				SO:0001651	inframe_deletion	653247							g.chr12:11546320_11546322delTTG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.690_692delCAA	12.37:g.11546323_11546325delTTG	ENSP00000374013:p.Asn230del						p.N230del	NM_006248	NP_006239			OV - Ovarian serous cystadenocarcinoma(49;0.185)		3	725_727	-		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)						O00599|P02811|P04281	In_Frame_Del	DEL	ENST00000389362.4	37	c.690_692delCAA	CCDS41757.2																																																																																				0.601	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
RYR3	6263	broad.mit.edu	37	15	34105755	34105755	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr15:34105755A>G	ENST00000389232.4	+	74	10547	c.10477A>G	c.(10477-10479)Atg>Gtg	p.M3493V	RYR3_ENST00000415757.3_Missense_Mutation_p.M3488V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3493	Interaction with CALM. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTGTTTCAGGATGGCCCCTCT	0.527																																						uc001zhi.2																			0				ovary(5)|central_nervous_system(4)|lung(1)	10						c.(10477-10479)ATG>GTG		ryanodine receptor 3							124.0	121.0	122.0					15																	34105755		1939	4127	6066	SO:0001583	missense	6263				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr15:34105755A>G		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10477A>G	15.37:g.34105755A>G	ENSP00000373884:p.Met3493Val					RYR3_uc010bar.2_Missense_Mutation_p.M3488V	p.M3493V	NM_001036	NP_001027	Q15413	RYR3_HUMAN		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	74	10547	+		all_lung(180;7.18e-09)	3493					O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	c.10477A>G	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504171	0.64410	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.97041	-4.22	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.98108	0.9376	M	0.75085	2.285	0.58432	D	0.999997	P;D	0.61080	0.917;0.989	D;D	0.74348	0.915;0.983	D	0.99066	1.0832	10	0.72032	D	0.01	.	15.0106	0.71547	1.0:0.0:0.0:0.0	.	3488;3493	Q15413-2;Q15413	.;RYR3_HUMAN	V	3493;3493;3488	ENSP00000373884:M3493V	ENSP00000354735:M3488V	M	+	1	0	RYR3	31893047	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.087000	0.94110	2.123000	0.65237	0.533000	0.62120	ATG		0.527	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
THBS1	7057	broad.mit.edu	37	15	39874573	39874573	+	Missense_Mutation	SNP	C	C	T	rs571353083		TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr15:39874573C>T	ENST00000260356.5	+	3	412	c.247C>T	c.(247-249)Cgg>Tgg	p.R83W		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	83	Heparin-binding.|Laminin G-like.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GGATGCTGTGCGGGCAGAAAA	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		19259	0.001		0.0	False		,,,				2504	0.0					uc001zkh.2																			0				ovary(3)|central_nervous_system(3)	6						c.(247-249)CGG>TGG		thrombospondin 1 precursor	Becaplermin(DB00102)						62.0	58.0	60.0					15																	39874573		2200	4297	6497	SO:0001583	missense	7057				activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding	g.chr15:39874573C>T		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.247C>T	15.37:g.39874573C>T	ENSP00000260356:p.Arg83Trp						p.R83W	NM_003246	NP_003237	P07996	TSP1_HUMAN		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	3	426	+		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)	83			TSP N-terminal.|Heparin-binding.		A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	c.247C>T	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.162114	0.57368	.	.	ENSG00000137801	ENST00000260356;ENST00000397591	T;T	0.02236	4.38;4.38	5.28	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.247598	0.21277	N	0.077205	T	0.03348	0.0097	L	0.54323	1.7	0.45097	D	0.998117	D	0.63880	0.993	B	0.40825	0.341	T	0.57688	-0.7768	10	0.40728	T	0.16	-16.0528	12.8047	0.57607	0.0:0.9219:0.0:0.0781	.	83	P07996	TSP1_HUMAN	W	83	ENSP00000260356:R83W;ENSP00000380720:R83W	ENSP00000260356:R83W	R	+	1	2	THBS1	37661865	1.000000	0.71417	0.995000	0.50966	0.610000	0.37248	3.021000	0.49651	1.453000	0.47775	0.563000	0.77884	CGG		0.617	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
PAQR5	54852	broad.mit.edu	37	15	69652448	69652448	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr15:69652448T>C	ENST00000340965.3	+	3	697	c.29T>C	c.(28-30)tTt>tCt	p.F10S	PAQR5_ENST00000561153.1_Missense_Mutation_p.F10S|PAQR5_ENST00000395407.2_Missense_Mutation_p.F10S|PAQR5_ENST00000561027.1_3'UTR	NM_001104554.1	NP_001098024.1	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	10					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)|steroid binding (GO:0005496)			endometrium(3)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|skin(1)	11						CCCAGGCTGTTTAGCATAGAC	0.542																																						uc002arz.2																			0				ovary(2)	2						c.(28-30)TTT>TCT		progestin and adipoQ receptor family member V							138.0	123.0	128.0					15																	69652448		2200	4298	6498	SO:0001583	missense	54852				cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding	g.chr15:69652448T>C		CCDS10232.1	15q22.31	2012-08-10			ENSG00000137819	ENSG00000137819			29645	protein-coding gene	gene with protein product	"""membrane progestin receptor gamma"""	607781				12574519	Standard	NM_001104554		Approved	FLJ20190, MPRG	uc002arz.2	Q9NXK6	OTTHUMG00000133322	ENST00000340965.3:c.29T>C	15.37:g.69652448T>C	ENSP00000343877:p.Phe10Ser					PAQR5_uc002asa.2_Missense_Mutation_p.F10S	p.F10S	NM_017705	NP_060175	Q9NXK6	MPRG_HUMAN			3	407	+			10			Cytoplasmic (Potential).		Q8IXU2	Missense_Mutation	SNP	ENST00000340965.3	37	c.29T>C	CCDS10232.1	.	.	.	.	.	.	.	.	.	.	T	7.344	0.621561	0.14193	.	.	ENSG00000137819	ENST00000395407;ENST00000340965	T;T	0.22743	1.94;1.94	5.02	3.89	0.44902	.	0.715119	0.14464	N	0.317987	T	0.24392	0.0591	M	0.65975	2.015	0.09310	N	1	B	0.26775	0.159	B	0.29353	0.101	T	0.22487	-1.0215	10	0.72032	D	0.01	-2.5843	8.02	0.30404	0.1806:0.0:0.0:0.8194	.	10	Q9NXK6	MPRG_HUMAN	S	10	ENSP00000378803:F10S;ENSP00000343877:F10S	ENSP00000343877:F10S	F	+	2	0	PAQR5	67439502	0.147000	0.22687	0.031000	0.17742	0.033000	0.12548	3.334000	0.52097	0.921000	0.36994	-0.516000	0.04426	TTT		0.542	PAQR5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416671.1	NM_017705	
CLEC3A	10143	broad.mit.edu	37	16	78064695	78064695	+	Missense_Mutation	SNP	G	G	A	rs201495730		TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr16:78064695G>A	ENST00000575655.1	+	3	632	c.551G>A	c.(550-552)cGc>cAc	p.R184H	CLEC3A_ENST00000299642.4_Missense_Mutation_p.R193H|RP11-281J9.2_ENST00000563114.1_RNA|CLEC3A_ENST00000565808.1_3'UTR	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	184	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						GAGGCCTGTCGCAGCAGCAAG	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		19546	0.001		0.0	False		,,,				2504	0.0					uc002ffh.3																			0					0						c.(550-552)CGC>CAC		C-type lectin domain family 3 member A							94.0	94.0	94.0					16																	78064695		2198	4300	6498	SO:0001583	missense	10143				skeletal system development	extracellular region	sugar binding	g.chr16:78064695G>A	AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"""C-type lectin domain containing"""	2052	protein-coding gene	gene with protein product		613588	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"""	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.551G>A	16.37:g.78064695G>A	ENSP00000460682:p.Arg184His						p.R184H	NM_005752	NP_005743	O75596	CLC3A_HUMAN			3	632	+			184			C-type lectin.		B2R8C4|Q3SX91|Q6UXF5	Missense_Mutation	SNP	ENST00000575655.1	37	c.551G>A		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	18.22	3.575240	0.65878	.	.	ENSG00000166509	ENST00000299642	.	.	.	6.07	5.13	0.70059	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.045357	0.85682	N	0.000000	T	0.59348	0.2187	L	0.52905	1.665	0.80722	D	1	B	0.16166	0.016	B	0.15484	0.013	T	0.58393	-0.7644	9	0.62326	D	0.03	-9.969	15.0897	0.72183	0.0682:0.0:0.9318:0.0	.	184	O75596	CLC3A_HUMAN	H	184	.	ENSP00000299642:R184H	R	+	2	0	CLEC3A	76622196	1.000000	0.71417	0.968000	0.41197	0.717000	0.41224	5.489000	0.66875	1.586000	0.49944	0.655000	0.94253	CGC		0.493	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005752	
HOXB5	3215	broad.mit.edu	37	17	46670992	46670992	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr17:46670992T>C	ENST00000239151.5	-	1	331	c.53A>G	c.(52-54)gAc>gGc	p.D18G	HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000467155.2_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	18					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						CAACTGATAGTCCGGGCCATT	0.507																																						uc002inr.2																			0					0						c.(52-54)GAC>GGC		homeobox B5							48.0	50.0	49.0					17																	46670992		1951	3900	5851	SO:0001583	missense	3215					nucleus	sequence-specific DNA binding	g.chr17:46670992T>C		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"""Homeoboxes / ANTP class : HOXL subclass"""	5116	protein-coding gene	gene with protein product		142960	"""homeo box B5"""	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.53A>G	17.37:g.46670992T>C	ENSP00000239151:p.Asp18Gly						p.D18G	NM_002147	NP_002138	P09067	HXB5_HUMAN			1	112	-			18					B2RC69|P09069|Q17RP4	Missense_Mutation	SNP	ENST00000239151.5	37	c.53A>G	CCDS11530.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.118777	0.56505	.	.	ENSG00000120075	ENST00000239151	D	0.93763	-3.28	5.44	5.44	0.79542	.	0.057310	0.64402	D	0.000003	D	0.94823	0.8328	M	0.90425	3.115	0.80722	D	1	P	0.46784	0.884	B	0.43274	0.414	D	0.95627	0.8686	10	0.87932	D	0	.	15.4969	0.75662	0.0:0.0:0.0:1.0	.	18	P09067	HXB5_HUMAN	G	18	ENSP00000239151:D18G	ENSP00000239151:D18G	D	-	2	0	HOXB5	44025991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.062000	0.61559	0.454000	0.30748	GAC		0.507	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2		
FUT3	2525	broad.mit.edu	37	19	5844280	5844280	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr19:5844280C>T	ENST00000303225.6	-	3	1205	c.571G>A	c.(571-573)Gag>Aag	p.E191K	FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.E191K|FUT3_ENST00000589918.1_Missense_Mutation_p.E191K|FUT3_ENST00000589620.1_Missense_Mutation_p.E191K	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	191					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						GCCACCAGCTCGGTCTTGGCC	0.667																																					Esophageal Squamous(82;745 1728 24593 44831)	uc002mdk.2																			0					0						c.(571-573)GAG>AAG		fucosyltransferase 3							28.0	30.0	29.0					19																	5844280		2202	4297	6499	SO:0001583	missense	2525				protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity	g.chr19:5844280C>T		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.571G>A	19.37:g.5844280C>T	ENSP00000305603:p.Glu191Lys					FUT3_uc002mdm.2_Missense_Mutation_p.E191K|FUT3_uc002mdj.2_Missense_Mutation_p.E191K|FUT3_uc002mdl.2_Missense_Mutation_p.E191K	p.E191K	NM_001097641	NP_001091110	P21217	FUT3_HUMAN			2	668	-			191			Lumenal (Potential).		B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	c.571G>A	CCDS12153.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.869945	0.00542	.	.	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.18960	2.18;2.18	1.89	-1.56	0.08532	.	0.330873	0.24516	N	0.037846	T	0.03695	0.0105	N	0.00661	-1.28	0.25328	N	0.989056	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.003;0.003;0.003	T	0.37502	-0.9703	10	0.02654	T	1	.	6.0579	0.19822	0.0:0.28:0.0:0.72	.	191;191;191;191	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	K	191	ENSP00000305603:E191K;ENSP00000416443:E191K	ENSP00000305603:E191K	E	-	1	0	FUT3	5795280	0.000000	0.05858	0.966000	0.40874	0.084000	0.17831	-0.477000	0.06583	-0.576000	0.05974	0.194000	0.17425	GAG		0.667	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
MUC16	94025	broad.mit.edu	37	19	9003616	9003616	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr19:9003616G>A	ENST00000397910.4	-	49	40227	c.40024C>T	c.(40024-40026)Cgc>Tgc	p.R13342C	MUC16_ENST00000380951.5_5'Flank	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13344	SEA 9. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGCCAGGGCGACGCATGTCC	0.552																																						uc002mkp.2																			0				lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						c.(40024-40026)CGC>TGC		mucin 16							246.0	203.0	217.0					19																	9003616		2034	4185	6219	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9003616G>A	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40024C>T	19.37:g.9003616G>A	ENSP00000381008:p.Arg13342Cys					MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.R159C|MUC16_uc010xki.1_Intron	p.R13342C	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			49	40228	-			13344			Extracellular (Potential).|SEA 9.		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.40024C>T	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	7.339	0.620604	0.14193	.	.	ENSG00000181143	ENST00000397910	T	0.29917	1.55	3.24	-1.05	0.10036	SEA (1);	.	.	.	.	T	0.45558	0.1348	M	0.73598	2.24	.	.	.	P;D	0.65815	0.938;0.995	P;D	0.69307	0.469;0.963	T	0.50725	-0.8794	8	0.87932	D	0	0.0858	3.0157	0.06059	0.3282:0.2321:0.4396:0.0	.	20987;13342	Q8WXI7;B5ME49	MUC16_HUMAN;.	C	13342	ENSP00000381008:R13342C	ENSP00000381008:R13342C	R	-	1	0	MUC16	8864616	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.421000	0.07053	0.092000	0.17331	0.455000	0.32223	CGC		0.552	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CCDC37	348807	broad.mit.edu	37	3	126133023	126133023	+	Splice_Site	SNP	G	G	A	rs150312379	byFrequency	TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr3:126133023G>A	ENST00000352312.1	+	4	324		c.e4+1		CCDC37_ENST00000510833.1_Missense_Mutation_p.V76M|CCDC37_ENST00000505024.1_Splice_Site|CCDC37_ENST00000393425.1_Splice_Site	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37											NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GGCTCTCTCCGTGAGTATCCA	0.557													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19671	0.0		0.0	False		,,,				2504	0.0					uc003eiu.1																			0				ovary(1)|skin(1)	2						c.e4+1		coiled-coil domain containing 37		G		2,4404	4.2+/-10.8	0,2,2201	149.0	148.0	148.0			4.6	0.9	3	dbSNP_134	148	0,8600		0,0,4300	yes	splice-5	CCDC37	NM_182628.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154			126133023	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	348807							g.chr3:126133023G>A	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.225+1G>A	3.37:g.126133023G>A						CCDC37_uc010hsg.1_Splice_Site_p.S75_splice	p.S75_splice	NM_182628	NP_872434	Q494V2	CCD37_HUMAN		GBM - Glioblastoma multiforme(114;0.166)	4	324	+								D3DNA8|Q494V1|Q494V4|Q8N838	Splice_Site	SNP	ENST00000352312.1	37	c.225_splice	CCDS3037.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	10.09|10.09	1.256253|1.256253	0.22965|0.22965	4.54E-4|4.54E-4	0.0|0.0	ENSG00000163885|ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024|ENST00000510833	.|.	.|.	.|.	4.6|4.6	4.6|4.6	0.57074|0.57074	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68760	.|0.3036	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.67106	.|-0.5754	.|4	.|.	.|.	.|.	.|.	13.6375|13.6375	0.62230|0.62230	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	.|M	-1|76	.|.	.|.	.|V	+|+	.|1	.|0	CCDC37|CCDC37	127615713|127615713	0.995000|0.995000	0.38212|0.38212	0.920000|0.920000	0.36463|0.36463	0.007000|0.007000	0.05969|0.05969	2.972000|2.972000	0.49256|0.49256	2.502000|2.502000	0.84385|0.84385	0.585000|0.585000	0.79938|0.79938	.|GTG		0.557	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	Intron
PCDHA1	56147	broad.mit.edu	37	5	140167216	140167216	+	Silent	SNP	C	C	T	rs369392034		TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr5:140167216C>T	ENST00000504120.2	+	1	1341	c.1341C>T	c.(1339-1341)gaC>gaT	p.D447D	PCDHA1_ENST00000378133.3_Silent_p.D447D|PCDHA1_ENST00000394633.3_Silent_p.D447D	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	447	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGGCCGACGTGAATGACA	0.667																																						uc003lhb.2																			0				skin(1)	1						c.(1339-1341)GAC>GAT		protocadherin alpha 1 isoform 1 precursor							77.0	81.0	80.0					5																	140167216		2203	4299	6502	SO:0001819	synonymous_variant	56147				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding	g.chr5:140167216C>T	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1341C>T	5.37:g.140167216C>T						PCDHA1_uc003lha.2_Silent_p.D447D|PCDHA1_uc003lgz.2_Silent_p.D447D	p.D447D	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1341	+			447			Cadherin 4.|Extracellular (Potential).		O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	c.1341C>T	CCDS54913.1																																																																																				0.667	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
PPARGC1B	133522	broad.mit.edu	37	5	149210432	149210432	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr5:149210432C>T	ENST00000309241.5	+	4	600	c.568C>T	c.(568-570)Cgg>Tgg	p.R190W	PPARGC1B_ENST00000360453.4_Intron|PPARGC1B_ENST00000403750.1_Intron|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.R190W	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	190					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TAAAAGTCAACGGCCTTGTGT	0.562																																						uc003lrc.2																			0					0						c.(568-570)CGG>TGG		peroxisome proliferator-activated receptor							92.0	93.0	93.0					5																	149210432		2203	4300	6503	SO:0001583	missense	133522				estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity	g.chr5:149210432C>T	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.568C>T	5.37:g.149210432C>T	ENSP00000312649:p.Arg190Trp					PPARGC1B_uc003lrb.1_Missense_Mutation_p.R190W|PPARGC1B_uc003lrd.2_Intron|PPARGC1B_uc003lrf.2_Missense_Mutation_p.R169W|PPARGC1B_uc003lre.1_Missense_Mutation_p.R169W	p.R190W	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		4	610	+			190					A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	c.568C>T	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.797741	0.70567	.	.	ENSG00000155846	ENST00000394320;ENST00000309241	T;T	0.13307	2.6;2.62	5.29	2.23	0.28157	.	0.373012	0.25625	N	0.029394	T	0.32734	0.0839	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.971;0.971;0.936;0.999	T	0.09185	-1.0686	10	0.72032	D	0.01	-9.4841	13.6285	0.62181	0.4044:0.5956:0.0:0.0	.	169;169;190;190	Q86YN6-2;Q86YN6-4;Q86YN6;Q86YN6-3	.;.;PRGC2_HUMAN;.	W	190	ENSP00000377855:R190W;ENSP00000312649:R190W	ENSP00000312649:R190W	R	+	1	2	PPARGC1B	149190625	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	1.608000	0.36847	0.665000	0.31066	0.561000	0.74099	CGG		0.562	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
TDRD6	221400	broad.mit.edu	37	6	46658843	46658843	+	Missense_Mutation	SNP	C	C	T	rs369734344		TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr6:46658843C>T	ENST00000316081.6	+	1	2978	c.2978C>T	c.(2977-2979)aCg>aTg	p.T993M	RP11-446F17.3_ENST00000434329.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.T993M	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	993					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GTTTATATAACGCATATTGAT	0.333																																						uc003oyj.2																			0				breast(3)|ovary(2)|skin(1)	6						c.(2977-2979)ACG>ATG		tudor domain containing 6		C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	50.0	54.0	53.0		2978,2978	5.4	0.9	6		53	0,8598		0,0,4299	no	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	81,81	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	993/2097,993/2067	46658843	1,13003	2203	4299	6502	SO:0001583	missense	221400				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding	g.chr6:46658843C>T	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.2978C>T	6.37:g.46658843C>T	ENSP00000346065:p.Thr993Met					TDRD6_uc010jze.2_Missense_Mutation_p.T987M	p.T993M	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	Lung(136;0.192)		1	2978	+			993					B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	c.2978C>T	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527533	0.64860	2.27E-4	0.0	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.11930	2.73;2.73	5.36	5.36	0.76844	Maternal tudor protein (1);	0.097072	0.64402	D	0.000001	T	0.41903	0.1179	M	0.91972	3.26	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.54268	-0.8319	10	0.66056	D	0.02	0.0033	19.0785	0.93173	0.0:1.0:0.0:0.0	.	993;993	F5H5M3;O60522	.;TDRD6_HUMAN	M	993	ENSP00000443299:T993M;ENSP00000346065:T993M	ENSP00000346065:T993M	T	+	2	0	TDRD6	46766802	1.000000	0.71417	0.864000	0.33941	0.761000	0.43186	7.456000	0.80751	2.498000	0.84270	0.655000	0.94253	ACG		0.333	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
RAMP3	10268	broad.mit.edu	37	7	45222997	45222997	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr7:45222997G>A	ENST00000242249.4	+	3	471	c.433G>A	c.(433-435)Gac>Aac	p.D145N	RAMP3_ENST00000481345.1_Missense_Mutation_p.D145N|RAMP3_ENST00000496212.1_Missense_Mutation_p.D145N	NM_005856.2	NP_005847.1	O60896	RAMP3_HUMAN	receptor (G protein-coupled) activity modifying protein 3	145					calcium ion transport (GO:0006816)|cellular response to estradiol stimulus (GO:0071392)|G-protein coupled receptor signaling pathway involved in heart process (GO:0086103)|intracellular protein transport (GO:0006886)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of receptor recycling (GO:0001921)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.D145N(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	11					Pramlintide(DB01278)	CAAACGCACCGACACGCTGCT	0.627																																						uc003tnb.2																			1	Substitution - Missense(1)		large_intestine(1)		0						c.(433-435)GAC>AAC		receptor activity modifying protein 3 precursor	Pramlintide(DB01278)						97.0	89.0	92.0					7																	45222997		2203	4300	6503	SO:0001583	missense	10268				intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity	g.chr7:45222997G>A	AJ001016	CCDS5503.1	7p13-p12	2006-11-21	2006-11-21		ENSG00000122679	ENSG00000122679		"""Receptor (G protein-coupled) activity modifying proteins"""	9845	protein-coding gene	gene with protein product		605155	"""receptor activity modifying protein 3"", ""receptor (calcitonin) activity modifying protein 3"""				Standard	NM_005856		Approved		uc003tnb.3	O60896	OTTHUMG00000023729	ENST00000242249.4:c.433G>A	7.37:g.45222997G>A	ENSP00000242249:p.Asp145Asn					RAMP3_uc003tnc.2_Missense_Mutation_p.D113N	p.D145N	NM_005856	NP_005847	O60896	RAMP3_HUMAN			3	494	+			145			Cytoplasmic (Potential).		Q7Z2Y1	Missense_Mutation	SNP	ENST00000242249.4	37	c.433G>A	CCDS5503.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149725	0.78001	.	.	ENSG00000122679	ENST00000242249;ENST00000481345;ENST00000496212	T;T;T	0.45668	0.89;0.89;0.89	4.37	3.46	0.39613	.	0.163209	0.52532	D	0.000077	T	0.62036	0.2395	M	0.78801	2.425	0.47994	D	0.999569	D	0.89917	1.0	D	0.69307	0.963	T	0.65429	-0.6170	10	0.72032	D	0.01	-25.0987	11.8561	0.52437	0.0:0.1786:0.8214:0.0	.	145	O60896	RAMP3_HUMAN	N	145	ENSP00000242249:D145N;ENSP00000419012:D145N;ENSP00000418460:D145N	ENSP00000242249:D145N	D	+	1	0	RAMP3	45189522	1.000000	0.71417	0.002000	0.10522	0.003000	0.03518	5.299000	0.65716	0.779000	0.33543	0.655000	0.94253	GAC		0.627	RAMP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251343.1	NM_005856	
TLR4	7099	broad.mit.edu	37	9	120466768	120466768	+	Silent	SNP	C	C	G			TCGA-06-0240-01A-03D-1491-08	TCGA-06-0240-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	20f74001-1cb8-451d-8173-5795fa93432b	276d21da-719b-4970-8733-aa745d09281a	g.chr9:120466768C>G	ENST00000355622.6	+	1	119	c.18C>G	c.(16-18)cgC>cgG	p.R6R	TLR4_ENST00000394487.4_5'UTR|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	6					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	CTGCCTCGCGCCTGGCTGGGA	0.602																																						uc004bjz.2																			0				lung(10)|ovary(4)|breast(1)|skin(1)	16						c.(16-18)CGC>CGG		toll-like receptor 4 precursor							66.0	63.0	64.0					9																	120466768		2203	4300	6503	SO:0001819	synonymous_variant	7099				activation of MAPK activity|cellular response to mechanical stimulus|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity	g.chr9:120466768C>G	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.18C>G	9.37:g.120466768C>G						TLR4_uc004bka.2_5'UTR|TLR4_uc004bkb.2_5'UTR	p.R6R	NM_138554	NP_612564	O00206	TLR4_HUMAN			1	309	+			6					A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Silent	SNP	ENST00000355622.6	37	c.18C>G	CCDS6818.1																																																																																				0.602	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
