#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
MTOR	2475	broad.mit.edu	37	1	11217231	11217231	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:11217231A>G	ENST00000361445.4	-	30	4523	c.4447T>C	c.(4447-4449)Tgc>Cgc	p.C1483R		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1483	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	GCCTCGAGGCAGCGCATGCGG	0.527																																						uc001asd.2																			0				central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						c.(4447-4449)TGC>CGC		FK506 binding protein 12-rapamycin associated							191.0	178.0	182.0					1																	11217231		2203	4300	6503	SO:0001583	missense	2475				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity	g.chr1:11217231A>G	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4447T>C	1.37:g.11217231A>G	ENSP00000354558:p.Cys1483Arg						p.C1483R	NM_004958	NP_004949	P42345	MTOR_HUMAN			30	4568	-			1483			FAT.		Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	c.4447T>C	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386530	0.82902	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.70045	-0.45	5.32	5.32	0.75619	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82042	0.4951	M	0.91920	3.255	0.80722	D	1	D	0.59357	0.985	P	0.55055	0.767	D	0.86805	0.1994	10	0.87932	D	0	-11.9694	15.2808	0.73784	1.0:0.0:0.0:0.0	.	1483	P42345	MTOR_HUMAN	R	1483	ENSP00000354558:C1483R	ENSP00000354558:C1483R	C	-	1	0	MTOR	11139818	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.871000	0.92346	2.011000	0.59026	0.533000	0.62120	TGC		0.527	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
KIF17	57576	broad.mit.edu	37	1	21031072	21031072	+	Missense_Mutation	SNP	G	G	A	rs139912475		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:21031072G>A	ENST00000247986.2	-	5	1301	c.991C>T	c.(991-993)Cgg>Tgg	p.R331W	KIF17_ENST00000375044.1_Missense_Mutation_p.R231W|KIF17_ENST00000400463.3_Missense_Mutation_p.R331W			Q9P2E2	KIF17_HUMAN	kinesin family member 17	331	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TTCTTGGCCCGGTTGGCGTAG	0.597																																						uc001bdr.3																			0				ovary(3)|skin(1)	4						c.(991-993)CGG>TGG		kinesin family member 17 isoform a		G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	165.0	125.0	138.0		991,991	3.2	1.0	1	dbSNP_134	138	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	331/1029,331/1030	21031072	1,13005	2203	4300	6503	SO:0001583	missense	57576				microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding	g.chr1:21031072G>A	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.991C>T	1.37:g.21031072G>A	ENSP00000247986:p.Arg331Trp					KIF17_uc001bds.3_Missense_Mutation_p.R331W	p.R331W	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)	5	1109	-		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)	331					A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	c.991C>T	CCDS213.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960050	0.74016	0.0	1.16E-4	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.79033	-1.23;-1.23;-1.23	5.26	3.21	0.36854	Kinesin, motor domain (3);	0.282457	0.17911	U	0.157832	D	0.92857	0.7728	H	0.99863	4.86	0.52501	D	0.99995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92581	0.6074	10	0.87932	D	0	.	9.0289	0.36247	0.0748:0.0:0.658:0.2672	.	331;331	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	W	231;331;331	ENSP00000364184:R231W;ENSP00000383311:R331W;ENSP00000247986:R331W	ENSP00000247986:R331W	R	-	1	2	KIF17	20903659	1.000000	0.71417	0.989000	0.46669	0.911000	0.54048	2.815000	0.48018	1.300000	0.44818	0.462000	0.41574	CGG		0.597	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
ELTD1	64123	broad.mit.edu	37	1	79412033	79412033	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:79412033C>G	ENST00000370742.3	-	3	314	c.251G>C	c.(250-252)tGt>tCt	p.C84S		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	84	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.C84Y(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TACACACATACAATAATAACT	0.363																																						uc001diq.3																			1	Substitution - Missense(1)		lung(1)	ovary(1)|skin(1)	2						c.(250-252)TGT>TCT		EGF, latrophilin and seven transmembrane domain							92.0	88.0	89.0					1																	79412033		1891	4120	6011	SO:0001583	missense	64123				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity	g.chr1:79412033C>G	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.251G>C	1.37:g.79412033C>G	ENSP00000359778:p.Cys84Ser						p.C84S	NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN		COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)	3	407	-			84			Extracellular (Potential).|EGF-like 2; calcium-binding (Potential).		B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	c.251G>C	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.343186	0.82022	.	.	ENSG00000162618	ENST00000370742	D	0.99429	-5.89	5.03	5.03	0.67393	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99739	0.9897	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97177	0.9848	9	.	.	.	.	18.3639	0.90384	0.0:1.0:0.0:0.0	.	84	Q9HBW9	ELTD1_HUMAN	S	84	ENSP00000359778:C84S	.	C	-	2	0	ELTD1	79184621	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.837000	0.69381	2.324000	0.78689	0.650000	0.86243	TGT		0.363	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
ABCA4	24	broad.mit.edu	37	1	94543367	94543367	+	Missense_Mutation	SNP	A	A	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:94543367A>T	ENST00000370225.3	-	11	1519	c.1433T>A	c.(1432-1434)aTc>aAc	p.I478N	ABCA4_ENST00000535735.1_Missense_Mutation_p.I478N	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	478					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GAAGTTTAGGATGGCTTCAGC	0.493																																						uc001dqh.2																			0				ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12						c.(1432-1434)ATC>AAC		ATP-binding cassette, sub-family A member 4							177.0	170.0	172.0					1																	94543367		2203	4300	6503	SO:0001583	missense	24				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances	g.chr1:94543367A>T	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1433T>A	1.37:g.94543367A>T	ENSP00000359245:p.Ile478Asn					ABCA4_uc010otn.1_Missense_Mutation_p.I478N	p.I478N	NM_000350	NP_000341	P78363	ABCA4_HUMAN		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)	11	1537	-		all_lung(203;0.000757)|Lung NSC(277;0.00335)	478			Extracellular.		O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	c.1433T>A	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.121902	0.56613	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.85339	-1.97;-1.97	5.24	2.71	0.32032	.	0.413350	0.24647	N	0.036749	D	0.83677	0.5306	M	0.73217	2.22	0.09310	N	1	P;B	0.52316	0.952;0.242	P;B	0.59056	0.851;0.105	T	0.76992	-0.2753	10	0.87932	D	0	.	8.4317	0.32761	0.815:0.0:0.185:0.0	.	478;478	F5H6E5;P78363	.;ABCA4_HUMAN	N	478	ENSP00000359245:I478N;ENSP00000437682:I478N	ENSP00000359245:I478N	I	-	2	0	ABCA4	94315955	0.268000	0.24133	0.000000	0.03702	0.877000	0.50540	4.636000	0.61339	0.357000	0.24183	0.533000	0.62120	ATC		0.493	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ATP1A2	477	broad.mit.edu	37	1	160106156	160106156	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:160106156G>C	ENST00000361216.3	+	18	2648	c.2559G>C	c.(2557-2559)caG>caC	p.Q853H	ATP1A2_ENST00000392233.3_Missense_Mutation_p.Q853H	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	853					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCTACGGACAGATCGGTGCGC	0.577																																						uc001fvc.2																			0				central_nervous_system(3)|ovary(2)|skin(2)	7						c.(2557-2559)CAG>CAC		Na+/K+ -ATPase alpha 2 subunit proprotein							63.0	64.0	64.0					1																	160106156		2203	4300	6503	SO:0001583	missense	477				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity	g.chr1:160106156G>C	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2559G>C	1.37:g.160106156G>C	ENSP00000354490:p.Gln853His					ATP1A2_uc001fvb.2_Missense_Mutation_p.Q853H|ATP1A2_uc001fvd.2_Missense_Mutation_p.Q589H	p.Q853H	NM_000702	NP_000693	P50993	AT1A2_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)		18	2691	+	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		853			Helical; (Potential).		D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	c.2559G>C	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.78|14.78	2.636324|2.636324	0.47049|0.47049	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866|ENST00000447527	D;D|.	0.95980|.	-3.87;-3.87|.	4.71|4.71	3.79|3.79	0.43588|0.43588	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.65801|0.65801	0.2726|0.2726	M|M	0.75264|0.75264	2.295|2.295	0.58432|0.58432	D|D	0.999996|0.999996	D;D|.	0.65815|.	0.993;0.995|.	D;D|.	0.72982|.	0.943;0.979|.	T|T	0.65981|0.65981	-0.6036|-0.6036	10|5	0.41790|.	T|.	0.15|.	.|.	12.5214|12.5214	0.56060|0.56060	0.0875:0.0:0.9125:0.0|0.0875:0.0:0.9125:0.0	.|.	753;853|.	F5GXJ7;P50993|.	.;AT1A2_HUMAN|.	H|T	853;853;556|564	ENSP00000354490:Q853H;ENSP00000376066:Q853H|.	ENSP00000354490:Q853H|.	Q|R	+|+	3|2	2|0	ATP1A2|ATP1A2	158372780|158372780	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	2.447000|2.447000	0.44917|0.44917	2.590000|2.590000	0.87494|0.87494	0.561000|0.561000	0.74099|0.74099	CAG|AGA		0.577	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
DUSP27	92235	broad.mit.edu	37	1	167064116	167064116	+	Silent	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:167064116G>A	ENST00000361200.2	+	2	196	c.30G>A	c.(28-30)gaG>gaA	p.E10E	DUSP27_ENST00000271385.5_Silent_p.E10E|DUSP27_ENST00000443333.1_Silent_p.E10E			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	10					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CAGAGGAGGAGCAGGTAGTCC	0.547																																						uc001geb.1																			0				ovary(3)	3						c.(28-30)GAG>GAA		dual specificity phosphatase 27							64.0	54.0	58.0					1																	167064116		2203	4300	6503	SO:0001819	synonymous_variant	92235				protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity	g.chr1:167064116G>A	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.30G>A	1.37:g.167064116G>A							p.E10E	NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN			1	30	+			10					A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	37	c.30G>A	CCDS30932.1																																																																																				0.547	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
DUSP27	92235	broad.mit.edu	37	1	167095182	167095182	+	Missense_Mutation	SNP	C	C	T	rs370272310		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:167095182C>T	ENST00000361200.2	+	6	980	c.814C>T	c.(814-816)Cgg>Tgg	p.R272W	DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_Missense_Mutation_p.R272W|DUSP27_ENST00000443333.1_Missense_Mutation_p.R272W			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	272					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GAAGCAGCTGCGGGAGCTCAA	0.582																																						uc001geb.1																			0				ovary(3)	3						c.(814-816)CGG>TGG		dual specificity phosphatase 27							68.0	70.0	70.0					1																	167095182		2203	4300	6503	SO:0001583	missense	92235				protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity	g.chr1:167095182C>T	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.814C>T	1.37:g.167095182C>T	ENSP00000354483:p.Arg272Trp						p.R272W	NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN			5	814	+			272					A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	c.814C>T	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.123181	0.77436	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	D;D;D	0.85955	-2.05;-2.05;-2.05	5.55	4.56	0.56223	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.92338	0.7569	M	0.86178	2.8	0.48135	D	0.999591	D	0.89917	1.0	D	0.97110	1.0	D	0.93238	0.6623	10	0.87932	D	0	-28.794	17.7161	0.88337	0.1623:0.8377:0.0:0.0	.	272	Q5VZP5	DUS27_HUMAN	W	272	ENSP00000354483:R272W;ENSP00000271385:R272W;ENSP00000404874:R272W	ENSP00000271385:R272W	R	+	1	2	DUSP27	165361806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.003000	0.40844	2.593000	0.87608	0.643000	0.83706	CGG		0.582	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
NLRP3	114548	broad.mit.edu	37	1	247587535	247587535	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr1:247587535G>T	ENST00000336119.3	+	3	1536	c.790G>T	c.(790-792)Gtg>Ttg	p.V264L	NLRP3_ENST00000391828.3_Missense_Mutation_p.V264L|NLRP3_ENST00000366497.2_Missense_Mutation_p.V264L|NLRP3_ENST00000391827.2_Missense_Mutation_p.V264L|NLRP3_ENST00000348069.2_Missense_Mutation_p.V264L|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366496.2_Missense_Mutation_p.V264L	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	264	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CTGTCGAGAGGTGAGCCTTGT	0.537																																						uc001icr.2																			0				lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26						c.(790-792)GTG>TTG		NLR family, pyrin domain containing 3 isoform a							68.0	68.0	68.0					1																	247587535		2203	4300	6503	SO:0001583	missense	114548				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding	g.chr1:247587535G>T	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.790G>T	1.37:g.247587535G>T	ENSP00000337383:p.Val264Leu					NLRP3_uc001ics.2_Missense_Mutation_p.V264L|NLRP3_uc001icu.2_Missense_Mutation_p.V264L|NLRP3_uc001icw.2_Missense_Mutation_p.V264L|NLRP3_uc001icv.2_Missense_Mutation_p.V264L|NLRP3_uc010pyw.1_Missense_Mutation_p.V262L|NLRP3_uc001ict.1_Missense_Mutation_p.V262L	p.V264L	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0141)		5	928	+	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	264			NACHT.		B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	c.790G>T	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	G	1.209	-0.630341	0.03610	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94;-0.94	4.04	1.06	0.20224	NACHT nucleoside triphosphatase (1);	0.292887	0.24793	N	0.035551	T	0.35422	0.0931	N	0.02111	-0.68	0.34866	D	0.743133	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.08055	0.001;0.001;0.002;0.001;0.003	T	0.38520	-0.9657	10	0.02654	T	1	.	2.5958	0.04854	0.1045:0.1872:0.5147:0.1936	.	264;264;264;264;264	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	L	264	ENSP00000375704:V264L;ENSP00000355453:V264L;ENSP00000337383:V264L;ENSP00000294752:V264L;ENSP00000355452:V264L;ENSP00000375703:V264L	ENSP00000337383:V264L	V	+	1	0	NLRP3	245654158	1.000000	0.71417	0.998000	0.56505	0.140000	0.21249	1.201000	0.32259	0.250000	0.21479	-0.261000	0.10672	GTG		0.537	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
MBL2	4153	broad.mit.edu	37	10	54531391	54531391	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr10:54531391G>T	ENST00000373968.3	-	1	69	c.5C>A	c.(4-6)tCc>tAc	p.S2Y		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	2					acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						TGGAAACAGGGACATGGTCCT	0.502																																						uc001jjt.2																			0				ovary(1)	1						c.(4-6)TCC>TAC		soluble mannose-binding lectin precursor							61.0	54.0	56.0					10																	54531391		2203	4300	6503	SO:0001583	missense	4153				acute-phase response|complement activation, classical pathway|complement activation, lectin pathway|defense response to Gram-positive bacterium|negative regulation of growth of symbiont in host|opsonization|response to oxidative stress	collagen|extracellular space	bacterial cell surface binding|calcium-dependent protein binding|eukaryotic cell surface binding|mannose binding|receptor binding	g.chr10:54531391G>T	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.5C>A	10.37:g.54531391G>T	ENSP00000363079:p.Ser2Tyr						p.S2Y	NM_000242	NP_000233	P11226	MBL2_HUMAN			1	70	-			2					Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	c.5C>A	CCDS7247.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.120104	0.00346	.	.	ENSG00000165471	ENST00000373968	T	0.71103	-0.54	4.24	-2.93	0.05598	.	1.551240	0.03799	N	0.264087	T	0.43122	0.1233	N	0.14661	0.345	0.09310	N	1	P	0.36616	0.561	B	0.31191	0.125	T	0.38478	-0.9659	10	0.02654	T	1	-0.4353	5.7981	0.18397	0.6066:0.1611:0.2323:0.0	.	2	P11226	MBL2_HUMAN	Y	2	ENSP00000363079:S2Y	ENSP00000363079:S2Y	S	-	2	0	MBL2	54201397	0.001000	0.12720	0.002000	0.10522	0.137000	0.21094	-0.385000	0.07379	-0.588000	0.05882	0.655000	0.94253	TCC		0.502	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
PCDH15	65217	broad.mit.edu	37	10	55839114	55839114	+	Missense_Mutation	SNP	C	C	G	rs368449190		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr10:55839114C>G	ENST00000320301.6	-	17	2462	c.2068G>C	c.(2068-2070)Gct>Cct	p.A690P	PCDH15_ENST00000395430.1_Missense_Mutation_p.A690P|PCDH15_ENST00000395438.1_Missense_Mutation_p.A690P|PCDH15_ENST00000361849.3_Missense_Mutation_p.A690P|PCDH15_ENST00000395432.2_Missense_Mutation_p.A653P|PCDH15_ENST00000395446.1_Missense_Mutation_p.A690P|PCDH15_ENST00000395433.1_Missense_Mutation_p.A668P|PCDH15_ENST00000373957.3_Missense_Mutation_p.A668P|PCDH15_ENST00000409834.1_Missense_Mutation_p.A301P|PCDH15_ENST00000373955.1_Missense_Mutation_p.A690P|PCDH15_ENST00000373965.2_Missense_Mutation_p.A697P|PCDH15_ENST00000437009.1_Missense_Mutation_p.A619P|PCDH15_ENST00000414778.1_Missense_Mutation_p.A695P|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.A697P|PCDH15_ENST00000395442.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	690	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CCATCTGAAGCTGTGATGATC	0.433										HNSCC(58;0.16)																												uc001jju.1																			0				pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13						c.(2068-2070)GCT>CCT		protocadherin 15 isoform CD1-4 precursor							247.0	218.0	228.0					10																	55839114		2203	4300	6503	SO:0001583	missense	65217				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding	g.chr10:55839114C>G	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2068G>C	10.37:g.55839114C>G	ENSP00000322604:p.Ala690Pro	HNSCC(58;0.16)				PCDH15_uc010qhq.1_Missense_Mutation_p.A695P|PCDH15_uc010qhr.1_Missense_Mutation_p.A690P|PCDH15_uc010qhs.1_Missense_Mutation_p.A702P|PCDH15_uc010qht.1_Missense_Mutation_p.A697P|PCDH15_uc010qhu.1_Missense_Mutation_p.A690P|PCDH15_uc001jjv.1_Missense_Mutation_p.A668P|PCDH15_uc010qhv.1_Missense_Mutation_p.A690P|PCDH15_uc010qhw.1_Missense_Mutation_p.A653P|PCDH15_uc010qhx.1_Missense_Mutation_p.A619P|PCDH15_uc010qhy.1_Missense_Mutation_p.A695P|PCDH15_uc010qhz.1_Missense_Mutation_p.A690P|PCDH15_uc010qia.1_Missense_Mutation_p.A668P|PCDH15_uc010qib.1_Missense_Mutation_p.A668P|PCDH15_uc001jjw.2_Missense_Mutation_p.A690P	p.A690P	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN			17	2463	-		Melanoma(3;0.117)|Lung SC(717;0.238)	690			Cadherin 6.|Extracellular (Potential).		A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	c.2068G>C	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813703	0.90790	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6;0.31;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.5;-0.6	5.9	5.9	0.94986	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.91486	0.7312	H	0.98980	4.39	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.998;1.0;1.0	D	0.94273	0.7512	9	0.87932	D	0	.	19.8634	0.96793	0.0:1.0:0.0:0.0	.	668;690;690;695;619;653;690;690;697;697;690;695;690;668;690	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	P	697;695;690;690;301;697;690;653;690;668;668;690;690;695;619;690	ENSP00000363076:A697P;ENSP00000410304:A695P;ENSP00000378826:A690P;ENSP00000386693:A301P;ENSP00000378832:A697P;ENSP00000378833:A690P;ENSP00000378820:A653P;ENSP00000354950:A690P;ENSP00000378821:A668P;ENSP00000363068:A668P;ENSP00000322604:A690P;ENSP00000378818:A690P;ENSP00000412628:A619P;ENSP00000363066:A690P	ENSP00000322604:A690P	A	-	1	0	PCDH15	55509120	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	5.408000	0.66368	2.800000	0.96347	0.591000	0.81541	GCT		0.433	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
MGMT	4255	broad.mit.edu	37	10	131506185	131506185	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr10:131506185C>T	ENST00000306010.7	+	3	277	c.245C>T	c.(244-246)gCg>gTg	p.A82V	MGMT_ENST00000462672.1_3'UTR	NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	51					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	GCCCCCGCTGCGGTTCTCGGA	0.602								Direct reversal of damage																														uc001lkh.2																			0				ovary(1)|breast(1)	2						c.(244-246)GCG>GTG	Direct_reversal_of_damage	O-6-methylguanine-DNA methyltransferase							63.0	68.0	66.0					10																	131506185		2203	4300	6503	SO:0001583	missense	4255							g.chr10:131506185C>T	M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.245C>T	10.37:g.131506185C>T	ENSP00000302111:p.Ala82Val						p.A82V	NM_002412	NP_002403	P16455	MGMT_HUMAN		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	3	271	+		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)	51					Q5VY78	Missense_Mutation	SNP	ENST00000306010.7	37	c.245C>T	CCDS7660.2	.	.	.	.	.	.	.	.	.	.	C	11.82	1.754112	0.31046	.	.	ENSG00000170430	ENST00000306010	T	0.14766	2.48	4.79	3.66	0.41972	.	0.332375	0.28510	N	0.015084	T	0.06096	0.0158	N	0.03608	-0.345	0.21290	N	0.99973	B	0.19200	0.034	B	0.08055	0.003	T	0.33675	-0.9859	10	0.31617	T	0.26	.	11.1375	0.48383	0.8431:0.1569:0.0:0.0	.	82	B4DEE8	.	V	82	ENSP00000302111:A82V	ENSP00000302111:A82V	A	+	2	0	MGMT	131396175	1.000000	0.71417	0.043000	0.18650	0.002000	0.02628	1.651000	0.37302	0.976000	0.38417	-0.256000	0.11100	GCG		0.602	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
PDE3B	5140	broad.mit.edu	37	11	14853295	14853295	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr11:14853295G>A	ENST00000282096.4	+	9	2419	c.2066G>A	c.(2065-2067)gGa>gAa	p.G689E	PDE3B_ENST00000455098.2_Missense_Mutation_p.G638E	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	689					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	GAAAAGATGGGAGAGAAATCA	0.294																																						uc001mln.2																			0					0						c.(2065-2067)GGA>GAA		phosphodiesterase 3B							61.0	67.0	65.0					11																	14853295		2199	4292	6491	SO:0001583	missense	5140				cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding	g.chr11:14853295G>A	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"""Phosphodiesterases"""	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.2066G>A	11.37:g.14853295G>A	ENSP00000282096:p.Gly689Glu					PDE3B_uc010rcr.1_Missense_Mutation_p.G638E	p.G689E	NM_000922	NP_000913	Q13370	PDE3B_HUMAN			9	2419	+			689					B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	37	c.2066G>A	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703738	0.88924	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.76316	-1.01;-1.01	5.82	5.82	0.92795	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.88262	0.6389	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87880	0.2677	10	0.59425	D	0.04	.	20.0951	0.97834	0.0:0.0:1.0:0.0	.	638;689	B7ZM37;Q13370	.;PDE3B_HUMAN	E	689;638	ENSP00000282096:G689E;ENSP00000388644:G638E	ENSP00000282096:G689E	G	+	2	0	PDE3B	14809871	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	8.913000	0.92730	2.753000	0.94483	0.467000	0.42956	GGA		0.294	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922	
HIPK3	10114	broad.mit.edu	37	11	33375092	33375092	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr11:33375092T>C	ENST00000303296.4	+	17	3931	c.3626T>C	c.(3625-3627)cTc>cCc	p.L1209P	AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000379016.3_Missense_Mutation_p.L1188P|HIPK3_ENST00000525975.1_Missense_Mutation_p.L1188P|HIPK3_ENST00000456517.1_Missense_Mutation_p.L1188P	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	1209					apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						CCAACAAAACTCAGCCAGTAT	0.363																																						uc001mul.1																			0				large_intestine(1)|skin(1)|stomach(1)|ovary(1)|pancreas(1)	5						c.(3625-3627)CTC>CCC		homeodomain interacting protein kinase 3 isoform							66.0	59.0	62.0					11																	33375092		2202	4298	6500	SO:0001583	missense	10114				anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	ATP binding|protein serine/threonine kinase activity	g.chr11:33375092T>C	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"""homeodomain-interacting protein kinase 3"""			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.3626T>C	11.37:g.33375092T>C	ENSP00000304226:p.Leu1209Pro					HIPK3_uc001mum.1_Missense_Mutation_p.L1188P|HIPK3_uc009yjv.1_Missense_Mutation_p.L1188P	p.L1209P	NM_005734	NP_005725	Q9H422	HIPK3_HUMAN			17	3896	+			1209					O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	37	c.3626T>C	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798609	0.31777	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	6.03	4.92	0.64577	.	0.000000	0.52532	D	0.000074	T	0.65144	0.2663	L	0.51422	1.61	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.70227	0.968;0.929	T	0.67133	-0.5747	10	0.87932	D	0	.	11.9761	0.53091	0.0:0.0671:0.0:0.9329	.	1188;1209	Q9H422-2;Q9H422	.;HIPK3_HUMAN	P	1188;1209;1188;1188	ENSP00000431710:L1188P;ENSP00000304226:L1209P;ENSP00000368301:L1188P;ENSP00000398241:L1188P	ENSP00000304226:L1209P	L	+	2	0	HIPK3	33331668	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	5.793000	0.69060	1.118000	0.41863	0.455000	0.32223	CTC		0.363	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734	
OR5AS1	219447	broad.mit.edu	37	11	55798090	55798090	+	Missense_Mutation	SNP	T	T	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr11:55798090T>G	ENST00000313555.1	+	1	196	c.196T>G	c.(196-198)Tta>Gta	p.L66V		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					TCTTAGCAACTTATCTTTCTT	0.348																																						uc010riw.1																			0				ovary(3)|liver(1)|skin(1)	5						c.(196-198)TTA>GTA		olfactory receptor, family 5, subfamily AS,							57.0	58.0	57.0					11																	55798090		2201	4296	6497	SO:0001583	missense	219447				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55798090T>G	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.196T>G	11.37:g.55798090T>G	ENSP00000324111:p.Leu66Val						p.L66V	NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN			1	196	+	Esophageal squamous(21;0.00693)		66			Helical; Name=2; (Potential).		Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	37	c.196T>G	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.564005	0.45694	.	.	ENSG00000181785	ENST00000313555	T	0.00587	6.38	5.65	1.67	0.24075	GPCR, rhodopsin-like superfamily (1);	0.000000	0.25106	U	0.033095	T	0.03564	0.0102	H	0.95260	3.645	0.26582	N	0.973356	D	0.76494	0.999	D	0.78314	0.991	T	0.09378	-1.0677	10	0.87932	D	0	.	7.5607	0.27849	0.0:0.4291:0.0:0.5709	.	66	Q8N127	O5AS1_HUMAN	V	66	ENSP00000324111:L66V	ENSP00000324111:L66V	L	+	1	2	OR5AS1	55554666	0.000000	0.05858	0.997000	0.53966	0.512000	0.34134	-0.557000	0.05985	0.434000	0.26340	-0.269000	0.10298	TTA		0.348	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
OR5M9	390162	broad.mit.edu	37	11	56229973	56229973	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr11:56229973G>C	ENST00000279791.1	-	1	904	c.905C>G	c.(904-906)gCa>gGa	p.A302G		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					CTTGGTGATTGCTTTGTTGAC	0.378																																						uc010rjj.1																			0				skin(2)|ovary(1)|central_nervous_system(1)	4						c.(904-906)GCA>GGA		olfactory receptor, family 5, subfamily M,							129.0	117.0	121.0					11																	56229973		2201	4296	6497	SO:0001583	missense	390162				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:56229973G>C	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"""GPCR / Class A : Olfactory receptors"""	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.905C>G	11.37:g.56229973G>C	ENSP00000279791:p.Ala302Gly						p.A302G	NM_001004743	NP_001004743	Q8NGP3	OR5M9_HUMAN			1	905	-	Esophageal squamous(21;0.00448)		302			Cytoplasmic (Potential).		Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	37	c.905C>G	CCDS31531.1	.	.	.	.	.	.	.	.	.	.	G	2.608	-0.291465	0.05568	.	.	ENSG00000150269	ENST00000279791	T	0.38077	1.16	3.89	0.254	0.15557	.	0.333939	0.21557	N	0.072633	T	0.20981	0.0505	N	0.21324	0.655	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16335	-1.0406	10	0.72032	D	0.01	1.4509	6.7833	0.23659	0.5512:0.0:0.4488:0.0	.	302	Q8NGP3	OR5M9_HUMAN	G	302	ENSP00000279791:A302G	ENSP00000279791:A302G	A	-	2	0	OR5M9	55986549	0.007000	0.16637	0.050000	0.19076	0.135000	0.20990	-0.620000	0.05565	-0.039000	0.13602	0.478000	0.44815	GCA		0.378	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743	
DTX4	23220	broad.mit.edu	37	11	58949878	58949878	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr11:58949878A>G	ENST00000227451.3	+	2	982	c.878A>G	c.(877-879)aAt>aGt	p.N293S	DTX4_ENST00000532982.1_Missense_Mutation_p.N187S	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	293					innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				GCCACCTTGAATCGTACCAAC	0.612																																						uc001nns.2																			0				lung(2)|central_nervous_system(1)	3						c.(877-879)AAT>AGT		deltex 4 homolog							30.0	38.0	35.0					11																	58949878		1995	4164	6159	SO:0001583	missense	23220				Notch signaling pathway	cytoplasm	zinc ion binding	g.chr11:58949878A>G	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"""RING-type (C3HC4) zinc fingers"""	29151	protein-coding gene	gene with protein product			"""deltex 4 homolog (Drosophila)"", ""deltex homolog 4 (Drosophila)"""			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.878A>G	11.37:g.58949878A>G	ENSP00000227451:p.Asn293Ser					DTX4_uc001nnr.2_Missense_Mutation_p.N187S	p.N293S	NM_015177	NP_055992	Q9Y2E6	DTX4_HUMAN			2	1135	+		all_epithelial(135;0.125)	293					Q0VF38	Missense_Mutation	SNP	ENST00000227451.3	37	c.878A>G	CCDS44612.1	.	.	.	.	.	.	.	.	.	.	A	2.969	-0.212938	0.06140	.	.	ENSG00000110042	ENST00000532982;ENST00000227451	T;T	0.11169	2.8;3.0	4.53	2.23	0.28157	.	0.766532	0.12326	N	0.478821	T	0.07593	0.0191	L	0.42581	1.335	0.29231	N	0.873283	B	0.02656	0.0	B	0.01281	0.0	T	0.44498	-0.9324	10	0.02654	T	1	.	6.6579	0.22998	0.8042:0.0:0.1958:0.0	.	293	Q9Y2E6	DTX4_HUMAN	S	187;293	ENSP00000434055:N187S;ENSP00000227451:N293S	ENSP00000227451:N293S	N	+	2	0	DTX4	58706454	1.000000	0.71417	0.980000	0.43619	0.782000	0.44232	2.401000	0.44513	0.293000	0.22520	0.533000	0.62120	AAT		0.612	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213	
PCNXL3	399909	broad.mit.edu	37	11	65402835	65402835	+	Silent	SNP	G	G	A	rs375263170		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr11:65402835G>A	ENST00000355703.3	+	31	5639	c.5100G>A	c.(5098-5100)gcG>gcA	p.A1700A	MIR4690_ENST00000578459.1_RNA|SIPA1_ENST00000534313.1_5'Flank	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1700						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCCTGCTGGCGCTGCGCCATG	0.632													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17409	0.0		0.0	False		,,,				2504	0.0					uc001oey.2																			0					0						c.(5098-5100)GCG>GCA		pecanex-like 3		G		10,4146		0,10,2068	21.0	22.0	22.0		5100	-8.1	0.7	11		22	0,8386		0,0,4193	no	coding-synonymous	PCNXL3	NM_032223.2		0,10,6261	AA,AG,GG		0.0,0.2406,0.0797		1700/2035	65402835	10,12532	2078	4193	6271	SO:0001819	synonymous_variant	399909					integral to membrane		g.chr11:65402835G>A	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.5100G>A	11.37:g.65402835G>A						PCNXL3_uc001oez.2_Silent_p.A587A	p.A1700A	NM_032223	NP_115599	Q9H6A9	PCX3_HUMAN			31	5100	+			1700					Q6MZN8	Silent	SNP	ENST00000355703.3	37	c.5100G>A	CCDS44650.1																																																																																				0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
CACNA1C	775	broad.mit.edu	37	12	2716205	2716205	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr12:2716205C>T	ENST00000347598.4	+	27	3325	c.3325C>T	c.(3325-3327)Cgc>Tgc	p.R1109C	CACNA1C_ENST00000399603.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000402845.3_Missense_Mutation_p.R1089C|CACNA1C_ENST00000480911.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399621.1_Missense_Mutation_p.R1089C|CACNA1C-AS3_ENST00000543559.1_RNA|CACNA1C_ENST00000399649.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399595.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399591.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399601.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000406454.3_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399617.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399606.1_Missense_Mutation_p.R1109C|CACNA1C_ENST00000344100.3_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399655.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399597.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399641.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399629.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000327702.7_Missense_Mutation_p.R1089C|CACNA1C_ENST00000335762.5_Missense_Mutation_p.R1114C|CACNA1C_ENST00000399644.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399638.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399637.1_Missense_Mutation_p.R1089C|CACNA1C_ENST00000399634.1_Missense_Mutation_p.R1089C	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1109	Dihydropyridine binding. {ECO:0000250}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CATCCAACCCCGCAGCTGGGA	0.542																																						uc009zdu.1																			0				ovary(10)|central_nervous_system(1)	11						c.(3325-3327)CGC>TGC		calcium channel, voltage-dependent, L type,	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)						61.0	67.0	65.0					12																	2716205		2138	4271	6409	SO:0001583	missense	775				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity	g.chr12:2716205C>T	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.3325C>T	12.37:g.2716205C>T	ENSP00000266376:p.Arg1109Cys					CACNA1C_uc009zdv.1_Missense_Mutation_p.R1086C|CACNA1C_uc001qkb.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkc.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qke.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkf.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qjz.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkd.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkg.2_Missense_Mutation_p.R1089C|CACNA1C_uc009zdw.1_Missense_Mutation_p.R1089C|CACNA1C_uc001qkh.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkl.2_Missense_Mutation_p.R1109C|CACNA1C_uc001qkn.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qko.2_Missense_Mutation_p.R1109C|CACNA1C_uc001qkp.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkr.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qku.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkq.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qks.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qkt.2_Missense_Mutation_p.R1089C|CACNA1C_uc001qka.1_Missense_Mutation_p.R624C|CACNA1C_uc001qki.1_Missense_Mutation_p.R825C|CACNA1C_uc001qkj.1_Missense_Mutation_p.R825C|CACNA1C_uc001qkk.1_Missense_Mutation_p.R825C|CACNA1C_uc001qkm.1_Missense_Mutation_p.R825C	p.R1109C	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	27	3638	+			1109			Extracellular (Potential).|III.|Dihydropyridine binding (By similarity).		B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	c.3325C>T	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382840	0.82792	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98633	-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04;-5.04	4.87	4.87	0.63330	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99477	0.9814	H	0.96748	3.875	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.738;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.987;1.0	D;D;P;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;P;D	0.91635	0.997;0.999;0.908;0.997;0.999;0.999;0.999;0.999;0.999;0.999;0.997;0.476;0.999;0.998;0.999;0.995;0.997;0.999;0.999;0.995;0.999;0.999;0.998;0.555;0.996	D	0.98175	1.0454	10	0.87932	D	0	.	18.5538	0.91075	0.0:1.0:0.0:0.0	.	1089;1086;1109;1089;1089;1089;1089;1089;1089;1109;1089;1060;1109;1089;1089;1089;1089;1089;1089;1089;1089;1089;1089;1089;1089	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	C	1114;1089;1089;1089;1089;1089;1089;1089;1089;1089;1109;1109;1089;1089;1089;1089;1089;1089;1089;1089;1089;1089;1089;930	ENSP00000336982:R1114C;ENSP00000382563:R1089C;ENSP00000437936:R1089C;ENSP00000382552:R1089C;ENSP00000382547:R1089C;ENSP00000382506:R1089C;ENSP00000382530:R1089C;ENSP00000382546:R1089C;ENSP00000382500:R1089C;ENSP00000382549:R1089C;ENSP00000266376:R1109C;ENSP00000382515:R1109C;ENSP00000382510:R1089C;ENSP00000341092:R1089C;ENSP00000382537:R1089C;ENSP00000329877:R1089C;ENSP00000382557:R1089C;ENSP00000385724:R1089C;ENSP00000382512:R1089C;ENSP00000382542:R1089C;ENSP00000382526:R1089C;ENSP00000385896:R1089C;ENSP00000382504:R1089C	ENSP00000323129:R930C	R	+	1	0	CACNA1C	2586466	0.997000	0.39634	1.000000	0.80357	0.926000	0.56050	3.452000	0.52971	2.691000	0.91804	0.655000	0.94253	CGC		0.542	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
TMTC1	83857	broad.mit.edu	37	12	29669420	29669420	+	Splice_Site	SNP	C	C	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr12:29669420C>A	ENST00000539277.1	-	15	2228		c.e15-1		TMTC1_ENST00000552618.1_Splice_Site|TMTC1_ENST00000319685.8_Splice_Site|TMTC1_ENST00000551659.1_Splice_Site|TMTC1_ENST00000256062.5_Splice_Site	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1							integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AAACCTGAGCCTACAAAACCA	0.453																																						uc001rjb.2																			0					0						c.e15-1		transmembrane and tetratricopeptide repeat							109.0	101.0	104.0					12																	29669420		2203	4300	6503	SO:0001630	splice_region_variant	83857					integral to membrane	binding	g.chr12:29669420C>A		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2170-1G>T	12.37:g.29669420C>A						TMTC1_uc001riz.2_Splice_Site_p.A373_splice|TMTC1_uc001rja.2_Splice_Site_p.A460_splice|TMTC1_uc001riy.2_Splice_Site_p.A69_splice	p.A616_splice	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN			15	2320	-	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)							D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Splice_Site	SNP	ENST00000539277.1	37	c.1846_splice	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184004	0.78677	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6163	0.88068	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMTC1	29560687	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.914000	0.75764	2.733000	0.93635	0.655000	0.94253	.		0.453	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	Intron
ABCD2	225	broad.mit.edu	37	12	40001468	40001468	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr12:40001468G>A	ENST00000308666.3	-	3	1304	c.1169C>T	c.(1168-1170)aCc>aTc	p.T390I		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	390	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						TCGAGCAGTGGTAAAGGCTTC	0.323																																						uc001rmb.2																			0				ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6						c.(1168-1170)ACC>ATC		ATP-binding cassette, sub-family D, member 2							96.0	101.0	99.0					12																	40001468		2203	4300	6503	SO:0001583	missense	225				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding	g.chr12:40001468G>A	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"""ATP binding cassette transporters / subfamily D"""	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1169C>T	12.37:g.40001468G>A	ENSP00000310688:p.Thr390Ile						p.T390I	NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN			3	1595	-			390			ABC transmembrane type-1.		B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	c.1169C>T	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.406203	0.62288	.	.	ENSG00000173208	ENST00000308666	D	0.96365	-3.99	5.24	5.24	0.73138	.	0.054263	0.64402	D	0.000001	D	0.92156	0.7513	N	0.17312	0.475	0.58432	D	0.999999	P	0.39964	0.697	B	0.38500	0.275	D	0.91364	0.5114	9	.	.	.	-16.5524	18.8419	0.92188	0.0:0.0:1.0:0.0	.	390	Q9UBJ2	ABCD2_HUMAN	I	390	ENSP00000310688:T390I	.	T	-	2	0	ABCD2	38287735	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.394000	0.97261	2.454000	0.82982	0.563000	0.77884	ACC		0.323	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164	
PCDH20	64881	broad.mit.edu	37	13	61985826	61985826	+	Silent	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr13:61985826G>A	ENST00000409186.1	-	5	4511	c.2406C>T	c.(2404-2406)ggC>ggT	p.G802G	PCDH20_ENST00000409204.4_Silent_p.G802G			Q8N6Y1	PCD20_HUMAN	protocadherin 20	802	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		AAGTAATGTTGCCAGTTTTAG	0.488																																						uc001vid.3																			0				ovary(4)|breast(1)|central_nervous_system(1)	6						c.(2404-2406)GGC>GGT		protocadherin 20							98.0	93.0	95.0					13																	61985826		2203	4300	6503	SO:0001819	synonymous_variant	64881				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr13:61985826G>A	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.2406C>T	13.37:g.61985826G>A						PCDH20_uc010thj.1_Silent_p.G802G	p.G802G	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN		GBM - Glioblastoma multiforme(99;0.000118)	2	2770	-		Breast(118;0.195)|Prostate(109;0.229)	775			Cadherin 6.|Extracellular (Potential).		A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	37	c.2406C>T	CCDS9442.2																																																																																				0.488	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
CTAGE11P	647288	broad.mit.edu	37	13	75814288	75814288	+	IGR	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr13:75814288A>G								AL162571.1 (31115 upstream) : LINC01078 (10327 downstream)																							TAACCGATCTAAAACTTCTCC	0.378																																						uc010ths.1																			0					0						c.(187-189)TTT>TTC		Homo sapiens mRNA; cDNA DKFZp434F0327 (from clone DKFZp434F0327).																																				SO:0001628	intergenic_variant	647288							g.chr13:75814288A>G																													13.37:g.75814288A>G							p.F63F	NR_027466						1	230	-									Silent	SNP		37	c.189T>C																																																																																				0	0.378								
PCID2	55795	broad.mit.edu	37	13	113854813	113854813	+	Silent	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr13:113854813G>A	ENST00000337344.4	-	2	130	c.54C>T	c.(52-54)gaC>gaT	p.D18D	PCID2_ENST00000375457.2_Silent_p.D16D|PCID2_ENST00000375477.1_Silent_p.D18D|PCID2_ENST00000246505.5_Silent_p.D18D|PCID2_ENST00000375479.2_Silent_p.D18D|PCID2_ENST00000375459.1_Silent_p.D16D	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	18					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)					breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			CATCTCTGCTGTCGATGGCTT	0.418																																						uc010tju.1																			0					0						c.(52-54)GAC>GAT		PCI domain containing 2							117.0	117.0	117.0					13																	113854813		2203	4300	6503	SO:0001819	synonymous_variant	55795				negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of mitotic cell cycle spindle assembly checkpoint|positive regulation of transcription, DNA-dependent|regulation of mRNA stability|spleen development		protein binding	g.chr13:113854813G>A	AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.54C>T	13.37:g.113854813G>A						PCID2_uc010tjv.1_Silent_p.D18D|PCID2_uc010tjw.1_Silent_p.D18D|PCID2_uc001vte.2_5'UTR|PCID2_uc001vtd.2_5'UTR|PCID2_uc001vtf.2_5'UTR|PCID2_uc001vtg.1_RNA	p.D18D	NM_001127203	NP_001120675	Q5JVF3	PCID2_HUMAN	all cancers(43;0.104)		2	135	-	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	18					A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Silent	SNP	ENST00000337344.4	37	c.54C>T	CCDS9532.2																																																																																				0.418	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386	
AHNAK2	113146	broad.mit.edu	37	14	105404844	105404844	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr14:105404844C>T	ENST00000333244.5	-	7	17063	c.16944G>A	c.(16942-16944)tgG>tgA	p.W5648*	AHNAK2_ENST00000557457.1_Nonsense_Mutation_p.W646*	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5648						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGTTTGGAAGCCAAAACCAGA	0.478																																						uc010axc.1																			0				ovary(1)	1						c.(16942-16944)TGG>TGA		AHNAK nucleoprotein 2							41.0	37.0	38.0					14																	105404844		1885	4123	6008	SO:0001587	stop_gained	113146					nucleus		g.chr14:105404844C>T	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.16944G>A	14.37:g.105404844C>T	ENSP00000353114:p.Trp5648*					AHNAK2_uc001ypx.2_Nonsense_Mutation_p.W5548*	p.W5648*	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		7	17064	-		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	5648					Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Nonsense_Mutation	SNP	ENST00000333244.5	37	c.16944G>A	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	C	56	27.038432	0.99970	.	.	ENSG00000185567	ENST00000557457;ENST00000333244	.	.	.	5.55	5.55	0.83447	.	0.000000	0.42821	U	0.000656	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	15.0366	0.71751	0.0:0.8583:0.1417:0.0	.	.	.	.	X	646;5648	.	ENSP00000353114:W5648X	W	-	3	0	AHNAK2	104475889	1.000000	0.71417	0.993000	0.49108	0.205000	0.24178	2.272000	0.43373	2.612000	0.88384	0.655000	0.94253	TGG		0.478	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
EIF3J	8669	broad.mit.edu	37	15	44829531	44829532	+	Frame_Shift_Ins	INS	-	-	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr15:44829531_44829532insT	ENST00000535391.1	+	2	65_66	c.53_54insT	c.(52-57)gctttcfs	p.AF18fs	EIF3J_ENST00000424492.3_Frame_Shift_Ins_p.AF18fs|EIF3J_ENST00000261868.5_Frame_Shift_Ins_p.AF18fs|EIF3J-AS1_ENST00000313807.4_lincRNA					eukaryotic translation initiation factor 3, subunit J											endometrium(1)|large_intestine(5)|liver(2)|skin(1)	9		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		GACGCCGACGCTTTCTCCGTGG	0.708																																						uc001ztv.2																			0					0						c.(52-54)GCTfs		eukaryotic translation initiation factor 3,																																				SO:0001589	frameshift_variant	8669					cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity	g.chr15:44829531_44829532insT	U97670	CCDS10111.1, CCDS61612.1, CCDS61613.1	15q21.1	2014-05-13	2007-07-27	2007-07-27	ENSG00000104131	ENSG00000104131			3270	protein-coding gene	gene with protein product		603910	"""eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa"""	EIF3S1		9822659	Standard	NM_001284335		Approved	eIF3-p35, eIF3-alpha, eIF3j	uc001ztv.3	O75822	OTTHUMG00000131158	ENST00000535391.1:c.56dupT	15.37:g.44829534_44829534dupT	ENSP00000440221:p.Ala18fs					uc001ztu.2_5'Flank|EIF3J_uc010ueg.1_Frame_Shift_Ins_p.A18fs|EIF3J_uc001ztw.2_Frame_Shift_Ins_p.A18fs	p.A18fs	NM_003758	NP_003749	O75822	EIF3J_HUMAN		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)	2	180_181	+		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)	18			Sufficient for interaction with EIF3B.			Frame_Shift_Ins	INS	ENST00000535391.1	37	c.53_54insT																																																																																					0.708	EIF3J-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396804.1	NM_003758	
CEP152	22995	broad.mit.edu	37	15	49054660	49054660	+	Silent	SNP	T	T	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr15:49054660T>G	ENST00000380950.2	-	18	2677	c.2490A>C	c.(2488-2490)atA>atC	p.I830I	CEP152_ENST00000325747.5_Silent_p.I737I|CEP152_ENST00000399334.3_Silent_p.I830I	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	830					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		CCTTGATGGCTATGTCCTTCT	0.358																																						uc001zwy.2																			0				lung(2)	2						c.(2488-2490)ATA>ATC		centrosomal protein 152kDa							167.0	154.0	158.0					15																	49054660		1851	4087	5938	SO:0001819	synonymous_variant	22995				centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding	g.chr15:49054660T>G	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2490A>C	15.37:g.49054660T>G						CEP152_uc001zwz.2_Silent_p.I830I|CEP152_uc001zxa.1_Silent_p.I737I	p.I830I	NM_014985	NP_055800	O94986	CE152_HUMAN		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)	18	2524	-		all_lung(180;0.0428)	830					E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	37	c.2490A>C	CCDS58361.1																																																																																				0.358	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	RNA	SNP	G	G	A	rs201972834		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr15:102515299G>A	ENST00000557932.1	+	0	1145				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.G374S(10)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						TGGGGGCATCGGCAAGGCCAA	0.652																																						uc002cdi.2																			10	Substitution - Missense(10)		kidney(7)|prostate(2)|endometrium(1)		0						c.(523-525)GGC>AGC		RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;																																						374666							g.chr15:102515299G>A			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102515299G>A						WASH3P_uc002cdl.2_Missense_Mutation_p.G175S|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Missense_Mutation_p.G175S|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	p.G175S	NR_003659						9	1943	+									Missense_Mutation	SNP	ENST00000557932.1	37	c.523G>A		.	.	.	.	.	.	.	.	.	.	g	2.376	-0.343229	0.05243	.	.	ENSG00000185596	ENST00000338304;ENST00000398121	.	.	.	1.01	1.01	0.19927	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	.	.	.	.	.	.	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	-23.1056	7.9382	0.29941	0.0:0.0:1.0:0.0	.	.	.	.	S	383;374	.	.	G	+	1	0	WASH3P	100332822	1.000000	0.71417	0.997000	0.53966	0.230000	0.25150	8.205000	0.89743	0.863000	0.35553	0.184000	0.17185	GGC		0.652	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163	
HYDIN	54768	broad.mit.edu	37	16	70913364	70913364	+	Missense_Mutation	SNP	C	C	T	rs373714588		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr16:70913364C>T	ENST00000393567.2	-	62	10543	c.10393G>A	c.(10393-10395)Gtg>Atg	p.V3465M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3465					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATGTCAAACACGAGGCCTCGG	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		21396	0.001		0.0	False		,,,				2504	0.0					uc002ezr.2																			0				ovary(1)|skin(1)	2						c.(10390-10392)GTG>ATG		hydrocephalus inducing isoform a		C	MET/VAL	1,3819		0,1,1909	41.0	45.0	44.0		10390	-4.1	0.2	16		44	0,8274		0,0,4137	no	missense	HYDIN	NM_032821.2	21	0,1,6046	TT,TC,CC		0.0,0.0262,0.0083	benign	3464/5121	70913364	1,12093	1910	4137	6047	SO:0001583	missense	54768							g.chr16:70913364C>T	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.10393G>A	16.37:g.70913364C>T	ENSP00000377197:p.Val3465Met						p.V3464M	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN			62	10518	-		Ovarian(137;0.0654)	3465					A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	c.10390G>A	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.437646	0.25900	2.62E-4	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00902	5.56	5.19	-4.1	0.03940	.	1.409600	0.05592	U	0.574901	T	0.01092	0.0036	L	0.56769	1.78	0.09310	N	1	B	0.27286	0.174	B	0.24269	0.052	T	0.46498	-0.9187	10	0.41790	T	0.15	.	2.4787	0.04582	0.2125:0.1648:0.1066:0.5162	.	3464	F8WD23	.	M	3465;3464	ENSP00000377197:V3465M	ENSP00000313052:V3464M	V	-	1	0	HYDIN	69470865	0.000000	0.05858	0.159000	0.22649	0.562000	0.35680	-1.512000	0.02258	-0.245000	0.09625	-0.409000	0.06214	GTG		0.567	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
SLC4A1	6521	broad.mit.edu	37	17	42330498	42330498	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr17:42330498C>T	ENST00000262418.6	-	17	2454	c.2299G>A	c.(2299-2301)Gct>Act	p.A767T		NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	767	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		ACAAGCACAGCGACCAGGAGT	0.637																																						uc002igf.3																			0				ovary(1)|central_nervous_system(1)|skin(1)	3						c.(2299-2301)GCT>ACT		solute carrier family 4, anion exchanger, member							73.0	67.0	69.0					17																	42330498		2203	4300	6503	SO:0001583	missense	6521				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity	g.chr17:42330498C>T		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2299G>A	17.37:g.42330498C>T	ENSP00000262418:p.Ala767Thr						p.A767T	NM_000342	NP_000333	P02730	B3AT_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.115)	17	2448	-		Breast(137;0.014)|Prostate(33;0.0181)	767			Helical; (Potential).|Membrane (anion exchange).		G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	c.2299G>A	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.538657	0.65085	.	.	ENSG00000004939	ENST00000262418	T	0.80033	-1.33	4.95	-1.75	0.08031	Bicarbonate transporter, C-terminal (1);	0.346172	0.30437	N	0.009624	D	0.84638	0.5516	M	0.89715	3.055	0.37514	D	0.91727	B	0.32382	0.368	B	0.38428	0.273	T	0.81280	-0.1004	10	0.33141	T	0.24	.	19.3172	0.94220	0.2369:0.7631:0.0:0.0	.	767	P02730	B3AT_HUMAN	T	767	ENSP00000262418:A767T	ENSP00000262418:A767T	A	-	1	0	SLC4A1	39686024	0.379000	0.25123	0.141000	0.22245	0.894000	0.52154	1.162000	0.31786	-0.731000	0.04862	-0.364000	0.07487	GCT		0.637	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
FBF1	85302	broad.mit.edu	37	17	73914257	73914257	+	Silent	SNP	G	G	A	rs375382563		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr17:73914257G>A	ENST00000586717.1	-	20	2463	c.2190C>T	c.(2188-2190)gcC>gcT	p.A730A	FBF1_ENST00000389570.4_Silent_p.A730A|FBF1_ENST00000319129.5_Silent_p.A729A			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	730					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGTGGGAGGTGGCACTGGTGG	0.662																																						uc002jqc.2																			0					0						c.(2185-2187)GCC>GCT		Fas (TNFRSF6) binding factor 1		G		1,4219		0,1,2109	33.0	42.0	39.0		2187	1.6	1.0	17		39	0,8452		0,0,4226	no	coding-synonymous	FBF1	NM_001080542.1		0,1,6335	AA,AG,GG		0.0,0.0237,0.0079		729/1134	73914257	1,12671	2110	4226	6336	SO:0001819	synonymous_variant	85302							g.chr17:73914257G>A	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2190C>T	17.37:g.73914257G>A						FBF1_uc002jqa.1_RNA|FBF1_uc010wsp.1_Silent_p.A720A|FBF1_uc002jqd.1_Silent_p.A730A|FBF1_uc002jqb.2_RNA|FBF1_uc010dgr.1_Silent_p.A40A	p.A729A	NM_001080542	NP_001074011	Q8TES7	FBF1_HUMAN			20	2461	-			729					B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37	c.2187C>T																																																																																					0.662	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
AANAT	15	broad.mit.edu	37	17	74465812	74465812	+	Silent	SNP	C	C	T	rs200468284	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr17:74465812C>T	ENST00000392492.3	+	4	618	c.384C>T	c.(382-384)cgC>cgT	p.R128R	AANAT_ENST00000250615.3_Silent_p.R173R	NM_001088.2	NP_001079.1	Q16613	SNAT_HUMAN	aralkylamine N-acetyltransferase	128	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|melatonin biosynthetic process (GO:0030187)|N-terminal protein amino acid acetylation (GO:0006474)|response to calcium ion (GO:0051592)|response to copper ion (GO:0046688)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to insulin (GO:0032868)|response to light stimulus (GO:0009416)|response to prostaglandin E (GO:0034695)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	aralkylamine N-acetyltransferase activity (GO:0004059)|arylamine N-acetyltransferase activity (GO:0004060)			lung(1)	1						CCGTGCACCGCGCCTTCCGGC	0.701													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16240	0.001		0.0	False		,,,				2504	0.0041					uc002jro.2																			0					0						c.(382-384)CGC>CGT		arylalkylamine N-acetyltransferase							8.0	8.0	8.0					17																	74465812		2176	4236	6412	SO:0001819	synonymous_variant	15				circadian rhythm|melatonin biosynthetic process	cytosol	aralkylamine N-acetyltransferase activity	g.chr17:74465812C>T	U40347	CCDS11745.1, CCDS54169.1	17q25.1	2013-10-15	2010-05-07		ENSG00000129673	ENSG00000129673	2.3.1.87		19	protein-coding gene	gene with protein product	"""serotonin N-acetyltransferase"""	600950	"""arylalkylamine N-acetyltransferase"""			8661026	Standard	NM_001088		Approved	SNAT	uc002jro.3	Q16613	OTTHUMG00000180179	ENST00000392492.3:c.384C>T	17.37:g.74465812C>T						AANAT_uc010wte.1_RNA	p.R128R	NM_001088	NP_001079	Q16613	SNAT_HUMAN			4	618	+			128			N-acetyltransferase.		A0AVF2|J3KMZ5|Q562F4	Silent	SNP	ENST00000392492.3	37	c.384C>T	CCDS11745.1																																																																																				0.701	AANAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450130.1	NM_001088	
EPB41L3	23136	broad.mit.edu	37	18	5489008	5489008	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr18:5489008G>A	ENST00000341928.2	-	2	515	c.175C>T	c.(175-177)Cgg>Tgg	p.R59W	EPB41L3_ENST00000544123.1_Missense_Mutation_p.R59W|EPB41L3_ENST00000400111.3_Missense_Mutation_p.R59W|EPB41L3_ENST00000342933.3_Missense_Mutation_p.R59W|EPB41L3_ENST00000540638.2_Missense_Mutation_p.R59W	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	59					apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						ACCTCCCTCCGCACCGGGGTG	0.672																																						uc002kmt.1																			0				ovary(5)	5						c.(175-177)CGG>TGG		erythrocyte membrane protein band 4.1-like 3							24.0	26.0	25.0					18																	5489008		2200	4295	6495	SO:0001583	missense	23136				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity	g.chr18:5489008G>A	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.175C>T	18.37:g.5489008G>A	ENSP00000343158:p.Arg59Trp					EPB41L3_uc010wzh.1_Missense_Mutation_p.R59W|EPB41L3_uc002kmu.1_Missense_Mutation_p.R59W|EPB41L3_uc010dkq.1_5'UTR|EPB41L3_uc010dks.1_Missense_Mutation_p.R81W|EPB41L3_uc002kmv.1_5'UTR	p.R59W	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN			2	261	-			59					B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	c.175C>T	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313834	0.60414	.	.	ENSG00000082397	ENST00000341928;ENST00000544123;ENST00000342933;ENST00000400111;ENST00000542652	D;D;D;D	0.83250	-1.54;-1.67;-1.54;-1.7	5.25	0.176	0.15049	.	10.463700	0.00166	N	0.000002	D	0.87418	0.6172	L	0.43152	1.355	0.58432	D	0.999998	D;D;P;D	0.61697	0.99;0.968;0.688;0.983	P;P;B;P	0.58391	0.838;0.6;0.433;0.48	T	0.73808	-0.3866	10	0.87932	D	0	.	13.4383	0.61096	0.0:0.0:0.2949:0.7051	.	59;59;59;59	F5GX05;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	W	59;59;59;59;140	ENSP00000343158:R59W;ENSP00000441174:R59W;ENSP00000341138:R59W;ENSP00000382981:R59W	ENSP00000343158:R59W	R	-	1	2	EPB41L3	5479008	1.000000	0.71417	0.108000	0.21378	0.794000	0.44872	2.303000	0.43646	-0.198000	0.10333	-0.321000	0.08615	CGG		0.672	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
LAMA3	3909	broad.mit.edu	37	18	21338466	21338466	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr18:21338466G>A	ENST00000313654.9	+	7	1295	c.1054G>A	c.(1054-1056)Gag>Aag	p.E352K	LAMA3_ENST00000399516.3_Missense_Mutation_p.E352K	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	352	Domain V.|Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GCAGAGCCACGAGTGTGAAGG	0.647																																						uc002kuq.2																			0				ovary(8)|skin(2)|central_nervous_system(1)	11						c.(1054-1056)GAG>AAG		laminin alpha 3 subunit isoform 1	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)						21.0	26.0	24.0					18																	21338466		1951	4123	6074	SO:0001583	missense	3909				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity	g.chr18:21338466G>A	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1054G>A	18.37:g.21338466G>A	ENSP00000324532:p.Glu352Lys					LAMA3_uc010dlv.1_Missense_Mutation_p.E352K|LAMA3_uc002kur.2_Missense_Mutation_p.E352K	p.E352K	NM_198129	NP_937762	Q16787	LAMA3_HUMAN			7	1140	+	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)		352			Laminin EGF-like 1.|Domain V.		B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	c.1054G>A	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.453277	0.26161	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669;ENST00000538801	T;T	0.63096	-0.02;-0.02	5.23	5.23	0.72850	EGF-like, laminin (3);	.	.	.	.	T	0.65616	0.2708	M	0.88377	2.95	0.80722	D	1	D;D;P	0.53885	0.959;0.963;0.776	B;B;B	0.43536	0.423;0.311;0.157	T	0.67321	-0.5700	9	0.14252	T	0.57	.	11.2375	0.48949	0.0932:0.0:0.9068:0.0	.	352;352;352	F5H8G3;Q6VU67;Q16787	.;.;LAMA3_HUMAN	K	352;352;350;352	ENSP00000324532:E352K;ENSP00000382432:E352K	ENSP00000324532:E352K	E	+	1	0	LAMA3	19592464	1.000000	0.71417	0.913000	0.36048	0.212000	0.24457	6.884000	0.75600	2.442000	0.82660	0.655000	0.94253	GAG		0.647	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
TAF4B	6875	broad.mit.edu	37	18	23873445	23873445	+	Silent	SNP	A	A	G	rs201212556		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr18:23873445A>G	ENST00000269142.5	+	9	2780	c.1782A>G	c.(1780-1782)gcA>gcG	p.A594A	TAF4B_ENST00000578121.1_Silent_p.A599A|TAF4B_ENST00000400466.2_Silent_p.A594A	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	594					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CACTTCAAGCATCTCCTACTC	0.269													A|||	1	0.000199681	0.0	0.0	5008	,	,		15317	0.001		0.0	False		,,,				2504	0.0					uc002kvu.3																			0				lung(1)|central_nervous_system(1)|skin(1)	3						c.(1780-1782)GCA>GCG		TAF4b RNA polymerase II, TATA box binding							41.0	40.0	40.0					18																	23873445		1789	4048	5837	SO:0001819	synonymous_variant	6875				transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity	g.chr18:23873445A>G	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1782A>G	18.37:g.23873445A>G						TAF4B_uc002kvs.3_RNA|TAF4B_uc002kvt.3_Silent_p.A599A	p.A594A	NM_005640	NP_005631	Q92750	TAF4B_HUMAN	Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)		9	2271	+	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		594					Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	c.1782A>G	CCDS42421.1																																																																																				0.269	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
BEST2	54831	broad.mit.edu	37	19	12864093	12864093	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:12864093C>T	ENST00000549706.1	+	3	496	c.172C>T	c.(172-174)Cag>Tag	p.Q58*	BEST2_ENST00000042931.1_Nonsense_Mutation_p.Q58*|BEST2_ENST00000553030.1_Nonsense_Mutation_p.Q58*			Q8NFU1	BEST2_HUMAN	bestrophin 2	58					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						GACCGAAGGGCAGAAGCGCTA	0.567																																						uc002mux.2																			0				ovary(1)|pancreas(1)	2						c.(172-174)CAG>TAG		vitelliform macular dystrophy 2-like 1							162.0	153.0	156.0					19																	12864093		2044	4184	6228	SO:0001587	stop_gained	54831				membrane depolarization|sensory perception of smell	chloride channel complex|cilium|plasma membrane	chloride channel activity	g.chr19:12864093C>T	AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17107	protein-coding gene	gene with protein product		607335	"""vitelliform macular dystrophy 2-like 1"""	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.172C>T	19.37:g.12864093C>T	ENSP00000448310:p.Gln58*						p.Q58*	NM_017682	NP_060152	Q8NFU1	BEST2_HUMAN			2	172	+			58			Extracellular (Potential).		Q53YQ8|Q9NXP0	Nonsense_Mutation	SNP	ENST00000549706.1	37	c.172C>T	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	C	37	5.983886	0.97173	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	.	.	.	3.95	3.95	0.45737	.	0.000000	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-24.4543	15.148	0.72674	0.0:1.0:0.0:0.0	.	.	.	.	X	58	.	ENSP00000042931:Q58X	Q	+	1	0	BEST2	12725093	1.000000	0.71417	0.977000	0.42913	0.455000	0.32408	7.704000	0.84595	1.944000	0.56390	0.313000	0.20887	CAG		0.567	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	
OR7A10	390892	broad.mit.edu	37	19	14951796	14951796	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:14951796C>A	ENST00000248058.1	-	1	893	c.894G>T	c.(892-894)aaG>aaT	p.K298N		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					TCATAGCACCCTTTATGTGTT	0.468																																						uc002mzx.1																			0					0						c.(892-894)AAG>AAT		olfactory receptor, family 7, subfamily A,							83.0	81.0	82.0					19																	14951796		2203	4300	6503	SO:0001583	missense	390892				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr19:14951796C>A		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.894G>T	19.37:g.14951796C>A	ENSP00000248058:p.Lys298Asn						p.K298N	NM_001005190	NP_001005190	O76100	OR7AA_HUMAN			1	894	-	Ovarian(108;0.203)		298			Cytoplasmic (Potential).		Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	c.894G>T	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	c	4.232	0.041921	0.08196	.	.	ENSG00000127515	ENST00000248058	T	0.40756	1.02	2.75	2.75	0.32379	.	0.391216	0.17888	U	0.158616	T	0.58308	0.2113	H	0.95260	3.645	0.22034	N	0.999403	B	0.33198	0.401	B	0.39771	0.309	T	0.59220	-0.7495	10	0.66056	D	0.02	.	9.2305	0.37434	0.0:1.0:0.0:0.0	.	298	O76100	OR7AA_HUMAN	N	298	ENSP00000248058:K298N	ENSP00000248058:K298N	K	-	3	2	OR7A10	14812796	0.000000	0.05858	0.048000	0.18961	0.154000	0.21943	-0.884000	0.04166	1.590000	0.49995	0.134000	0.15878	AAG		0.468	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
MAP1S	55201	broad.mit.edu	37	19	17838511	17838511	+	Missense_Mutation	SNP	G	G	A	rs540976741		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:17838511G>A	ENST00000324096.4	+	5	2469	c.2318G>A	c.(2317-2319)cGg>cAg	p.R773Q	MAP1S_ENST00000544059.2_Missense_Mutation_p.R747Q|MAP1S_ENST00000597681.1_3'UTR|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	773	Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for the microtubule-organizing center localization.|Pro-rich.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						TCACAGGAACGGGCAGGTGGG	0.687													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13468	0.0		0.0	False		,,,				2504	0.0					uc002nhe.1																			0				central_nervous_system(1)	1						c.(2317-2319)CGG>CAG		BPY2 interacting protein 1							18.0	19.0	18.0					19																	17838511		2194	4293	6487	SO:0001583	missense	55201				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding	g.chr19:17838511G>A	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2318G>A	19.37:g.17838511G>A	ENSP00000325313:p.Arg773Gln					MAP1S_uc010eba.1_Intron|MAP1S_uc002nhf.1_Missense_Mutation_p.R21Q|MAP1S_uc010xpv.1_Missense_Mutation_p.R747Q	p.R773Q	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN			5	2327	+			773			Pro-rich.|Necessary for the microtubule-organizing center localization.|Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.		B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	c.2318G>A	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223332	0.39300	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.16457	2.34;2.35	4.81	-1.75	0.08031	.	0.506800	0.16684	N	0.203813	T	0.10465	0.0256	L	0.45581	1.43	0.09310	N	1	B;B	0.24618	0.04;0.107	B;B	0.15870	0.009;0.014	T	0.22068	-1.0227	10	0.56958	D	0.05	-18.5764	1.0813	0.01643	0.188:0.1273:0.2876:0.3972	.	747;773	B4DH53;Q66K74	.;MAP1S_HUMAN	Q	773;747	ENSP00000325313:R773Q;ENSP00000439243:R747Q	ENSP00000325313:R773Q	R	+	2	0	MAP1S	17699511	1.000000	0.71417	0.169000	0.22859	0.006000	0.05464	1.621000	0.36986	0.091000	0.17302	-0.291000	0.09656	CGG		0.687	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
CEACAM5	1048	broad.mit.edu	37	19	42218934	42218934	+	Missense_Mutation	SNP	G	G	A	rs368068137		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:42218934G>A	ENST00000221992.6	+	3	583	c.469G>A	c.(469-471)Gtg>Atg	p.V157M	CEACAM5_ENST00000398599.4_Missense_Mutation_p.V157M|CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000405816.1_Missense_Mutation_p.V157M	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	157	Ig-like 2.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CTCCAAACCCGTGGAGGACAA	0.562																																						uc002ork.2																			0				skin(2)	2						c.(469-471)GTG>ATG		carcinoembryonic antigen-related cell adhesion		G	MET/VAL	0,4406		0,0,2203	135.0	124.0	128.0		469	0.6	0.0	19		128	2,8594		0,2,4296	no	missense	CEACAM5	NM_004363.2	21	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	157/703	42218934	2,13000	2203	4298	6501	SO:0001583	missense	1048					anchored to membrane|basolateral plasma membrane|integral to plasma membrane		g.chr19:42218934G>A	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.469G>A	19.37:g.42218934G>A	ENSP00000221992:p.Val157Met					CEACAM5_uc010ehz.1_Missense_Mutation_p.V157M|CEACAM5_uc002orj.1_Missense_Mutation_p.V157M|CEACAM5_uc002orl.2_Missense_Mutation_p.V157M	p.V157M	NM_004363	NP_004354	P06731	CEAM5_HUMAN		OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)	3	590	+			157			Ig-like 2.		H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	c.469G>A	CCDS12584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	10.89|10.89	1.479585|1.479585	0.26511|0.26511	0.0|0.0	2.33E-4|2.33E-4	ENSG00000105388|ENSG00000105388	ENST00000398599|ENST00000221992;ENST00000405816	.|T;T	.|0.56275	.|0.47;0.47	2.94|2.94	0.547|0.547	0.17202|0.17202	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.67420|0.67420	0.2891|0.2891	M|M	0.82716|0.82716	2.605|2.605	0.09310|0.09310	N|N	1|1	.|P;D;D	.|0.63880	.|0.755;0.993;0.976	.|B;D;P	.|0.65684	.|0.389;0.937;0.887	T|T	0.54642|0.54642	-0.8263|-0.8263	5|9	.|0.49607	.|T	.|0.09	.|.	5.9987|5.9987	0.19509|0.19509	0.2771:0.0:0.7229:0.0|0.2771:0.0:0.7229:0.0	.|.	.|157;157;157	.|Q8N4D0;P06731;Q53G30	.|.;CEAM5_HUMAN;.	H|M	153|157	.|ENSP00000221992:V157M;ENSP00000385072:V157M	.|ENSP00000221992:V157M	R|V	+|+	2|1	0|0	CEACAM5|CEACAM5	46910774|46910774	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.017000|0.017000	0.09413|0.09413	-0.939000|-0.939000	0.03933|0.03933	-0.039000|-0.039000	0.13602|0.13602	-1.112000|-1.112000	0.02068|0.02068	CGT|GTG		0.562	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
FUT1	2523	broad.mit.edu	37	19	49253828	49253828	+	Silent	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:49253828G>A	ENST00000310160.3	-	4	1685	c.711C>T	c.(709-711)ggC>ggT	p.G237G	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	237					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		AGGCGCTGTCGCCCACCACAC	0.657																																						uc002pkk.2																			0				ovary(1)	1						c.(709-711)GGC>GGT		fucosyltransferase 1							77.0	70.0	72.0					19																	49253828		2203	4299	6502	SO:0001819	synonymous_variant	2523				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to plasma membrane|membrane fraction	galactoside 2-alpha-L-fucosyltransferase activity	g.chr19:49253828G>A		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"""Blood group antigens"", ""Fucosyltransferases"""	4012	protein-coding gene	gene with protein product		211100	"""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)"", ""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"""	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.711C>T	19.37:g.49253828G>A							p.G237G	NM_000148	NP_000139	P19526	FUT1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)	4	1686	-		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)	237			Lumenal (Potential).		O14505|O14506|O14507	Silent	SNP	ENST00000310160.3	37	c.711C>T	CCDS12733.1																																																																																				0.657	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148	
NLRP12	91662	broad.mit.edu	37	19	54314476	54314476	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:54314476C>T	ENST00000324134.6	-	3	605	c.437G>A	c.(436-438)cGc>cAc	p.R146H	NLRP12_ENST00000354278.3_Missense_Mutation_p.R146H|NLRP12_ENST00000391772.1_Missense_Mutation_p.R146H|NLRP12_ENST00000535162.1_Missense_Mutation_p.R146H|NLRP12_ENST00000345770.5_Missense_Mutation_p.R146H|NLRP12_ENST00000351894.4_Missense_Mutation_p.R146H|NLRP12_ENST00000391773.1_Missense_Mutation_p.R146H|NLRP12_ENST00000391775.3_Missense_Mutation_p.R146H	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	146					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.R146L(1)|p.R146H(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TTCCCCTAGGCGCGCATTGCG	0.567																																						uc002qch.3																			2	Substitution - Missense(2)		large_intestine(1)|lung(1)	ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7						c.(436-438)CGC>CAC		NLR family, pyrin domain containing 12 isoform							91.0	88.0	89.0					19																	54314476		2203	4300	6503	SO:0001583	missense	91662				negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding	g.chr19:54314476C>T	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.437G>A	19.37:g.54314476C>T	ENSP00000319377:p.Arg146His					NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.R146H|NLRP12_uc002qcj.3_Missense_Mutation_p.R146H|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.R146H	p.R146H	NM_144687	NP_653288	P59046	NAL12_HUMAN		GBM - Glioblastoma multiforme(134;0.026)	3	657	-	Ovarian(34;0.19)		146					A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	c.437G>A	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	C	13.70	2.314812	0.40996	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48;-2.48;-2.48	4.47	4.47	0.54385	.	0.000000	0.42294	D	0.000728	D	0.92831	0.7720	M	0.78801	2.425	0.26209	N	0.979335	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.68621	0.925;0.926;0.959;0.945	D	0.85993	0.1490	10	0.33940	T	0.23	.	11.0466	0.47863	0.0:0.8111:0.1889:0.0	.	146;146;146;146	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	H	146	ENSP00000319377:R146H;ENSP00000438030:R146H;ENSP00000340473:R146H;ENSP00000346231:R146H;ENSP00000375655:R146H;ENSP00000375653:R146H;ENSP00000375652:R146H	ENSP00000319377:R146H	R	-	2	0	NLRP12	59006288	0.005000	0.15991	0.678000	0.29963	0.982000	0.71751	1.658000	0.37376	2.228000	0.72767	0.306000	0.20318	CGC		0.567	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
PPP6R1	22870	broad.mit.edu	37	19	55742009	55742009	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr19:55742009G>T	ENST00000412770.2	-	23	3180	c.2614C>A	c.(2614-2616)Ccg>Acg	p.P872T	TMEM86B_ENST00000327042.4_5'Flank|PPP6R1_ENST00000587283.1_Missense_Mutation_p.P872T	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	872	Pro-rich.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGCCCTTCCGGGGCAGAGCCA	0.677																																						uc002qjw.3																			0					0						c.(2614-2616)CCG>ACG		SAPS domain family, member 1							29.0	34.0	32.0					19																	55742009		2025	4182	6207	SO:0001583	missense	22870				regulation of phosphoprotein phosphatase activity	cytoplasm	protein phosphatase binding	g.chr19:55742009G>T	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.2614C>A	19.37:g.55742009G>T	ENSP00000414202:p.Pro872Thr					TMEM86B_uc002qjt.2_5'Flank|TMEM86B_uc002qju.2_5'Flank|SAPS1_uc002qjv.2_Missense_Mutation_p.P934T	p.P872T	NM_014931	NP_055746	Q9UPN7	PP6R1_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)	23	2856	-		Renal(1328;0.245)	872			Pro-rich.		Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	c.2614C>A	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	G	4.589	0.109471	0.08780	.	.	ENSG00000105063	ENST00000444538;ENST00000412770	T	0.53640	0.61	3.74	-2.4	0.06583	.	0.330843	0.22228	N	0.062855	T	0.21631	0.0521	N	0.19112	0.55	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.11329	0.002;0.006	T	0.05162	-1.0902	10	0.30854	T	0.27	-4.4596	0.584	0.00717	0.203:0.1594:0.3116:0.326	.	872;234	Q9UPN7;Q96ID3	PP6R1_HUMAN;.	T	387;872	ENSP00000414202:P872T	ENSP00000414202:P872T	P	-	1	0	PPP6R1	60433821	0.005000	0.15991	0.001000	0.08648	0.001000	0.01503	0.461000	0.21940	-0.298000	0.08921	-1.130000	0.01982	CCG		0.677	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
SLC9A4	389015	broad.mit.edu	37	2	103095456	103095456	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr2:103095456G>A	ENST00000295269.4	+	2	872	c.415G>A	c.(415-417)Gtt>Att	p.V139I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	139					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GCCACCCATCGTTCTGGAGGG	0.617																																						uc002tbz.3																			0				skin(2)|central_nervous_system(1)	3						c.(415-417)GTT>ATT		solute carrier family 9 (sodium/hydrogen							69.0	64.0	66.0					2																	103095456		2203	4300	6503	SO:0001583	missense	389015				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity	g.chr2:103095456G>A		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.415G>A	2.37:g.103095456G>A	ENSP00000295269:p.Val139Ile						p.V139I	NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN			2	872	+			139			Helical; Name=D/M4; (Potential).		Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	c.415G>A	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.412111	0.25465	.	.	ENSG00000180251	ENST00000295269	T	0.13901	2.55	5.92	5.05	0.67936	Cation/H+ exchanger (1);	0.063660	0.64402	D	0.000005	T	0.05547	0.0146	N	0.04162	-0.26	0.42471	D	0.992825	B	0.22909	0.077	B	0.21360	0.034	T	0.17592	-1.0364	10	0.02654	T	1	.	11.6442	0.51250	0.1858:0.0:0.8142:0.0	.	139	Q6AI14	SL9A4_HUMAN	I	139	ENSP00000295269:V139I	ENSP00000295269:V139I	V	+	1	0	SLC9A4	102461888	1.000000	0.71417	0.968000	0.41197	0.911000	0.54048	3.315000	0.51951	1.509000	0.48786	0.655000	0.94253	GTT		0.617	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
ANAPC1	64682	broad.mit.edu	37	2	112541977	112541977	+	Splice_Site	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr2:112541977C>T	ENST00000341068.3	-	41	5690	c.4918G>A	c.(4918-4920)Ggc>Agc	p.G1640S		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1640					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						CACTGAGTGCCCTTTACAAAT	0.458																																						uc002thi.2																			0				skin(2)	2						c.(4918-4920)GGC>AGC		anaphase promoting complex subunit 1							63.0	51.0	55.0					2																	112541977		2201	4280	6481	SO:0001630	splice_region_variant	64682				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm		g.chr2:112541977C>T	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.4918-1G>A	2.37:g.112541977C>T							p.G1640S	NM_022662	NP_073153	Q9H1A4	APC1_HUMAN			41	5165	-			1640					Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	c.4918G>A	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.61|16.61	3.170359|3.170359	0.57584|0.57584	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000427997|ENST00000341068	.|.	.|.	.|.	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	0.000000|0.000000	0.56097|0.56097	D|D	0.000028|0.000028	T|T	0.47229|0.47229	0.1434|0.1434	N|N	0.25647|0.25647	0.755|0.755	0.80722|0.80722	D|D	1|1	.|B	.|0.11235	.|0.004	.|B	.|0.08055	.|0.003	T|T	0.44436|0.44436	-0.9328|-0.9328	6|9	.|0.06757	.|T	.|0.87	-12.5857|-12.5857	17.5134|17.5134	0.87766|0.87766	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1640	.|Q9H1A4	.|APC1_HUMAN	E|S	1174|1640	.|.	.|ENSP00000339109:G1640S	G|G	-|-	2|1	0|0	ANAPC1|ANAPC1	112258448|112258448	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	5.809000|5.809000	0.69172|0.69172	2.108000|2.108000	0.64289|0.64289	0.555000|0.555000	0.69702|0.69702	GGG|GGC		0.458	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	Missense_Mutation
TTN	7273	broad.mit.edu	37	2	179542530	179542530	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr2:179542530A>G	ENST00000591111.1	-	144	33382	c.33158T>C	c.(33157-33159)gTt>gCt	p.V11053A	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V10126A|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V11370A|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	10191	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCAGGTAGAACTTCCTCTTC	0.448																																						uc010zfg.1																			0				ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153						c.(30376-30378)GTT>GCT		titin isoform N2-A							125.0	124.0	124.0					2																	179542530		1853	4086	5939	SO:0001583	missense	7273						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr2:179542530A>G	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.33158T>C	2.37:g.179542530A>G	ENSP00000465570:p.Val11053Ala					TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.V6787A|TTN_uc010fre.1_Intron|TTN_uc002una.1_RNA|TTN_uc010frf.1_RNA	p.V10126A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		143	30601	-			11053					A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37	c.30377T>C		.	.	.	.	.	.	.	.	.	.	A	11.43	1.635845	0.29068	.	.	ENSG00000155657	ENST00000342992	T	0.68624	-0.34	5.79	4.61	0.57282	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.59046	0.2165	.	.	.	0.22656	N	0.998885	B	0.10296	0.003	B	0.06405	0.002	T	0.54417	-0.8297	8	0.87932	D	0	.	11.959	0.52997	0.9317:0.0:0.0683:0.0	.	11053	Q8WZ42	TITIN_HUMAN	A	10126	ENSP00000343764:V10126A	ENSP00000343764:V10126A	V	-	2	0	TTN	179250775	0.054000	0.20591	0.479000	0.27329	0.838000	0.47535	3.460000	0.53028	0.985000	0.38656	0.533000	0.62120	GTT		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ALPI	248	broad.mit.edu	37	2	233323014	233323014	+	Missense_Mutation	SNP	C	C	T	rs146257849	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr2:233323014C>T	ENST00000295463.3	+	9	1156	c.1079C>T	c.(1078-1080)gCg>gTg	p.A360V		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	360					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		ATTGAGAGGGCGGGCCAGCTC	0.627													C|||	2	0.000399361	0.0	0.0	5008	,	,		18080	0.0		0.002	False		,,,				2504	0.0					uc002vst.3																			0				central_nervous_system(1)	1						c.(1078-1080)GCG>GTG		intestinal alkaline phosphatase precursor		C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	87.0	74.0	78.0		1079	4.5	0.0	2	dbSNP_134	78	5,8595	3.7+/-12.6	0,5,4295	yes	missense	ALPI	NM_001631.3	64	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	probably-damaging	360/529	233323014	6,13000	2203	4300	6503	SO:0001583	missense	248				phosphorylation	anchored to membrane|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding|protein binding	g.chr2:233323014C>T	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.1079C>T	2.37:g.233323014C>T	ENSP00000295463:p.Ala360Val					ALPI_uc002vsu.3_Missense_Mutation_p.A271V	p.A360V	NM_001631	NP_001622	P09923	PPBI_HUMAN		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)	9	1156	+		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)	360					B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	37	c.1079C>T	CCDS2492.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	27.8	4.864521	0.91511	2.27E-4	5.81E-4	ENSG00000163295	ENST00000295463	D	0.96396	-4.0	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.054525	0.64402	D	0.000001	D	0.97717	0.9251	M	0.75884	2.315	0.58432	D	0.999996	D	0.89917	1.0	D	0.73708	0.981	D	0.98331	1.0533	10	0.66056	D	0.02	.	15.8578	0.78994	0.0:1.0:0.0:0.0	.	360	P09923	PPBI_HUMAN	V	360	ENSP00000295463:A360V	ENSP00000295463:A360V	A	+	2	0	ALPI	233031258	1.000000	0.71417	0.020000	0.16555	0.013000	0.08279	4.780000	0.62382	2.318000	0.78349	0.561000	0.74099	GCG		0.627	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
PDCD1	5133	broad.mit.edu	37	2	242800933	242800933	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr2:242800933G>A	ENST00000334409.5	-	1	127	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W		NM_005018.2	NP_005009.2	Q15116	PDCD1_HUMAN	programmed cell death 1	20					apoptotic process (GO:0006915)|humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			endometrium(1)|lung(2)|ovary(1)|prostate(3)|skin(1)	8		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)		CATCCTGGCCGCCAGCCCAGT	0.677																																						uc002wcq.3																			0				ovary(1)	1						c.(58-60)CGG>TGG		programmed cell death 1 precursor							37.0	36.0	36.0					2																	242800933		2195	4292	6487	SO:0001583	missense	5133				apoptosis|humoral immune response|multicellular organismal development|T cell costimulation	integral to membrane	protein tyrosine phosphatase activity|signal transducer activity	g.chr2:242800933G>A	AY206416	CCDS33428.1	2q37.3	2014-01-29			ENSG00000188389	ENSG00000188389		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	8760	protein-coding gene	gene with protein product		600244	"""systemic lupus erythematosus susceptibility 2"""	SLEB2		7851902, 12402038	Standard	NM_005018		Approved	CD279, PD1, hSLE1	uc002wcq.4	Q15116	OTTHUMG00000151342	ENST00000334409.5:c.58C>T	2.37:g.242800933G>A	ENSP00000335062:p.Arg20Trp					PDCD1_uc010fzt.2_RNA	p.R20W	NM_005018	NP_005009	Q15116	PDCD1_HUMAN		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)	1	126	-		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)	20					O00517|Q8IX89	Missense_Mutation	SNP	ENST00000334409.5	37	c.58C>T	CCDS33428.1	.	.	.	.	.	.	.	.	.	.	.	10.47	1.359107	0.24598	.	.	ENSG00000188389	ENST00000334409;ENST00000539073	T	0.67698	-0.28	3.31	-6.15	0.02105	.	1.517800	0.04795	N	0.432427	T	0.38585	0.1046	N	0.04880	-0.145	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.19257	-1.0311	10	0.49607	T	0.09	-0.7107	3.4871	0.07624	0.4071:0.0:0.3137:0.2791	.	20	Q15116	PDCD1_HUMAN	W	20	ENSP00000335062:R20W	ENSP00000335062:R20W	R	-	1	2	PDCD1	242449606	0.004000	0.15560	0.077000	0.20336	0.724000	0.41520	-1.052000	0.03503	-1.621000	0.01562	0.305000	0.20034	CGG		0.677	PDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322313.1	NM_005018	
C20orf196	149840	broad.mit.edu	37	20	5843987	5843987	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr20:5843987G>T	ENST00000303142.6	+	3	583	c.496G>T	c.(496-498)Gac>Tac	p.D166Y		NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	166										endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						GCATTCCAGGGACACCCACTT	0.512																																						uc002wmf.2																			0					0						c.(496-498)GAC>TAC		hypothetical protein LOC149840							79.0	76.0	77.0					20																	5843987		2203	4300	6503	SO:0001583	missense	149840							g.chr20:5843987G>T	AK057796	CCDS13091.1	20p12.3	2006-07-07			ENSG00000171984	ENSG00000171984			26318	protein-coding gene	gene with protein product						12477932	Standard	NM_152504		Approved	FLJ25067	uc002wmf.3	Q8IYI0	OTTHUMG00000031813	ENST00000303142.6:c.496G>T	20.37:g.5843987G>T	ENSP00000305875:p.Asp166Tyr						p.D166Y	NM_152504	NP_689717	Q8IYI0	CT196_HUMAN			3	583	+			166					A8K9J3|Q5TGA9|Q96LU1	Missense_Mutation	SNP	ENST00000303142.6	37	c.496G>T	CCDS13091.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.535822	0.27475	.	.	ENSG00000171984	ENST00000303142	T	0.53857	0.6	5.86	2.73	0.32206	.	0.375145	0.25845	N	0.027940	T	0.62122	0.2402	M	0.62723	1.935	0.09310	N	1	D	0.76494	0.999	D	0.65874	0.939	T	0.51601	-0.8685	10	0.87932	D	0	-3.0241	5.926	0.19112	0.1667:0.1555:0.6778:0.0	.	166	Q8IYI0	CT196_HUMAN	Y	166	ENSP00000305875:D166Y	ENSP00000305875:D166Y	D	+	1	0	C20orf196	5791987	0.889000	0.30405	0.010000	0.14722	0.004000	0.04260	1.752000	0.38349	0.836000	0.34901	-0.126000	0.14955	GAC		0.512	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077882.2	NM_152504	
DLGAP4	22839	broad.mit.edu	37	20	35060659	35060659	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr20:35060659G>A	ENST00000373907.2	+	2	738	c.539G>A	c.(538-540)cGg>cAg	p.R180Q	DLGAP4_ENST00000373913.3_Missense_Mutation_p.R180Q|DLGAP4_ENST00000339266.5_Missense_Mutation_p.R180Q|DLGAP4_ENST00000401952.2_Missense_Mutation_p.R180Q			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	180					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				GGCAAGGGCCGGAGGGCCAAA	0.647																																						uc002xff.2																			0				skin(2)|ovary(1)	3						c.(538-540)CGG>CAG		disks large-associated protein 4 isoform a							37.0	44.0	42.0					20																	35060659		2203	4300	6503	SO:0001583	missense	22839				cell-cell signaling	membrane	protein binding	g.chr20:35060659G>A	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.539G>A	20.37:g.35060659G>A	ENSP00000363014:p.Arg180Gln					DLGAP4_uc010zvp.1_Missense_Mutation_p.R180Q	p.R180Q	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN			3	974	+	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)	180					E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	37	c.539G>A		.	.	.	.	.	.	.	.	.	.	G	23.4	4.412960	0.83449	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266	T;T;T;T	0.18810	2.19;2.19;2.19;2.19	5.53	4.59	0.56863	.	0.298816	0.36972	N	0.002312	T	0.44746	0.1308	M	0.70275	2.135	0.52099	D	0.999946	D	0.89917	1.0	D	0.85130	0.997	T	0.38908	-0.9639	10	0.49607	T	0.09	.	13.3659	0.60684	0.0755:0.0:0.9245:0.0	.	180	Q9Y2H0-1	.	Q	180	ENSP00000363023:R180Q;ENSP00000384954:R180Q;ENSP00000363014:R180Q;ENSP00000341633:R180Q	ENSP00000341633:R180Q	R	+	2	0	DLGAP4	34494073	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.863000	0.99569	1.334000	0.45468	0.561000	0.74099	CGG		0.647	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902	
NFATC2	4773	broad.mit.edu	37	20	50133367	50133367	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr20:50133367G>A	ENST00000396009.3	-	3	1507	c.1288C>T	c.(1288-1290)Cga>Tga	p.R430*	NFATC2_ENST00000414705.1_Nonsense_Mutation_p.R410*|NFATC2_ENST00000609507.1_Nonsense_Mutation_p.R211*|NFATC2_ENST00000371564.3_Nonsense_Mutation_p.R430*|NFATC2_ENST00000610033.1_Nonsense_Mutation_p.R211*|NFATC2_ENST00000609943.1_Nonsense_Mutation_p.R410*	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	430	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					ACAGCCCCTCGGCTGCCTTCT	0.557																																						uc002xwd.2																			0				ovary(2)	2						c.(1288-1290)CGA>TGA		nuclear factor of activated T-cells,							87.0	78.0	81.0					20																	50133367		2203	4300	6503	SO:0001587	stop_gained	4773				B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity	g.chr20:50133367G>A	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1288C>T	20.37:g.50133367G>A	ENSP00000379330:p.Arg430*					NFATC2_uc002xwc.2_Nonsense_Mutation_p.R430*|NFATC2_uc010zyv.1_Nonsense_Mutation_p.R211*|NFATC2_uc010zyw.1_Nonsense_Mutation_p.R211*|NFATC2_uc010zyx.1_Nonsense_Mutation_p.R410*|NFATC2_uc010zyy.1_Nonsense_Mutation_p.R211*|NFATC2_uc010zyz.1_Nonsense_Mutation_p.R211*|NFATC2_uc002xwe.2_Nonsense_Mutation_p.R410*	p.R430*	NM_173091	NP_775114	Q13469	NFAC2_HUMAN			3	1508	-	Hepatocellular(150;0.248)		430			RHD.		B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Nonsense_Mutation	SNP	ENST00000396009.3	37	c.1288C>T	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	G	39	7.579528	0.98371	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	.	.	.	5.25	4.29	0.51040	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6532	15.2933	0.73882	0.0:0.0:0.8589:0.1411	.	.	.	.	X	430;430;211;410	.	ENSP00000360619:R430X	R	-	1	2	NFATC2	49566774	1.000000	0.71417	0.998000	0.56505	0.536000	0.34869	2.331000	0.43894	1.204000	0.43247	-0.175000	0.13238	CGA		0.557	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
COL20A1	57642	broad.mit.edu	37	20	61943349	61943349	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr20:61943349G>A	ENST00000358894.6	+	14	1845	c.1745G>A	c.(1744-1746)aGg>aAg	p.R582K	COL20A1_ENST00000435874.1_Missense_Mutation_p.R589K|COL20A1_ENST00000422202.1_Missense_Mutation_p.R589K|COL20A1_ENST00000326996.6_Missense_Mutation_p.R582K	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	582	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GGTGCCCCGAGGCCTGTGCGC	0.682																																						uc011aau.1																			0				central_nervous_system(1)	1						c.(1744-1746)AGG>AAG		collagen, type XX, alpha 1							23.0	28.0	27.0					20																	61943349		1990	4156	6146	SO:0001583	missense	57642				cell adhesion	collagen|extracellular space	structural molecule activity	g.chr20:61943349G>A	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.1745G>A	20.37:g.61943349G>A	ENSP00000351767:p.Arg582Lys					COL20A1_uc011aav.1_Missense_Mutation_p.R403K	p.R582K	NM_020882	NP_065933	Q9P218	COKA1_HUMAN			14	1845	+	all_cancers(38;1.39e-10)		582			Fibronectin type-III 4.		Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	c.1745G>A	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	G	1.185	-0.636897	0.03557	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	T;T;T;T	0.04360	3.64;3.64;3.64;3.64	3.62	1.57	0.23409	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.754958	0.12311	N	0.480234	T	0.07773	0.0195	L	0.42245	1.32	0.09310	N	1	P;D	0.53462	0.951;0.96	P;P	0.54270	0.631;0.747	T	0.34502	-0.9826	10	0.20046	T	0.44	.	5.5243	0.16949	0.1184:0.201:0.6805:0.0	.	589;582	Q9P218-2;Q9P218	.;COKA1_HUMAN	K	582;582;589;589	ENSP00000351767:R582K;ENSP00000323077:R582K;ENSP00000408690:R589K;ENSP00000414753:R589K	ENSP00000323077:R582K	R	+	2	0	COL20A1	61413794	0.000000	0.05858	0.031000	0.17742	0.081000	0.17604	-0.554000	0.06006	0.161000	0.19458	0.313000	0.20887	AGG		0.682	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
KRTAP10-11	386678	broad.mit.edu	37	21	46066409	46066409	+	Missense_Mutation	SNP	G	G	A	rs190235053		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr21:46066409G>A	ENST00000334670.8	+	1	79	c.34G>A	c.(34-36)Gct>Act	p.A12T	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	12						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CTGCTCCAGCGCTTACTCCGA	0.667													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14545	0.0		0.0	False		,,,				2504	0.0					uc002zfr.3																			0				ovary(1)	1						c.(34-36)GCT>ACT		keratin associated protein 10-11							68.0	73.0	71.0					21																	46066409		2202	4298	6500	SO:0001583	missense	386678					keratin filament		g.chr21:46066409G>A	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.34G>A	21.37:g.46066409G>A	ENSP00000334197:p.Ala12Thr					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	p.A12T	NM_198692	NP_941965	P60412	KR10B_HUMAN			1	79	+			12					A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	c.34G>A	CCDS42962.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	4.947	0.175992	0.09443	.	.	ENSG00000243489	ENST00000334670	T	0.14640	2.49	3.83	0.936	0.19488	.	.	.	.	.	T	0.10637	0.0260	L	0.50333	1.59	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.45086	-0.9285	9	0.02654	T	1	.	10.0224	0.42051	0.2004:0.0:0.7996:0.0	.	12	P60412	KR10B_HUMAN	T	12	ENSP00000334197:A12T	ENSP00000334197:A12T	A	+	1	0	KRTAP10-11	44890837	0.001000	0.12720	0.918000	0.36340	0.006000	0.05464	-1.757000	0.01811	-0.138000	0.11434	-1.327000	0.01280	GCT		0.667	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
SLC19A1	6573	broad.mit.edu	37	21	46950811	46950811	+	Missense_Mutation	SNP	C	C	T	rs142899279		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr21:46950811C>T	ENST00000311124.4	-	4	1176	c.1024G>A	c.(1024-1026)Gtc>Atc	p.V342I	SLC19A1_ENST00000567670.1_Missense_Mutation_p.V342I|SLC19A1_ENST00000380010.4_Missense_Mutation_p.V342I|SLC19A1_ENST00000485649.2_Missense_Mutation_p.V302I	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	342					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	GTGGCCGTGACGCCCGCGATG	0.697																																						uc002zhl.1																			0					0						c.(1024-1026)GTC>ATC		solute carrier family 19 member 1							17.0	18.0	18.0					21																	46950811		2187	4282	6469	SO:0001583	missense	6573				folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity	g.chr21:46950811C>T	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.1024G>A	21.37:g.46950811C>T	ENSP00000308895:p.Val342Ile					SLC19A1_uc010gpy.1_Missense_Mutation_p.V342I|SLC19A1_uc011aft.1_Missense_Mutation_p.V302I|SLC19A1_uc002zhm.1_Missense_Mutation_p.V342I|SLC19A1_uc010gpz.1_Missense_Mutation_p.V221I	p.V342I	NM_194255	NP_919231	P41440	S19A1_HUMAN		Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	4	1143	-			342			Helical; (Probable).		B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	37	c.1024G>A	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	c	10.26	1.300894	0.23650	.	.	ENSG00000173638	ENST00000380014;ENST00000311124;ENST00000380010;ENST00000485649	D;D;D	0.86230	-2.09;-2.09;-2.09	4.16	2.28	0.28536	Major facilitator superfamily domain, general substrate transporter (1);	0.197420	0.43110	N	0.000601	D	0.83672	0.5305	L	0.33137	0.985	0.36274	D	0.855373	D;D;P;D	0.63880	0.993;0.993;0.902;0.993	P;P;B;P	0.53722	0.733;0.733;0.266;0.733	T	0.82016	-0.0666	10	0.23302	T	0.38	-39.1739	9.8994	0.41338	0.0:0.8118:0.0:0.1882	.	302;364;342;342	B7Z8C3;D3DSM6;E9PFY4;P41440	.;.;.;S19A1_HUMAN	I	89;342;342;302	ENSP00000308895:V342I;ENSP00000369347:V342I;ENSP00000441772:V302I	ENSP00000308895:V342I	V	-	1	0	SLC19A1	45775239	0.952000	0.32445	0.006000	0.13384	0.129000	0.20672	1.887000	0.39698	0.874000	0.35823	0.289000	0.19496	GTC		0.697	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
CCT8L2	150160	broad.mit.edu	37	22	17073274	17073274	+	Missense_Mutation	SNP	C	C	T	rs567911712	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr22:17073274C>T	ENST00000359963.3	-	1	426	c.167G>A	c.(166-168)cGg>cAg	p.R56Q		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	56					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				GAACTTCTGCCGGCCGTGGGG	0.642													c|||	2	0.000399361	0.0	0.0	5008	,	,		17834	0.002		0.0	False		,,,				2504	0.0					uc002zlp.1																			0				ovary(1)	1						c.(166-168)CGG>CAG		T-complex protein 1							64.0	65.0	65.0					22																	17073274		2203	4300	6503	SO:0001583	missense	150160				cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity	g.chr22:17073274C>T	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.167G>A	22.37:g.17073274C>T	ENSP00000353048:p.Arg56Gln						p.R56Q	NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN			1	427	-	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)	56					A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	c.167G>A	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	c	15.80	2.941709	0.53079	.	.	ENSG00000198445	ENST00000359963	T	0.80738	-1.41	2.0	2.0	0.26442	.	0.269489	0.18804	U	0.130720	T	0.78799	0.4340	L	0.53249	1.67	0.25771	N	0.984833	D	0.58620	0.983	P	0.50378	0.639	T	0.69873	-0.5027	10	0.66056	D	0.02	-8.6772	7.4831	0.27417	0.0:1.0:0.0:0.0	.	56	Q96SF2	TCPQM_HUMAN	Q	56	ENSP00000353048:R56Q	ENSP00000353048:R56Q	R	-	2	0	CCT8L2	15453274	0.098000	0.21812	0.953000	0.39169	0.690000	0.40134	0.377000	0.20552	1.126000	0.42016	0.393000	0.25936	CGG		0.642	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
GNB1L	54584	broad.mit.edu	37	22	19799872	19799872	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr22:19799872C>T	ENST00000329517.6	-	5	589	c.353G>A	c.(352-354)aGc>aAc	p.S118N	GNB1L_ENST00000460402.1_5'UTR|GNB1L_ENST00000405009.1_Missense_Mutation_p.S118N|GNB1L_ENST00000403325.1_Missense_Mutation_p.S118N	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	118					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					CAGGATGCTGCTCCGGCAGAA	0.692																																						uc002zqe.1																			0				breast(1)	1						c.(352-354)AGC>AAC		guanine nucleotide binding protein							37.0	33.0	34.0					22																	19799872		2203	4300	6503	SO:0001583	missense	54584				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular		g.chr22:19799872C>T	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"""WD repeat domain containing"""	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.353G>A	22.37:g.19799872C>T	ENSP00000331313:p.Ser118Asn					GNB1L_uc002zqd.1_5'UTR|GNB1L_uc002zqf.1_Missense_Mutation_p.S118N	p.S118N	NM_053004	NP_443730	Q9BYB4	GNB1L_HUMAN			4	747	-	Colorectal(54;0.0993)		118					Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	37	c.353G>A	CCDS13768.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.619076	0.28801	.	.	ENSG00000185838	ENST00000329517;ENST00000403325;ENST00000405009;ENST00000453108	T;T;T;T	0.56275	1.16;1.16;4.79;0.47	4.96	3.92	0.45320	WD40 repeat-like-containing domain (1);	0.755422	0.11905	U	0.518223	T	0.36358	0.0964	N	0.24115	0.695	0.25008	N	0.991429	P	0.36465	0.554	B	0.32583	0.148	T	0.06303	-1.0834	10	0.13853	T	0.58	-17.8133	13.5059	0.61483	0.0:0.8432:0.1568:0.0	.	118	Q9BYB4	GNB1L_HUMAN	N	118;118;118;76	ENSP00000331313:S118N;ENSP00000385154:S118N;ENSP00000384626:S118N;ENSP00000389412:S76N	ENSP00000331313:S118N	S	-	2	0	GNB1L	18179872	1.000000	0.71417	0.510000	0.27712	0.169000	0.22640	4.193000	0.58385	1.049000	0.40321	0.563000	0.77884	AGC		0.692	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1		
BPIFC	254240	broad.mit.edu	37	22	32833790	32833790	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr22:32833790C>T	ENST00000397452.1	-	8	814	c.704G>A	c.(703-705)aGt>aAt	p.S235N	BPIFC_ENST00000534972.1_5'UTR|BPIFC_ENST00000432451.2_Missense_Mutation_p.S49N|BPIFC_ENST00000300399.3_Missense_Mutation_p.S235N			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	235						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										TTCTGGAGAACTGATTAGGGA	0.353																																						uc003amn.2																			0				ovary(1)|skin(1)	2						c.(703-705)AGT>AAT		bactericidal/permeability-increasing							103.0	96.0	98.0					22																	32833790		2203	4300	6503	SO:0001583	missense	254240					extracellular region	lipopolysaccharide binding|phospholipid binding	g.chr22:32833790C>T	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.704G>A	22.37:g.32833790C>T	ENSP00000380594:p.Ser235Asn					BPIL2_uc010gwo.2_Missense_Mutation_p.S49N|BPIL2_uc011amb.1_5'UTR	p.S235N	NM_174932	NP_777592	Q8NFQ6	BPIL2_HUMAN			7	704	-			235					A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	c.704G>A	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485141	0.26598	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000432451	T;T;T	0.05447	3.44;3.44;3.44	5.68	2.15	0.27550	.	0.987485	0.08313	N	0.965061	T	0.06917	0.0176	L	0.47016	1.485	0.19300	N	0.999974	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.42481	-0.9449	10	0.31617	T	0.26	-0.5005	6.175	0.20439	0.0:0.3556:0.0:0.6444	.	49;235	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	N	235;235;49	ENSP00000380594:S235N;ENSP00000300399:S235N;ENSP00000408920:S49N	ENSP00000300399:S235N	S	-	2	0	BPIFC	31163790	0.004000	0.15560	0.293000	0.24932	0.983000	0.72400	0.186000	0.16978	0.233000	0.21120	-0.345000	0.07892	AGT		0.353	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
SYN3	8224	broad.mit.edu	37	22	33402361	33402361	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr22:33402361A>G	ENST00000358763.2	-	2	529	c.287T>C	c.(286-288)gTg>gCg	p.V96A	SYN3_ENST00000332840.5_Missense_Mutation_p.V96A	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	96	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						ATCATCGATCACCAACAGGAT	0.547																																						uc003amx.2																			0				skin(1)	1						c.(286-288)GTG>GCG		synapsin III isoform IIIa							117.0	112.0	114.0					22																	33402361		2203	4300	6503	SO:0001583	missense	8224				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity	g.chr22:33402361A>G	AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.287T>C	22.37:g.33402361A>G	ENSP00000351614:p.Val96Ala					SYN3_uc003amy.2_Missense_Mutation_p.V96A|SYN3_uc003amz.2_Missense_Mutation_p.V96A	p.V96A	NM_003490	NP_003481	O14994	SYN3_HUMAN			1	446	-			96			C; actin-binding and synaptic-vesicle binding.		B1B1F9	Missense_Mutation	SNP	ENST00000358763.2	37	c.287T>C	CCDS13908.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.541255	0.65085	.	.	ENSG00000185666	ENST00000358763;ENST00000332840;ENST00000390686;ENST00000441821;ENST00000412575	T;T	0.55052	0.54;0.54	5.21	5.21	0.72293	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Synapsin, pre-ATP-grasp domain (1);	0.000000	0.64402	D	0.000002	T	0.75917	0.3915	M	0.87617	2.895	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.85130	0.997;0.995;0.997	T	0.80226	-0.1470	10	0.56958	D	0.05	-6.4115	15.3817	0.74661	1.0:0.0:0.0:0.0	.	96;96;96	Q17R54;B1B1F9;O14994	.;.;SYN3_HUMAN	A	96	ENSP00000351614:V96A;ENSP00000330219:V96A	ENSP00000330219:V96A	V	-	2	0	SYN3	31732361	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.111000	0.94308	2.077000	0.62373	0.455000	0.32223	GTG		0.547	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4		
ATP2B2	491	broad.mit.edu	37	3	10413514	10413514	+	Silent	SNP	G	G	A	rs148841263	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:10413514G>A	ENST00000352432.4	-	11	1707	c.1638C>T	c.(1636-1638)agC>agT	p.S546S	ATP2B2_ENST00000383800.4_Silent_p.S501S|ATP2B2_ENST00000397077.1_Silent_p.S501S|ATP2B2_ENST00000360273.2_Silent_p.S546S|ATP2B2_ENST00000343816.4_Silent_p.S532S			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	546					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TGGTGTAGGCGCTGTTGATGG	0.547													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19399	0.0		0.0	False		,,,				2504	0.0				Ovarian(125;1619 1709 15675 19819 38835)	uc003bvt.2																			0				ovary(3)|skin(2)|central_nervous_system(1)	6						c.(1636-1638)AGC>AGT		plasma membrane calcium ATPase 2 isoform 1		G	,	16,4390	23.3+/-48.9	0,16,2187	151.0	129.0	137.0		1638,1503	2.5	1.0	3	dbSNP_134	137	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	0,17,6486	AA,AG,GG		0.0116,0.3631,0.1307	,	546/1244,501/1199	10413514	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	491				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding	g.chr3:10413514G>A	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1638C>T	3.37:g.10413514G>A						ATP2B2_uc003bvv.2_Silent_p.S501S|ATP2B2_uc003bvw.2_Silent_p.S501S|ATP2B2_uc010hdo.2_Silent_p.S251S	p.S546S	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN			12	2077	-			546			Cytoplasmic (Potential).		O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	c.1638C>T	CCDS33701.1																																																																																				0.547	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
NR2C2	7182	broad.mit.edu	37	3	15070193	15070193	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:15070193A>G	ENST00000425241.1	+	8	1261	c.899A>G	c.(898-900)cAg>cGg	p.Q300R	NR2C2_ENST00000478572.1_3'UTR|NR2C2_ENST00000393102.3_Missense_Mutation_p.Q300R|NR2C2_ENST00000323373.6_Missense_Mutation_p.Q319R|NR2C2_ENST00000406272.2_Missense_Mutation_p.Q300R			P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	300					cell differentiation (GO:0030154)|gene expression (GO:0010467)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TCAGAAATCCAGCCAGAGGAC	0.542																																						uc003bzj.3																			0					0						c.(898-900)CAG>CGG		nuclear receptor subfamily 2, group C, member 2							91.0	77.0	82.0					3																	15070193		2203	4300	6503	SO:0001583	missense	7182				cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding	g.chr3:15070193A>G	L27586	CCDS2621.1, CCDS74905.1	3p25	2013-01-16			ENSG00000177463	ENSG00000177463		"""Nuclear hormone receptors"""	7972	protein-coding gene	gene with protein product		601426		TR4		8661150, 8016112	Standard	XM_005265428		Approved	TAK1, TR2R1, hTAK1	uc003bzi.3	P49116	OTTHUMG00000129839	ENST00000425241.1:c.899A>G	3.37:g.15070193A>G	ENSP00000388387:p.Gln300Arg					NR2C2_uc003bzi.2_Missense_Mutation_p.Q319R	p.Q300R	NM_003298	NP_003289	P49116	NR2C2_HUMAN			8	1116	+			300					A8K3H5|B6ZGT8|P55092	Missense_Mutation	SNP	ENST00000425241.1	37	c.899A>G		.	.	.	.	.	.	.	.	.	.	A	14.98	2.696054	0.48202	.	.	ENSG00000177463	ENST00000425241;ENST00000323373;ENST00000393102;ENST00000406272	D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31	5.81	3.34	0.38264	Nuclear hormone receptor, ligand-binding (1);	0.098571	0.64402	D	0.000001	D	0.89252	0.6662	L	0.50333	1.59	0.43399	D	0.995529	B;B	0.16603	0.0;0.018	B;B	0.14023	0.001;0.01	T	0.81176	-0.1052	10	0.12430	T	0.62	.	12.6703	0.56864	0.7389:0.261:0.0:0.0	.	300;319	P49116;F2YGU2	NR2C2_HUMAN;.	R	300;319;300;300	ENSP00000388387:Q300R;ENSP00000320447:Q319R;ENSP00000376814:Q300R;ENSP00000384463:Q300R	ENSP00000320447:Q319R	Q	+	2	0	NR2C2	15045197	1.000000	0.71417	0.977000	0.42913	0.961000	0.63080	5.584000	0.67490	0.422000	0.26005	0.482000	0.46254	CAG		0.542	NR2C2-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000340729.1	NM_003298	
LRRC3B	116135	broad.mit.edu	37	3	26751737	26751737	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:26751737G>A	ENST00000396641.2	+	2	1166	c.574G>A	c.(574-576)Gct>Act	p.A192T	AC114877.3_ENST00000446601.1_lincRNA|LRRC3B_ENST00000456208.2_Missense_Mutation_p.A192T|LRRC3B_ENST00000417744.1_Missense_Mutation_p.A192T	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	192	LRRCT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						TGCCAACGACGCTGACCTTTG	0.468																																						uc003cdp.2																			0				pancreas(2)|ovary(1)|skin(1)	4						c.(574-576)GCT>ACT		leucine rich repeat containing 3B precursor							78.0	71.0	73.0					3																	26751737		2203	4300	6503	SO:0001583	missense	116135					integral to membrane		g.chr3:26751737G>A	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.574G>A	3.37:g.26751737G>A	ENSP00000379880:p.Ala192Thr					LRRC3B_uc003cdq.2_Missense_Mutation_p.A192T	p.A192T	NM_052953	NP_443185	Q96PB8	LRC3B_HUMAN			2	1163	+			192			LRRCT.		Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	37	c.574G>A	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.703768	0.30232	.	.	ENSG00000179796	ENST00000396641;ENST00000417744;ENST00000456208	T;T;T	0.59083	0.29;0.29;0.29	6.17	6.17	0.99709	.	0.047974	0.85682	D	0.000000	T	0.37785	0.1016	N	0.04508	-0.205	0.58432	D	0.999999	B	0.19935	0.04	B	0.12156	0.007	T	0.27571	-1.0070	10	0.15499	T	0.54	-12.6247	19.8676	0.96824	0.0:0.0:1.0:0.0	.	192	Q96PB8	LRC3B_HUMAN	T	192	ENSP00000379880:A192T;ENSP00000406370:A192T;ENSP00000394940:A192T	ENSP00000379880:A192T	A	+	1	0	LRRC3B	26726741	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	4.564000	0.60830	2.941000	0.99782	0.655000	0.94253	GCT		0.468	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
MST1R	4486	broad.mit.edu	37	3	49940194	49940194	+	Silent	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:49940194A>G	ENST00000296474.3	-	1	876	c.849T>C	c.(847-849)ctT>ctC	p.L283L	CTD-2330K9.2_ENST00000435478.1_RNA|CTD-2330K9.3_ENST00000419183.1_5'Flank|MST1R_ENST00000344206.4_Silent_p.L283L	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	283	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		CAGTGGCGCTAAGCCGTGCCA	0.622																																						uc003cxy.3																			0				ovary(5)|lung(1)	6						c.(847-849)CTT>CTC		macrophage stimulating 1 receptor precursor							74.0	78.0	77.0					3																	49940194		2203	4300	6503	SO:0001819	synonymous_variant	4486				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding	g.chr3:49940194A>G	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"""CD molecules"""	7381	protein-coding gene	gene with protein product		600168	"""PTK8 protein tyrosine kinase 8"""	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.849T>C	3.37:g.49940194A>G						MST1R_uc011bdd.1_Silent_p.L283L|MST1R_uc011bde.1_Silent_p.L283L|MST1R_uc011bdf.1_Silent_p.L283L|MST1R_uc011bdg.1_Silent_p.L283L	p.L283L	NM_002447	NP_002438	Q04912	RON_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)	1	1113	-			283			Extracellular (Potential).|Sema.		B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	37	c.849T>C	CCDS2807.1																																																																																				0.622	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
ITIH4	3700	broad.mit.edu	37	3	52851043	52851043	+	Silent	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:52851043C>T	ENST00000266041.4	-	21	2424	c.2328G>A	c.(2326-2328)gaG>gaA	p.E776E	ITIH4_ENST00000346281.5_Silent_p.E760E|ITIH4_ENST00000406595.1_Silent_p.E746E|ITIH4_ENST00000485816.1_Silent_p.E781E|RP5-966M1.6_ENST00000468472.1_3'UTR	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	776					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		ACCCAGCCTTCTCCCTCTCAT	0.592																																						uc003dfz.2																			0				ovary(2)|central_nervous_system(1)	3						c.(2326-2328)GAG>GAA		inter-alpha (globulin) inhibitor H4							112.0	114.0	113.0					3																	52851043		2203	4300	6503	SO:0001819	synonymous_variant	3700				acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity	g.chr3:52851043C>T	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.2328G>A	3.37:g.52851043C>T						ITIH4_uc011bel.1_Silent_p.E490E|ITIH4_uc003dfy.2_Silent_p.E571E|ITIH4_uc011bem.1_Silent_p.E781E|ITIH4_uc011ben.1_Silent_p.E746E	p.E776E	NM_002218	NP_002209	Q14624	ITIH4_HUMAN		BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)	21	2364	-			776					B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	c.2328G>A	CCDS2865.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.608871	0.00842	.	.	ENSG00000055955	ENST00000441637	T	0.11712	2.75	4.83	2.46	0.29980	.	1.363480	0.04608	N	0.399859	T	0.06462	0.0166	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32079	-0.9920	7	0.19147	T	0.46	-8.3478	4.0104	0.09619	0.0:0.5975:0.2338:0.1686	.	.	.	.	K	565	ENSP00000395634:E565K	ENSP00000395634:E565K	E	-	1	0	ITIH4	52826083	0.001000	0.12720	0.074000	0.20217	0.021000	0.10359	-0.295000	0.08298	2.239000	0.73571	0.561000	0.74099	GAA		0.592	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
ARL6	84100	broad.mit.edu	37	3	97506846	97506846	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:97506846G>A	ENST00000463745.1	+	6	839	c.362G>A	c.(361-363)cGt>cAt	p.R121H	ARL6_ENST00000335979.2_Missense_Mutation_p.R121H|ARL6_ENST00000394206.1_Missense_Mutation_p.R121H|ARL6_ENST00000496713.1_3'UTR	NM_001278293.1	NP_001265222.1	Q9H0F7	ARL6_HUMAN	ADP-ribosylation factor-like 6	121					cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|melanosome transport (GO:0032402)|protein polymerization (GO:0051258)|protein targeting to membrane (GO:0006612)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	axonemal microtubule (GO:0005879)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane coat (GO:0030117)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)			large_intestine(1)|lung(4)	5		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)		ATTAAACACCGTCGAATTCCA	0.323																																						uc003drv.2																			0					0						c.(361-363)CGT>CAT		ADP-ribosylation factor-like 6							72.0	74.0	73.0					3																	97506846		2202	4297	6499	SO:0001583	missense	84100	Bardet-Biedl_syndrome			cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding	g.chr3:97506846G>A	BC024239	CCDS2928.1	3q11.2	2014-05-09			ENSG00000113966	ENSG00000113966		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	13210	protein-coding gene	gene with protein product		608845		BBS3		15258860, 15314642, 21282186	Standard	NM_032146		Approved	RP55	uc003drv.3	Q9H0F7	OTTHUMG00000159189	ENST00000463745.1:c.362G>A	3.37:g.97506846G>A	ENSP00000419619:p.Arg121His					ARL6_uc003drw.2_RNA|ARL6_uc003dru.2_Missense_Mutation_p.R121H|ARL6_uc010hoy.2_Missense_Mutation_p.R121H	p.R121H	NM_177976	NP_816931	Q9H0F7	ARL6_HUMAN		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)	7	675	+		Lung NSC(201;0.0193)|Prostate(884;0.174)	121					A8KA93|D3DN31	Missense_Mutation	SNP	ENST00000463745.1	37	c.362G>A	CCDS2928.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.8|23.8	4.461017|4.461017	0.84317|0.84317	.|.	.|.	ENSG00000113966|ENSG00000113966	ENST00000463745;ENST00000462412;ENST00000335979;ENST00000394206|ENST00000476753	D;T;D;D|.	0.82619|.	-1.63;-1.21;-1.63;-1.63|.	5.49|5.49	5.49|5.49	0.81192|0.81192	Small GTP-binding protein domain (1);|.	0.110332|.	0.64402|.	D|.	0.000011|.	T|T	0.76234|0.76234	0.3959|0.3959	M|M	0.74467|0.74467	2.265|2.265	0.58432|0.58432	D|D	0.999993|0.999993	D|.	0.67145|.	0.996|.	B|.	0.43301|.	0.415|.	T|T	0.75496|0.75496	-0.3297|-0.3297	10|5	0.87932|.	D|.	0|.	.|.	17.5189|17.5189	0.87782|0.87782	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	121|.	Q9H0F7|.	ARL6_HUMAN|.	H|I	121|16	ENSP00000419619:R121H;ENSP00000418740:R121H;ENSP00000337722:R121H;ENSP00000377756:R121H|.	ENSP00000337722:R121H|.	R|V	+|+	2|1	0|0	ARL6|ARL6	98989536|98989536	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.898000|0.898000	0.52572|0.52572	4.926000|4.926000	0.63433|0.63433	2.733000|2.733000	0.93635|0.93635	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.323	ARL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353756.1	NM_032146	
OR5K1	26339	broad.mit.edu	37	3	98189167	98189167	+	Silent	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:98189167A>G	ENST00000332650.5	+	1	844	c.747A>G	c.(745-747)tcA>tcG	p.S249S		NM_001004736.2	NP_001004736.2	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K, member 1	249						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(4)|lung(21)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGTCAGTTTCATTATTCTATG	0.333																																						uc003dsm.2																			0				large_intestine(1)	1						c.(745-747)TCA>TCG		olfactory receptor, family 5, subfamily K,							98.0	101.0	100.0					3																	98189167		2185	4293	6478	SO:0001819	synonymous_variant	26339				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr3:98189167A>G	X64984	CCDS43115.1	3q11.2	2013-09-23			ENSG00000232382	ENSG00000232382		"""GPCR / Class A : Olfactory receptors"""	8349	protein-coding gene	gene with protein product						1370859	Standard	NM_001004736		Approved	HTPCRX10, HSHTPCRX10	uc003dsm.3	Q8NHB7	OTTHUMG00000160048	ENST00000332650.5:c.747A>G	3.37:g.98189167A>G							p.S249S	NM_001004736	NP_001004736	Q8NHB7	OR5K1_HUMAN			1	747	+			249			Helical; Name=6; (Potential).		B9EGY5|Q6IF46	Silent	SNP	ENST00000332650.5	37	c.747A>G	CCDS43115.1																																																																																				0.333	OR5K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359019.1		
ST3GAL6	10402	broad.mit.edu	37	3	98507190	98507190	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:98507190G>C	ENST00000483910.1	+	8	928	c.639G>C	c.(637-639)aaG>aaC	p.K213N	ST3GAL6_ENST00000462152.1_3'UTR|ST3GAL6_ENST00000265261.6_Missense_Mutation_p.K95N|ST3GAL6_ENST00000394162.1_Missense_Mutation_p.K213N	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	213					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						GTTTTTGGAAGAAACCAGCCT	0.323																																						uc003dsz.2																			0				ovary(1)	1						c.(637-639)AAG>AAC		alpha2,3-sialyltransferase VI							84.0	92.0	89.0					3																	98507190		2202	4300	6502	SO:0001583	missense	10402				amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity	g.chr3:98507190G>C	AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"""Sialyltransferases"""	18080	protein-coding gene	gene with protein product		607156	"""sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"""	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.639G>C	3.37:g.98507190G>C	ENSP00000417376:p.Lys213Asn					ST3GAL6_uc003dsy.2_Missense_Mutation_p.K127N|ST3GAL6_uc003dta.2_Missense_Mutation_p.K95N|ST3GAL6_uc003dtb.2_Missense_Mutation_p.K69N|ST3GAL6_uc003dtc.2_Missense_Mutation_p.K213N|ST3GAL6_uc010hpd.2_Missense_Mutation_p.K266N	p.K213N	NM_006100	NP_006091	Q9Y274	SIA10_HUMAN			8	875	+			213			Lumenal (Potential).		B2RCH2|B3KMI1|D3DN39|F8W6U0	Missense_Mutation	SNP	ENST00000483910.1	37	c.639G>C	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833741	0.71258	.	.	ENSG00000064225	ENST00000483910;ENST00000265261;ENST00000486334;ENST00000394162;ENST00000485391;ENST00000492254;ENST00000485145	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	4.84	4.84	0.62591	.	0.153008	0.45606	D	0.000357	T	0.56543	0.1992	M	0.87547	2.89	0.45066	D	0.998087	D;P;P	0.63880	0.993;0.954;0.619	P;P;P	0.58873	0.824;0.847;0.515	T	0.63510	-0.6621	10	0.56958	D	0.05	-28.4486	15.8184	0.78621	0.0:0.0:1.0:0.0	.	236;95;213	C9J480;F8W6U0;Q9Y274	.;.;SIA10_HUMAN	N	213;95;213;213;181;236;127	ENSP00000417376:K213N;ENSP00000265261:K95N;ENSP00000418896:K213N;ENSP00000377717:K213N;ENSP00000418650:K181N;ENSP00000417201:K236N;ENSP00000419202:K127N	ENSP00000265261:K95N	K	+	3	2	ST3GAL6	99989880	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.445000	0.52921	2.671000	0.90904	0.563000	0.77884	AAG		0.323	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100	
MYLK	4638	broad.mit.edu	37	3	123428617	123428617	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:123428617G>C	ENST00000475616.1	-	11	1927	c.1928C>G	c.(1927-1929)aCt>aGt	p.T643S	MYLK_ENST00000360772.3_Missense_Mutation_p.T643S|MYLK_ENST00000346322.5_Missense_Mutation_p.T574S|MYLK_ENST00000359169.1_Missense_Mutation_p.T643S|MYLK_ENST00000360304.3_Missense_Mutation_p.T643S			Q15746	MYLK_HUMAN	myosin light chain kinase	643	Ig-like C2-type 5.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CACTTGGACAGTCATAGTGAC	0.532																																						uc003ego.2																			0				ovary(6)|skin(2)|stomach(1)	9						c.(1927-1929)ACT>AGT		myosin light chain kinase isoform 1							251.0	267.0	262.0					3																	123428617		2203	4300	6503	SO:0001583	missense	4638				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity	g.chr3:123428617G>C	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.1928C>G	3.37:g.123428617G>C	ENSP00000418335:p.Thr643Ser					MYLK_uc011bjw.1_Missense_Mutation_p.T643S|MYLK_uc003egp.2_Missense_Mutation_p.T574S|MYLK_uc003egq.2_Missense_Mutation_p.T643S|MYLK_uc003egr.2_Missense_Mutation_p.T574S|MYLK_uc003egs.2_Missense_Mutation_p.T467S	p.T643S	NM_053025	NP_444253	Q15746	MYLK_HUMAN		GBM - Glioblastoma multiforme(114;0.0736)	14	2210	-		Lung NSC(201;0.0496)	643			Ig-like C2-type 5.		B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	c.1928C>G	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201836	0.58234	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25	5.05	5.05	0.67936	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.63165	0.2488	N	0.11560	0.145	0.80722	D	1	D;P;D;D;D	0.76494	0.999;0.947;0.997;0.999;0.999	D;P;D;D;D	0.83275	0.993;0.908;0.984;0.991;0.996	T	0.57406	-0.7817	9	0.09338	T	0.73	.	14.2295	0.65882	0.0:0.1491:0.8509:0.0	.	643;574;643;574;643	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	S	643;643;643;574;643	ENSP00000354004:T643S;ENSP00000353452:T643S;ENSP00000352088:T643S;ENSP00000320622:T574S;ENSP00000418335:T643S	ENSP00000320622:T574S	T	-	2	0	MYLK	124911307	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.749000	0.68704	2.622000	0.88805	0.650000	0.86243	ACT		0.532	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
TRIM42	287015	broad.mit.edu	37	3	140397090	140397090	+	Missense_Mutation	SNP	G	G	A	rs116143762		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:140397090G>A	ENST00000286349.3	+	1	210	c.19G>A	c.(19-21)Gtt>Att	p.V7I		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	7	Cys-rich.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TGCTATGTGCGTTTGCTGTCC	0.507																																						uc003eto.1																			0				lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7						c.(19-21)GTT>ATT		tripartite motif-containing 42		G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	368.0	307.0	328.0		19	0.6	1.0	3	dbSNP_132	328	0,8600		0,0,4300	no	missense	TRIM42	NM_152616.4	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	7/724	140397090	1,13005	2203	4300	6503	SO:0001583	missense	287015					intracellular	zinc ion binding	g.chr3:140397090G>A	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.19G>A	3.37:g.140397090G>A	ENSP00000286349:p.Val7Ile						p.V7I	NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN			1	210	+			7			Cys-rich.		A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	c.19G>A	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	G	8.384	0.838139	0.16891	2.27E-4	0.0	ENSG00000155890	ENST00000286349	T	0.37411	1.2	5.37	0.561	0.17285	.	0.904453	0.09312	N	0.819434	T	0.14874	0.0359	N	0.03608	-0.345	0.20764	N	0.999857	B	0.09022	0.002	B	0.04013	0.001	T	0.25082	-1.0142	10	0.29301	T	0.29	-13.3898	5.8185	0.18514	0.1808:0.4034:0.4158:0.0	.	7	Q8IWZ5	TRI42_HUMAN	I	7	ENSP00000286349:V7I	ENSP00000286349:V7I	V	+	1	0	TRIM42	141879780	0.019000	0.18553	0.964000	0.40570	0.414000	0.31173	0.278000	0.18753	0.657000	0.30906	-0.214000	0.12660	GTT		0.507	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
ZIC4	84107	broad.mit.edu	37	3	147114065	147114065	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:147114065C>T	ENST00000383075.3	-	3	774	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	ZIC4_ENST00000484399.1_Missense_Mutation_p.A88T|ZIC4_ENST00000491672.1_Intron|ZIC4_ENST00000525172.2_Missense_Mutation_p.A138T|ZIC4_ENST00000425731.3_Missense_Mutation_p.A126T|ZIC4_ENST00000473123.1_Missense_Mutation_p.A88T	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	88	Poly-Ala.					nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A88S(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						GCTGCCAGGGCGTCGCTGCGG	0.701																																						uc003ewd.1																			1	Substitution - Missense(1)		lung(1)	upper_aerodigestive_tract(1)|central_nervous_system(1)	2						c.(262-264)GCC>ACC		zinc finger protein of the cerebellum 4							11.0	14.0	13.0					3																	147114065		1998	4151	6149	SO:0001583	missense	84107					nucleus	DNA binding|zinc ion binding	g.chr3:147114065C>T	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"""Zinc fingers, C2H2-type"""	20393	protein-coding gene	gene with protein product		608948	"""zinc finger protein of the cerebellum 4"""				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.262G>A	3.37:g.147114065C>T	ENSP00000372553:p.Ala88Thr					ZIC4_uc003ewc.1_Missense_Mutation_p.A18T|ZIC4_uc011bno.1_Missense_Mutation_p.A138T	p.A88T	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN			3	535	-			88			Poly-Ala.		A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	37	c.262G>A	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.419041	0.42918	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000462748	T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31	4.98	0.736	0.18307	.	0.320500	0.22453	N	0.059871	T	0.09598	0.0236	N	0.02011	-0.69	0.80722	D	1	B;B	0.23650	0.089;0.007	B;B	0.13407	0.009;0.003	T	0.09997	-1.0649	10	0.17369	T	0.5	.	1.6191	0.02710	0.2391:0.4205:0.1009:0.2395	.	138;88	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	T	88;126;138;88;88;88	ENSP00000372553:A88T;ENSP00000397695:A126T;ENSP00000435509:A138T;ENSP00000417855:A88T;ENSP00000420775:A88T;ENSP00000420627:A88T	ENSP00000372553:A88T	A	-	1	0	ZIC4	148596755	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.915000	0.56409	0.488000	0.27723	-0.258000	0.10820	GCC		0.701	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1		
VPS8	23355	broad.mit.edu	37	3	184571960	184571960	+	Splice_Site	SNP	G	G	A	rs201816956		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:184571960G>A	ENST00000437079.3	+	13	1205	c.1034G>A	c.(1033-1035)cGg>cAg	p.R345Q	VPS8_ENST00000446204.2_Splice_Site_p.R343Q|VPS8_ENST00000287546.4_Splice_Site_p.R345Q|VPS8_ENST00000436792.2_Splice_Site_p.R343Q	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	345							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			CCCTATGGCCGGGTGAGTACG	0.413																																						uc003fpb.1																			0				ovary(1)	1						c.(1027-1029)CGG>CAG		vacuolar protein sorting 8 homolog isoform b		G	GLN/ARG,GLN/ARG	0,3812		0,0,1906	79.0	73.0	75.0		1034,1028	5.0	1.0	3		75	1,8257		0,1,4128	yes	missense-near-splice,missense-near-splice	VPS8	NM_001009921.2,NM_015303.3	43,43	0,1,6034	AA,AG,GG		0.0121,0.0,0.0083	benign,benign	345/1429,343/1427	184571960	1,12069	1906	4129	6035	SO:0001630	splice_region_variant	23355						zinc ion binding	g.chr3:184571960G>A	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.1035+1G>A	3.37:g.184571960G>A						VPS8_uc010hyd.1_Missense_Mutation_p.R343Q	p.R343Q	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)		12	1199	+	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		345					A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	c.1028G>A	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730114	0.48939	0.0	1.21E-4	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	5.04	5.04	0.67666	.	0.060399	0.64402	D	0.000003	T	0.14056	0.0340	N	0.08118	0	0.45930	D	0.998763	D;P	0.56521	0.976;0.766	P;B	0.45639	0.488;0.078	T	0.13495	-1.0507	10	0.11794	T	0.64	-14.0754	18.4014	0.90518	0.0:0.0:1.0:0.0	.	343;343	Q8N3P4-2;Q8N3P4-3	.;.	Q	345;345;343;343	ENSP00000287546:R345Q;ENSP00000397879:R345Q;ENSP00000404704:R343Q;ENSP00000405483:R343Q	ENSP00000287546:R345Q	R	+	2	0	VPS8	186054654	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.509000	0.81698	2.317000	0.78254	0.563000	0.77884	CGG		0.413	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	Missense_Mutation
LINC00969	440993	broad.mit.edu	37	3	195410687	195410687	+	lincRNA	SNP	T	T	A	rs6583274	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:195410687T>A	ENST00000445430.1	+	0	1884									long intergenic non-protein coding RNA 969																		CCCTTTGAGGTGCACTGGAGG	0.567													.|||	701	0.139976	0.0552	0.1571	5008	,	,		36746	0.1855		0.16	False		,,,				2504	0.1748					uc003fuw.2																			0					0						c.(583-585)GTG>GAG		SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);																																						727956							g.chr3:195410687T>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195410687T>A						SDHAP2_uc003fuv.2_RNA	p.V195E							13	1778	+									Missense_Mutation	SNP	ENST00000445430.1	37	c.584T>A																																																																																					0.567	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1		
MUC4	4585	broad.mit.edu	37	3	195505849	195505849	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr3:195505849G>A	ENST00000463781.3	-	2	13061	c.12602C>T	c.(12601-12603)gCa>gTa	p.A4201V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A4201V|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.592																																						uc011bto.1																			0					0						c.(12217-12219)GCA>GTA		mucin 4 isoform a							18.0	14.0	15.0					3																	195505849		690	1575	2265	SO:0001583	missense	4585				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity	g.chr3:195505849G>A	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12602C>T	3.37:g.195505849G>A	ENSP00000417498:p.Ala4201Val					MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	p.A4073V	NM_018406	NP_060876	Q99102	MUC4_HUMAN	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)	3	12678	-	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	c.12218C>T	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	2.680	-0.275604	0.05679	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.46063	0.88;0.97	.	.	.	.	.	.	.	.	T	0.16599	0.0399	N	0.08118	0	0.09310	N	1	B	0.21606	0.058	B	0.18263	0.021	T	0.18871	-1.0323	7	.	.	.	.	4.6311	0.12502	0.442:0.0:0.558:0.0	.	4073	E7ESK3	.	V	4201	ENSP00000417498:A4201V;ENSP00000420243:A4201V	.	A	-	2	0	MUC4	196990628	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-0.859000	0.04277	-1.727000	0.01368	-1.973000	0.00462	GCA		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TLR6	10333	broad.mit.edu	37	4	38830788	38830788	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr4:38830788C>T	ENST00000381950.1	-	1	372	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	TLR6_ENST00000436693.2_Missense_Mutation_p.E103K			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	103					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCCAAATATTCTAAATCCTGG	0.363																																						uc003gtm.2																			0				ovary(2)	2						c.(307-309)GAA>AAA		toll-like receptor 6 precursor							47.0	47.0	47.0					4																	38830788		2203	4300	6503	SO:0001583	missense	10333				activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity	g.chr4:38830788C>T		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.307G>A	4.37:g.38830788C>T	ENSP00000371376:p.Glu103Lys					TLR6_uc010ifg.1_Missense_Mutation_p.E103K	p.E103K	NM_006068	NP_006059	Q9Y2C9	TLR6_HUMAN			1	373	-			103			LRR 3.|Extracellular (Potential).		B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	c.307G>A	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	C	32	5.111187	0.94339	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542;ENST00000508254	T;T;T	0.56444	0.46;0.46;0.46	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	T	0.65344	0.2682	L	0.46670	1.46	0.58432	D	0.999999	P	0.50272	0.933	P	0.58391	0.838	T	0.65471	-0.6160	10	0.59425	D	0.04	.	19.5078	0.95127	0.0:1.0:0.0:0.0	.	103	Q9Y2C9	TLR6_HUMAN	K	103	ENSP00000389600:E103K;ENSP00000371376:E103K;ENSP00000424718:E103K	ENSP00000371376:E103K	E	-	1	0	TLR6	38507183	1.000000	0.71417	0.997000	0.53966	0.882000	0.50991	3.371000	0.52379	2.602000	0.87976	0.561000	0.74099	GAA		0.363	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
PRDM8	56978	broad.mit.edu	37	4	81123201	81123201	+	Silent	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr4:81123201C>T	ENST00000504452.1	+	8	1424	c.585C>T	c.(583-585)ggC>ggT	p.G195G	PRDM8_ENST00000339711.4_Silent_p.G195G|PRDM8_ENST00000415738.2_Silent_p.G195G			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	195	Gly-rich.				corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						AACAAggcggcggcgtgggca	0.617											OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc010ijo.2																			0				skin(1)	1						c.(583-585)GGC>GGT		PR domain containing 8							48.0	56.0	54.0					4																	81123201		2018	4170	6188	SO:0001819	synonymous_variant	56978				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr4:81123201C>T	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.585C>T	4.37:g.81123201C>T			OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1203	PRDM8_uc003hmb.3_Silent_p.G195G|PRDM8_uc003hmc.3_Silent_p.G195G	p.G195G	NM_020226	NP_064611	Q9NQV8	PRDM8_HUMAN			8	1424	+			195			Gly-rich.		A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	c.585C>T	CCDS43243.1																																																																																				0.617	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
HHIP	64399	broad.mit.edu	37	4	145580881	145580881	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr4:145580881G>A	ENST00000296575.3	+	4	1377	c.722G>A	c.(721-723)cGt>cAt	p.R241H	HHIP_ENST00000511314.1_3'UTR|HHIP_ENST00000434550.2_Missense_Mutation_p.R241H|HHIP-AS1_ENST00000512359.1_RNA	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	241					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		GGCTCGCAACGTCTCTTCATT	0.453																																						uc003ijs.1																			0				ovary(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6						c.(721-723)CGT>CAT		hedgehog-interacting protein precursor							123.0	131.0	128.0					4																	145580881		2203	4300	6503	SO:0001583	missense	64399					cytoplasm|extracellular region	catalytic activity|protein binding|zinc ion binding	g.chr4:145580881G>A	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"""hedgehog-interacting protein"""			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.722G>A	4.37:g.145580881G>A	ENSP00000296575:p.Arg241His					HHIP_uc003ijr.1_Missense_Mutation_p.R241H	p.R241H	NM_022475	NP_071920	Q96QV1	HHIP_HUMAN		GBM - Glioblastoma multiforme(119;0.0185)	4	1377	+	all_hematologic(180;0.151)		241					Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Missense_Mutation	SNP	ENST00000296575.3	37	c.722G>A	CCDS3762.1	.	.	.	.	.	.	.	.	.	.	G	33	5.289191	0.95517	.	.	ENSG00000164161	ENST00000296575;ENST00000434550	T;T	0.78924	2.75;-1.22	5.54	5.54	0.83059	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.90456	0.7011	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91774	0.5430	10	0.87932	D	0	-18.1383	19.4725	0.94969	0.0:0.0:1.0:0.0	.	241;241	Q96QV1;Q96QV1-2	HHIP_HUMAN;.	H	241	ENSP00000296575:R241H;ENSP00000408587:R241H	ENSP00000296575:R241H	R	+	2	0	HHIP	145800331	1.000000	0.71417	0.916000	0.36221	0.983000	0.72400	9.869000	0.99810	2.620000	0.88729	0.555000	0.69702	CGT		0.453	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2		
HCN1	348980	broad.mit.edu	37	5	45262309	45262309	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr5:45262309T>A	ENST00000303230.4	-	8	2444	c.2387A>T	c.(2386-2388)gAg>gTg	p.E796V		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	796					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						AGTGGACACCTCATGGGGCAG	0.632																																						uc003jok.2																			0				ovary(1)	1						c.(2386-2388)GAG>GTG		hyperpolarization activated cyclic							55.0	53.0	53.0					5																	45262309		2203	4300	6503	SO:0001583	missense	348980					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity	g.chr5:45262309T>A	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.2387A>T	5.37:g.45262309T>A	ENSP00000307342:p.Glu796Val						p.E796V	NM_021072	NP_066550	O60741	HCN1_HUMAN			8	2412	-			796			Cytoplasmic (Potential).			Missense_Mutation	SNP	ENST00000303230.4	37	c.2387A>T	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.668791	0.67814	.	.	ENSG00000164588	ENST00000303230	T	0.76839	-1.05	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000005	T	0.73745	0.3626	N	0.24115	0.695	0.54753	D	0.999983	D	0.57899	0.981	P	0.52109	0.69	T	0.73493	-0.3965	10	0.32370	T	0.25	.	15.0491	0.71850	0.0:0.0:0.0:1.0	.	796	O60741	HCN1_HUMAN	V	796	ENSP00000307342:E796V	ENSP00000307342:E796V	E	-	2	0	HCN1	45298066	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	5.973000	0.70456	2.016000	0.59253	0.533000	0.62120	GAG		0.632	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
PJA2	9867	broad.mit.edu	37	5	108680493	108680493	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr5:108680493C>A	ENST00000361189.2	-	8	2031	c.1792G>T	c.(1792-1794)Gca>Tca	p.A598S	PJA2_ENST00000361557.3_Missense_Mutation_p.A598S	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	598	Interaction with PRKAR1A, PRKAR2A and PRKAR2B.				long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		ACATCCACTGCAAGAGACTCT	0.408																																						uc003kos.3																			0				ovary(1)|skin(1)	2						c.(1792-1794)GCA>TCA		praja 2, RING-H2 motif containing							111.0	113.0	113.0					5																	108680493		2202	4300	6502	SO:0001583	missense	9867				long-term memory|regulation of protein kinase A signaling cascade	cell junction|endoplasmic reticulum membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	ligase activity|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|zinc ion binding	g.chr5:108680493C>A	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.1792G>T	5.37:g.108680493C>A	ENSP00000354775:p.Ala598Ser						p.A598S	NM_014819	NP_055634	O43164	PJA2_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)	8	2012	-		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)	598			Interaction with PRKAR1A, PRKAR2A and PRKAR2B.		A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	c.1792G>T	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613468	0.66672	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.11063	2.81;2.81	5.98	5.11	0.69529	.	0.000000	0.64402	D	0.000001	T	0.19406	0.0466	L	0.29908	0.895	0.41741	D	0.98961	D	0.64830	0.994	D	0.64410	0.925	T	0.00248	-1.1880	10	0.56958	D	0.05	-19.0524	12.8316	0.57748	0.0:0.8719:0.0:0.1281	.	598	O43164	PJA2_HUMAN	S	598	ENSP00000354775:A598S;ENSP00000355284:A598S	ENSP00000354775:A598S	A	-	1	0	PJA2	108708392	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.299000	0.51826	2.838000	0.97847	0.591000	0.81541	GCA		0.408	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
GNPDA1	10007	broad.mit.edu	37	5	141385836	141385838	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr5:141385836_141385838delGAA	ENST00000508177.1	-	3	1038_1040	c.280_282delTTC	c.(280-282)ttcdel	p.F94del	GNPDA1_ENST00000503794.1_In_Frame_Del_p.F94del|GNPDA1_ENST00000458112.2_In_Frame_Del_p.F60del|GNPDA1_ENST00000513454.1_In_Frame_Del_p.F94del|GNPDA1_ENST00000500692.2_In_Frame_Del_p.F94del|GNPDA1_ENST00000311337.6_In_Frame_Del_p.F94del|GNPDA1_ENST00000542860.1_Intron			P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	94					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucosamine catabolic process (GO:0006043)|N-acetylglucosamine metabolic process (GO:0006044)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			central_nervous_system(1)|lung(1)|skin(3)|stomach(1)	6		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAATGTGCTTGAAGAAGTTGTTC	0.527																																						uc003lmf.3																			0					0						c.(280-282)TTCdel		glucosamine-6-phosphate deaminase 1																																				SO:0001651	inframe_deletion	10007				generation of precursor metabolites and energy|glucosamine catabolic process|N-acetylglucosamine metabolic process|single fertilization	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity	g.chr5:141385836_141385838delGAA	AF048826	CCDS4272.1	5q21	2008-02-05	2003-10-17	2003-10-22	ENSG00000113552	ENSG00000113552	3.5.99.6		4417	protein-coding gene	gene with protein product	"""glucosamine-6-phosphate deaminase"", ""oscillin"""	601798	"""glucosamine-6-phosphate isomerase"""	GNPI		9714720, 9438414	Standard	NM_005471		Approved	GNPDA, HLN, GPI, KIAA0060	uc010jgh.3	P46926	OTTHUMG00000129657	ENST00000508177.1:c.280_282delTTC	5.37:g.141385839_141385841delGAA	ENSP00000423674:p.Phe94del					GNPDA1_uc003lmg.3_In_Frame_Del_p.F94del|GNPDA1_uc010jgh.2_In_Frame_Del_p.F94del|GNPDA1_uc003lmh.3_In_Frame_Del_p.F60del	p.F94del	NM_005471	NP_005462	P46926	GNPI1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		3	1039_1041	-		all_hematologic(541;0.118)	94					B7Z3X4|D3DQE7	In_Frame_Del	DEL	ENST00000508177.1	37	c.280_282delTTC	CCDS4272.1																																																																																				0.527	GNPDA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370631.1	NM_005471	
CPEB4	80315	broad.mit.edu	37	5	173317554	173317554	+	Frame_Shift_Del	DEL	A	A	-			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr5:173317554delA	ENST00000265085.5	+	1	2272	c.818delA	c.(817-819)catfs	p.H273fs	CPEB4_ENST00000334035.5_Frame_Shift_Del_p.H273fs|CPEB4_ENST00000520867.1_Frame_Shift_Del_p.H273fs|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000519835.1_Frame_Shift_Del_p.H273fs	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	273					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAGCTGCCTCATTTGGCGAAT	0.557																																						uc003mcs.3																			0					0						c.(817-819)CATfs		cytoplasmic polyadenylation element binding							192.0	204.0	200.0					5																	173317554		2203	4300	6503	SO:0001589	frameshift_variant	80315						nucleotide binding|RNA binding	g.chr5:173317554delA	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"""RNA binding motif (RRM) containing"""	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.818delA	5.37:g.173317554delA	ENSP00000265085:p.His273fs					CPEB4_uc010jju.1_Frame_Shift_Del_p.H273fs|CPEB4_uc010jjv.2_Frame_Shift_Del_p.H273fs|CPEB4_uc011dfg.1_Frame_Shift_Del_p.H273fs|CPEB4_uc003mct.3_5'Flank|CPEB4_uc003mcu.3_5'Flank	p.H273fs	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		1	2224	+	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	273					B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Frame_Shift_Del	DEL	ENST00000265085.5	37	c.818delA	CCDS4390.1																																																																																				0.557	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627	
PRSS16	10279	broad.mit.edu	37	6	27220721	27220721	+	Silent	SNP	C	C	T	rs191407230	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:27220721C>T	ENST00000230582.3	+	9	1158	c.1143C>T	c.(1141-1143)ttC>ttT	p.F381F	PRSS16_ENST00000377456.2_Intron|PRSS16_ENST00000421826.2_Silent_p.F124F	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	381					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)	p.F381F(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GTACCGAGTTCGGCTTCTGTA	0.507													C|||	2	0.000399361	0.0015	0.0	5008	,	,		21194	0.0		0.0	False		,,,				2504	0.0				NSCLC(178;1118 2105 17078 23587 44429)	uc003nja.2																			1	Substitution - coding silent(1)		large_intestine(1)	ovary(2)|central_nervous_system(2)|skin(1)	5						c.(1141-1143)TTC>TTT		protease, serine, 16 precursor		C		1,4405	2.1+/-5.4	0,1,2202	209.0	178.0	188.0		1143	-7.3	0.9	6		188	0,8600		0,0,4300	no	coding-synonymous	PRSS16	NM_005865.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		381/515	27220721	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10279				protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity	g.chr6:27220721C>T	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1143C>T	6.37:g.27220721C>T						PRSS16_uc011dkt.1_RNA|PRSS16_uc003njb.2_Silent_p.F124F|PRSS16_uc010jqq.1_Silent_p.F158F|PRSS16_uc010jqr.1_Silent_p.F132F|PRSS16_uc003njc.1_RNA|PRSS16_uc003njd.2_Intron	p.F381F	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN			9	1155	+			381					O75416	Silent	SNP	ENST00000230582.3	37	c.1143C>T	CCDS4623.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	8.864	0.947645	0.18356	2.27E-4	0.0	ENSG00000112812	ENST00000485993;ENST00000475106	.	.	.	4.26	-7.33	0.01431	.	.	.	.	.	T	0.37293	0.0998	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56896	-0.7903	4	.	.	.	-26.3792	11.6689	0.51389	0.0:0.535:0.0:0.465	.	.	.	.	W	134;160	.	.	R	+	1	2	PRSS16	27328700	0.105000	0.21958	0.949000	0.38748	0.911000	0.54048	-2.253000	0.01184	-1.143000	0.02866	-1.012000	0.02466	CGG		0.507	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
LYPLA2P1	653639	broad.mit.edu	37	6	33333916	33333916	+	IGR	SNP	G	G	T	rs211449	byFrequency	TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:33333916G>T								DAXX (43125 upstream) : KIFC1 (25396 downstream)																							TGTGCCCTGTGTCTCCAAGTC	0.562													G|||	2486	0.496406	0.4894	0.402	5008	,	,		17445	0.6548		0.3549	False		,,,				2504	0.5552					uc003shx.2																			0					0						c.(88-90)GAC>GAA		SubName: Full=Lysophospholipase II; Flags: Fragment;																																				SO:0001628	intergenic_variant	653639							g.chr6:33333916G>T																													6.37:g.33333916G>T							p.D30E	NR_001444						1	224	-									Missense_Mutation	SNP		37	c.90C>A																																																																																				0	0.562								
UHRF1BP1	54887	broad.mit.edu	37	6	34838669	34838669	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:34838669C>T	ENST00000192788.5	+	18	3928	c.3757C>T	c.(3757-3759)Cac>Tac	p.H1253Y	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.H1253Y	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	1253							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						GAAGACTGGCCACATCAGGCC	0.498																																						uc003oju.3																			0				ovary(3)	3						c.(3757-3759)CAC>TAC		ICBP90 binding protein 1							74.0	74.0	74.0					6																	34838669		1922	4136	6058	SO:0001583	missense	54887							g.chr6:34838669C>T	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.3757C>T	6.37:g.34838669C>T	ENSP00000192788:p.His1253Tyr					UHRF1BP1_uc010jvm.1_RNA|UHRF1BP1_uc010jvn.2_RNA|UHRF1BP1_uc010jvo.2_RNA	p.H1253Y	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN			18	3991	+			1253					Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	c.3757C>T	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	0.486	-0.877666	0.02550	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.08102	3.13;3.13	5.27	-1.69	0.08186	.	0.886574	0.10291	N	0.692343	T	0.01189	0.0039	N	0.14661	0.345	0.09310	N	1	B	0.15719	0.014	B	0.14578	0.011	T	0.47368	-0.9123	10	0.38643	T	0.18	-0.458	3.2135	0.06691	0.1719:0.4984:0.088:0.2418	.	1253	Q6BDS2	URFB1_HUMAN	Y	1253	ENSP00000192788:H1253Y;ENSP00000400628:H1253Y	ENSP00000192788:H1253Y	H	+	1	0	UHRF1BP1	34946647	0.000000	0.05858	0.018000	0.16275	0.285000	0.27093	-0.328000	0.07945	-0.254000	0.09500	-0.797000	0.03246	CAC		0.498	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
EEF1A1	1915	broad.mit.edu	37	6	74227627	74227627	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:74227627G>A	ENST00000316292.9	-	7	2286	c.1295C>T	c.(1294-1296)aCa>aTa	p.T432I	EEF1A1_ENST00000309268.6_Missense_Mutation_p.T432I|EEF1A1_ENST00000331523.2_Missense_Mutation_p.T432I|EEF1A1_ENST00000491404.1_Intron	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	432					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						CACCGCAACTGTCTGTCTCAT	0.403											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										uc003phi.2																			0					0						c.(1294-1296)ACA>ATA		eukaryotic translation elongation factor 1 alpha							41.0	44.0	43.0					6																	74227627		2203	4300	6503	SO:0001583	missense	1915					cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity	g.chr6:74227627G>A	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1295C>T	6.37:g.74227627G>A	ENSP00000339063:p.Thr432Ile		OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1151	EEF1A1_uc003phd.2_Missense_Mutation_p.T157I|EEF1A1_uc003phe.2_Missense_Mutation_p.T422I|EEF1A1_uc003phf.2_Missense_Mutation_p.T425I|EEF1A1_uc003phg.2_3'UTR|EEF1A1_uc003phh.2_Missense_Mutation_p.T278I|EEF1A1_uc003phj.2_Missense_Mutation_p.T432I|EEF1A1_uc003phk.2_Missense_Mutation_p.T432I|EEF1A1_uc003phl.2_Intron|EEF1A1_uc003phm.1_Intron	p.T432I	NM_001402	NP_001393	P68104	EF1A1_HUMAN			7	1332	-			432					P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	c.1295C>T	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257171	0.80246	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.56275	0.47;0.47;0.47	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.000000	0.85682	U	0.000000	T	0.80401	0.4616	H	0.98936	4.375	0.80722	D	1	D;D;D	0.52996	0.957;0.957;0.957	P;P;P	0.59948	0.866;0.866;0.866	D	0.88863	0.3327	10	0.87932	D	0	.	18.3119	0.90203	0.0:0.0:1.0:0.0	.	432;432;432	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	I	432;432;432;411	ENSP00000339063:T432I;ENSP00000339053:T432I;ENSP00000330054:T432I	ENSP00000339053:T432I	T	-	2	0	EEF1A1	74284348	1.000000	0.71417	0.976000	0.42696	0.877000	0.50540	9.332000	0.96446	2.381000	0.81170	0.556000	0.70494	ACA		0.403	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402	
TMEM30A	55754	broad.mit.edu	37	6	75968538	75968538	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:75968538G>C	ENST00000230461.6	-	6	1179	c.850C>G	c.(850-852)Cca>Gca	p.P284A	TMEM30A_ENST00000475111.2_Missense_Mutation_p.P248A|TMEM30A_ENST00000370050.5_Missense_Mutation_p.P165A	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	284					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGTAATGTTGGATGTAAATCA	0.388																																						uc003phw.2																			0					0						c.(850-852)CCA>GCA		transmembrane protein 30A isoform 1							99.0	95.0	96.0					6																	75968538		2203	4300	6503	SO:0001583	missense	55754					integral to membrane		g.chr6:75968538G>C	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.850C>G	6.37:g.75968538G>C	ENSP00000230461:p.Pro284Ala					TMEM30A_uc003phx.2_Missense_Mutation_p.P248A	p.P284A	NM_018247	NP_060717	Q9NV96	CC50A_HUMAN			6	1128	-			284					A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	37	c.850C>G	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204168	0.38905	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.34658	0.0905	L	0.27975	0.815	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.15052	0.011;0.012	T	0.32561	-0.9902	9	0.11485	T	0.65	.	19.4728	0.94969	0.0:0.0:1.0:0.0	.	248;284	Q9NV96-2;Q9NV96	.;CC50A_HUMAN	A	284;268;165;248	.	ENSP00000230461:P284A	P	-	1	0	TMEM30A	76025258	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	9.357000	0.97099	2.605000	0.88082	0.591000	0.81541	CCA		0.388	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
TTK	7272	broad.mit.edu	37	6	80746263	80746263	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:80746263G>C	ENST00000369798.2	+	17	2107	c.1996G>C	c.(1996-1998)Ggg>Cgg	p.G666R	TTK_ENST00000509894.1_Missense_Mutation_p.G665R|TTK_ENST00000230510.3_Missense_Mutation_p.G665R	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	666	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		AATTGATTTTGGGATTGCAAA	0.323																																						uc003pjc.2																			0				ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11						c.(1996-1998)GGG>CGG		TTK protein kinase							146.0	140.0	142.0					6																	80746263		2202	4298	6500	SO:0001583	missense	7272				mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr6:80746263G>C		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1996G>C	6.37:g.80746263G>C	ENSP00000358813:p.Gly666Arg					TTK_uc003pjb.3_Missense_Mutation_p.G665R	p.G666R	NM_003318	NP_003309	P33981	TTK_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0321)	17	2070	+		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)	666			Protein kinase.		A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	c.1996G>C	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482675	0.84747	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	D;D;D	0.89415	-2.51;-2.51;-2.51	6.08	5.21	0.72293	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96059	0.8716	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97641	1.0148	10	0.87932	D	0	-16.2953	15.9875	0.80174	0.0:0.0:0.8645:0.1355	.	666;665	P33981;A8K8U5	TTK_HUMAN;.	R	665;665;666	ENSP00000422936:G665R;ENSP00000230510:G665R;ENSP00000358813:G666R	ENSP00000230510:G665R	G	+	1	0	TTK	80802982	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	9.476000	0.97823	1.569000	0.49696	0.591000	0.81541	GGG		0.323	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
MYB	4602	broad.mit.edu	37	6	135514998	135514998	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr6:135514998C>T	ENST00000367814.4	+	7	971	c.785C>T	c.(784-786)cCt>cTt	p.P262L	MYB_ENST00000534121.1_Missense_Mutation_p.P262L|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000528774.1_Missense_Mutation_p.P262L|MYB_ENST00000442647.2_Missense_Mutation_p.P262L|MYB_ENST00000533624.1_Missense_Mutation_p.P262L|MYB_ENST00000316528.8_Missense_Mutation_p.P262L|MYB_ENST00000341911.5_Missense_Mutation_p.P262L|MYB_ENST00000534044.1_Missense_Mutation_p.P262L|MYB_ENST00000420123.2_Missense_Mutation_p.P238L|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000527615.1_Missense_Mutation_p.P262L|MYB_ENST00000525369.1_Missense_Mutation_p.P262L	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	262					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GTTCCATACCCTGTAGCGTTA	0.453			T	NFIB	adenoid cystic carcinoma																																	uc003qfc.2				Dom	yes		6	6q22-23	4602	T	v-myb myeloblastosis viral oncogene homolog			E	NFIB		adenoid cystic carcinoma		0				lung(1)	1						c.(784-786)CCT>CTT		v-myb myeloblastosis viral oncogene homolog							246.0	216.0	226.0					6																	135514998		2203	4300	6503	SO:0001583	missense	4602				blood coagulation|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone H3-K4 methylation|positive regulation of histone H3-K9 methylation|positive regulation of T-helper cell differentiation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear matrix	DNA binding|protein binding	g.chr6:135514998C>T		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.785C>T	6.37:g.135514998C>T	ENSP00000356788:p.Pro262Leu					MYB_uc003qfh.2_Missense_Mutation_p.P262L|MYB_uc003qfi.2_Missense_Mutation_p.P262L|MYB_uc010kgi.2_Missense_Mutation_p.P262L|MYB_uc003qfq.2_Missense_Mutation_p.P262L|MYB_uc010kgj.2_Missense_Mutation_p.P262L|MYB_uc003qfo.2_Missense_Mutation_p.P262L|MYB_uc003qfu.2_Missense_Mutation_p.P262L|MYB_uc003qfl.2_RNA|MYB_uc003qfv.2_RNA|MYB_uc003qfz.2_RNA|MYB_uc003qfx.2_RNA|MYB_uc003qga.2_RNA|MYB_uc003qgb.2_RNA|MYB_uc010kgk.2_RNA|MYB_uc003qfd.2_RNA|MYB_uc003qfe.2_RNA|MYB_uc003qfg.2_RNA|MYB_uc003qff.2_RNA|MYB_uc003qfj.2_RNA|MYB_uc003qfm.2_RNA|MYB_uc003qfp.2_RNA|MYB_uc003qfn.2_RNA|MYB_uc003qfk.2_RNA|MYB_uc003qfr.2_RNA|MYB_uc003qfs.2_5'UTR|MYB_uc003qft.2_RNA|MYB_uc003qfw.2_Missense_Mutation_p.P74L|MYB_uc003qfy.2_RNA|MYB_uc003qgc.2_RNA|MYB_uc003qfb.1_Missense_Mutation_p.P262L|MYB_uc003qgd.1_Missense_Mutation_p.P74L|MYB_uc003qge.1_5'Flank	p.P262L	NM_005375	NP_005366	P10242	MYB_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)	7	984	+	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)	262					E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	c.785C>T	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.903080	0.92035	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624;ENST00000430686	T;T;T;T;T;T;T;T;T;T	0.32515	2.7;2.21;2.2;2.22;1.45;1.92;2.69;2.69;1.88;2.22	5.23	5.23	0.72850	.	0.049512	0.85682	D	0.000000	T	0.49287	0.1548	M	0.67953	2.075	0.80722	D	1	D;D;P;D;D;P;D;D;D;D	0.89917	0.999;1.0;0.917;1.0;0.998;0.76;0.996;1.0;0.984;1.0	D;D;B;D;D;B;P;D;P;D	0.91635	0.994;0.998;0.367;0.999;0.959;0.343;0.893;0.999;0.632;0.999	T	0.53287	-0.8460	10	0.87932	D	0	-8.1358	18.8089	0.92050	0.0:1.0:0.0:0.0	.	262;262;238;262;262;262;262;262;262;262	E9PI07;E9PLZ5;E9PMQ0;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;.;MYB_HUMAN;.	L	262;262;262;262;262;262;238;262;262;262;262;262;216	ENSP00000339992:P262L;ENSP00000410825:P262L;ENSP00000326328:P262L;ENSP00000356788:P262L;ENSP00000433227:P262L;ENSP00000435938:P262L;ENSP00000434723:P262L;ENSP00000432851:P262L;ENSP00000435055:P262L;ENSP00000436605:P262L	ENSP00000237302:P262L	P	+	2	0	MYB	135556691	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.204000	0.72143	2.437000	0.82529	0.650000	0.86243	CCT		0.453	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
EGFR	1956	broad.mit.edu	37	7	55221822	55221823	+	Missense_Mutation	DNP	CC	CC	TT	rs149840192		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr7:55221822_55221823CC>TT	ENST00000275493.2	+	7	1043_1044	c.866_867CC>TT	c.(865-867)gCC>gTT	p.A289V	EGFR_ENST00000455089.1_Missense_Mutation_p.A244V|EGFR_ENST00000344576.2_Missense_Mutation_p.A289V|EGFR_ENST00000420316.2_Missense_Mutation_p.A289V|EGFR_ENST00000454757.2_Missense_Mutation_p.A236V|EGFR_ENST00000342916.3_Missense_Mutation_p.A289V|EGFR_ENST00000442591.1_Missense_Mutation_p.A289V	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	289			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.A289V(20)|p.A289D(3)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AGCTTTGGTGCCACCTGCGTGA	0.594		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		23	Substitution - Missense(23)	p.A289V(20)|p.V30_R297>G(5)|p.A289D(3)|p.A289T(3)	central_nervous_system(23)	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.(865-867)GCC>GTT		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)																																			SO:0001583	missense	1956	Lung_Cancer_Familial_Clustering_of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55221822_55221823CC>TT		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	Exception_encountered	7.37:g.55221822_55221823delinsTT	ENSP00000275493:p.Ala289Val	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc003tqh.2_Missense_Mutation_p.A289V|EGFR_uc003tqi.2_Missense_Mutation_p.A289V|EGFR_uc003tqj.2_Missense_Mutation_p.A289V|EGFR_uc010kzg.1_Missense_Mutation_p.A244V|EGFR_uc011kco.1_Missense_Mutation_p.A236V|EGFR_uc011kcp.1_5'Flank|EGFR_uc011kcq.1_5'Flank	p.A289V	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)		7	1112_1113	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		289			Approximate.|Extracellular (Potential).		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	DNP	ENST00000275493.2	37	c.866_867CC>TT	CCDS5514.1																																																																																				0.594	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
GPR85	54329	broad.mit.edu	37	7	112724771	112724771	+	Silent	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr7:112724771C>T	ENST00000297146.3	-	3	609	c.6G>A	c.(4-6)gcG>gcA	p.A2A	GPR85_ENST00000501255.2_Silent_p.A2A|GPR85_ENST00000424100.1_Silent_p.A2A|GPR85_ENST00000449591.1_Silent_p.A2A|GPR85_ENST00000487573.1_5'Flank	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	2					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						GGCTATAGTTCGCCATAGATG	0.403																																						uc010ljv.2																			0				ovary(1)|central_nervous_system(1)	2						c.(4-6)GCG>GCA		G protein-coupled receptor 85							28.0	28.0	28.0					7																	112724771		2203	4300	6503	SO:0001819	synonymous_variant	54329					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr7:112724771C>T	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"""GPCR / Class A : Orphans"""	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.6G>A	7.37:g.112724771C>T						GPR85_uc003vgp.1_Silent_p.A2A|GPR85_uc003vgq.2_Silent_p.A2A|GPR85_uc010ljw.1_Silent_p.A2A	p.A2A	NM_001146266	NP_001139738	P60893	GPR85_HUMAN			2	523	-			2			Extracellular (Potential).		Q9JHI6|Q9NPD1	Silent	SNP	ENST00000297146.3	37	c.6G>A	CCDS5758.1																																																																																				0.403	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2		
DENND2A	27147	broad.mit.edu	37	7	140267052	140267052	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr7:140267052T>C	ENST00000275884.6	-	8	2030	c.1613A>G	c.(1612-1614)aAc>aGc	p.N538S	DENND2A_ENST00000492720.1_Missense_Mutation_p.N538S|DENND2A_ENST00000537639.1_Missense_Mutation_p.N538S|DENND2A_ENST00000496613.1_Missense_Mutation_p.N538S			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	538					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					GGACTTCACGTTGACCAGGCG	0.567																																						uc010lnj.2																			0				ovary(3)|breast(1)	4						c.(1612-1614)AAC>AGC		DENN/MADD domain containing 2A							28.0	30.0	29.0					7																	140267052		1917	4152	6069	SO:0001583	missense	27147							g.chr7:140267052T>C	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.1613A>G	7.37:g.140267052T>C	ENSP00000275884:p.Asn538Ser					DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Missense_Mutation_p.N538S|DENND2A_uc003vvw.2_Missense_Mutation_p.N538S|DENND2A_uc003vvx.2_Missense_Mutation_p.N538S	p.N538S	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN			7	1758	-	Melanoma(164;0.00956)		538					C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	37	c.1613A>G	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.993880	0.35131	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613;ENST00000492720	T;T;T;T	0.09073	3.72;3.72;3.72;3.02	5.86	4.7	0.59300	.	0.475787	0.22572	N	0.058332	T	0.03827	0.0108	N	0.02539	-0.55	0.21802	N	0.99954	B;B	0.22003	0.063;0.003	B;B	0.20384	0.029;0.007	T	0.42464	-0.9450	10	0.19590	T	0.45	-11.2939	13.4022	0.60889	0.0:0.0:0.1313:0.8687	.	538;538	Q9ULE3-2;Q9ULE3	.;DEN2A_HUMAN	S	538	ENSP00000275884:N538S;ENSP00000442245:N538S;ENSP00000419654:N538S;ENSP00000419464:N538S	ENSP00000275884:N538S	N	-	2	0	DENND2A	139913521	1.000000	0.71417	0.876000	0.34364	0.954000	0.61252	3.341000	0.52151	1.048000	0.40298	-0.258000	0.10820	AAC		0.567	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
GBX1	2636	broad.mit.edu	37	7	150845924	150845924	+	Missense_Mutation	SNP	A	A	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr7:150845924A>T	ENST00000297537.4	-	2	843	c.844T>A	c.(844-846)Tgc>Agc	p.C282S	GBX1_ENST00000475831.1_5'Flank	NM_001098834.1	NP_001092304.1	Q14549	GBX1_HUMAN	gastrulation brain homeobox 1	282					adult walking behavior (GO:0007628)|neuron fate commitment (GO:0048663)|proprioception (GO:0019230)|regulation of transcription, DNA-templated (GO:0006355)|sensory neuron axon guidance (GO:0097374)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(5)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TATTTCTTGCAATGAAATTCC	0.557																																						uc011kvg.1																			0					0						c.(844-846)TGC>AGC		gastrulation brain homeo box 1							64.0	71.0	68.0					7																	150845924		2119	4243	6362	SO:0001583	missense	2636					nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:150845924A>T	L11239	CCDS43682.1	7q36.1	2012-03-09	2005-12-22		ENSG00000164900	ENSG00000164900		"""Homeoboxes / ANTP class : HOXL subclass"""	4185	protein-coding gene	gene with protein product		603354	"""gastrulation brain homeo box 1"""			7903253	Standard	NM_001098834		Approved		uc011kvg.2	Q14549	OTTHUMG00000158751	ENST00000297537.4:c.844T>A	7.37:g.150845924A>T	ENSP00000297537:p.Cys282Ser						p.C282S	NM_001098834	NP_001092304	Q14549	GBX1_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	2	1076	-			282			Homeobox.			Missense_Mutation	SNP	ENST00000297537.4	37	c.844T>A	CCDS43682.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.300076	0.60195	.	.	ENSG00000164900	ENST00000297537	D	0.95724	-3.79	4.75	4.75	0.60458	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.87144	0.6104	N	0.01505	-0.83	0.80722	D	1	B	0.20988	0.05	B	0.31290	0.127	D	0.83740	0.0203	10	0.32370	T	0.25	-34.0229	13.2065	0.59800	1.0:0.0:0.0:0.0	.	282	Q14549	GBX1_HUMAN	S	282	ENSP00000297537:C282S	ENSP00000297537:C282S	C	-	1	0	GBX1	150476857	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.067000	0.76741	2.012000	0.59069	0.482000	0.46254	TGC		0.557	GBX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352029.1		
RPS20	6224	broad.mit.edu	37	8	56985787	56985787	+	Silent	SNP	A	A	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr8:56985787A>T	ENST00000521262.1	-	4	475	c.222T>A	c.(220-222)tcT>tcA	p.S74S	SNORD54_ENST00000459159.1_RNA|RPS20_ENST00000519807.1_Silent_p.S74S|RPS20_ENST00000523936.1_3'UTR|RPS20_ENST00000009589.3_Silent_p.S74S|RPS20_ENST00000519606.1_3'UTR|CTA-397H3.3_ENST00000521403.1_RNA|RPS20_ENST00000520627.1_Silent_p.S19S|RPS20_ENST00000524349.1_Silent_p.S19S|RPS20_ENST00000520490.1_5'UTR			P60866	RS20_HUMAN	ribosomal protein S20	74					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)						all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.155)	Epithelial(17;0.00117)|all cancers(17;0.00879)			CCCACGTCTTAGAACCTTCAC	0.388																																						uc003xsn.2																			0					0						c.(220-222)TCT>TCA		ribosomal protein S20 isoform 2							103.0	107.0	106.0					8																	56985787		2059	3953	6012	SO:0001819	synonymous_variant	6224				endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome	g.chr8:56985787A>T	L06498	CCDS6163.1, CCDS55231.1	8q12.1	2011-04-05				ENSG00000008988		"""S ribosomal proteins"""	10405	protein-coding gene	gene with protein product		603682				9582194, 8479924	Standard	NM_001023		Approved	S20	uc003xsm.2	P60866		ENST00000521262.1:c.222T>A	8.37:g.56985787A>T						RPS20_uc003xsm.2_Silent_p.S74S	p.S74S	NM_001023	NP_001014	P60866	RS20_HUMAN	Epithelial(17;0.00117)|all cancers(17;0.00879)		4	420	-		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.155)	74					B2R4F4|B4DW28|P17075|Q5M8S9	Silent	SNP	ENST00000521262.1	37	c.222T>A																																																																																					0.388	RPS20-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378166.1	NM_001023	
ARFGEF1	10565	broad.mit.edu	37	8	68140324	68140327	+	Frame_Shift_Del	DEL	TAAT	TAAT	-	rs369152833		TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr8:68140324_68140327delTAAT	ENST00000262215.3	-	25	3851_3854	c.3462_3465delATTA	c.(3460-3465)gaattafs	p.EL1154fs	ARFGEF1_ENST00000518230.1_5'UTR|ARFGEF1_ENST00000520381.1_Frame_Shift_Del_p.EL608fs	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1154					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCGTGGAAAGTAATTCATCCATAG	0.343																																						uc003xxo.1																			0				ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8						c.(3460-3465)GAATTAfs		brefeldin A-inhibited guanine																																				SO:0001589	frameshift_variant	10565				exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding	g.chr8:68140324_68140327delTAAT	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.3462_3465delATTA	8.37:g.68140324_68140327delTAAT	ENSP00000262215:p.Glu1154fs					ARFGEF1_uc003xxl.1_Frame_Shift_Del_p.E608fs|ARFGEF1_uc003xxn.1_Frame_Shift_Del_p.E137fs	p.E1154fs	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)		25	3852_3855	-	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	1154_1155					Q9NV46|Q9UFV2|Q9UNL0	Frame_Shift_Del	DEL	ENST00000262215.3	37	c.3462_3465delATTA	CCDS6199.1																																																																																				0.343	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
AGO2	27161	broad.mit.edu	37	8	141570507	141570507	+	Silent	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr8:141570507C>T	ENST00000220592.5	-	5	733	c.621G>A	c.(619-621)cgG>cgA	p.R207R	AGO2_ENST00000519980.1_Silent_p.R207R	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	207					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										AGAGAGAAGGCCGGACGGACT	0.622																																						uc003yvn.2																			0					0						c.(619-621)CGG>CGA		argonaute 2 isoform 1							91.0	88.0	89.0					8																	141570507		2203	4300	6503	SO:0001819	synonymous_variant	27161				mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity	g.chr8:141570507C>T	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.621G>A	8.37:g.141570507C>T						EIF2C2_uc010men.2_Silent_p.R130R|EIF2C2_uc010meo.2_Silent_p.R207R	p.R207R	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.158)		5	661	-	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	207					Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	37	c.621G>A	CCDS6380.1																																																																																				0.622	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
IFNA10	3446	broad.mit.edu	37	9	21206995	21206995	+	Silent	SNP	A	A	G			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr9:21206995A>G	ENST00000357374.2	-	1	147	c.102T>C	c.(100-102)aaT>aaC	p.N34N		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	34					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		AGGCCCTCCTATTACCCAGGC	0.512																																						uc003zoq.1																			0					0						c.(100-102)AAT>AAC		interferon, alpha 10 precursor							64.0	73.0	70.0					9																	21206995		2202	4297	6499	SO:0001819	synonymous_variant	3446				blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding	g.chr9:21206995A>G		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"""Interferons"""	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.102T>C	9.37:g.21206995A>G						IFNA14_uc003zoo.1_Intron	p.N34N	NM_002171	NP_002162	P01566	IFN10_HUMAN		Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)	1	148	-			34					Q5VV13	Silent	SNP	ENST00000357374.2	37	c.102T>C	CCDS6499.1																																																																																				0.512	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
KIAA0368	23392	broad.mit.edu	37	9	114188086	114188086	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr9:114188086C>T	ENST00000338205.5	-	10	1292	c.1073G>A	c.(1072-1074)gGt>gAt	p.G358D	KIAA0368_ENST00000259335.4_Missense_Mutation_p.G536D			Q5VYK3	ECM29_HUMAN	KIAA0368	364					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TGTATTTGTACCAAAAAGTCC	0.254																																						uc004bfe.1																			0					0						c.(1606-1608)GGT>GAT		KIAA0368 protein							86.0	88.0	87.0					9																	114188086		1810	4063	5873	SO:0001583	missense	23392							g.chr9:114188086C>T	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1073G>A	9.37:g.114188086C>T	ENSP00000339889:p.Gly358Asp					KIAA0368_uc010muc.1_Missense_Mutation_p.G358D	p.G536D	NM_001080398	NP_001073867					12	1607	-								O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37	c.1607G>A		.	.	.	.	.	.	.	.	.	.	C	25.8	4.672238	0.88348	.	.	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.51071	0.72	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68449	0.3002	M	0.64567	1.98	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67321	-0.5700	10	0.54805	T	0.06	.	20.0016	0.97412	0.0:1.0:0.0:0.0	.	364	Q5VYK3	ECM29_HUMAN	D	358;536	ENSP00000259335:G536D	ENSP00000259335:G536D	G	-	2	0	KIAA0368	113227907	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.279000	0.78599	2.802000	0.96397	0.655000	0.94253	GGT		0.254	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
CDK5RAP2	55755	broad.mit.edu	37	9	123156840	123156840	+	Missense_Mutation	SNP	A	A	C			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr9:123156840A>C	ENST00000349780.4	-	36	5707	c.5528T>G	c.(5527-5529)aTg>aGg	p.M1843R	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.M1802R|CDK5RAP2_ENST00000480467.1_5'UTR|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.M1811R|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.M1764R	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1843	Interaction with PCNT and AKAP9.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						CAAAAGCTTCATGGTGTTTTG	0.428																																						uc004bkf.2																			0				ovary(2)|lung(1)|skin(1)	4						c.(5527-5529)ATG>AGG		CDK5 regulatory subunit associated protein 2							179.0	160.0	167.0					9																	123156840		2203	4300	6503	SO:0001583	missense	55755				brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding	g.chr9:123156840A>C	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.5528T>G	9.37:g.123156840A>C	ENSP00000343818:p.Met1843Arg					CDK5RAP2_uc010mvi.2_Missense_Mutation_p.M852R|CDK5RAP2_uc004bke.2_Missense_Mutation_p.M1128R|CDK5RAP2_uc004bkg.2_Missense_Mutation_p.M1764R|CDK5RAP2_uc011lxw.1_Missense_Mutation_p.M1108R|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_Missense_Mutation_p.M1108R|CDK5RAP2_uc011lya.1_Missense_Mutation_p.M1108R|CDK5RAP2_uc004bkh.1_Missense_Mutation_p.M1613R	p.M1843R	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN			36	5709	-			1843			Interaction with PCNT and AKAP9.		Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	c.5528T>G	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	A	9.767	1.171560	0.21704	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647	T;T;T;T;T;T	0.23348	3.9;3.8;3.9;3.81;2.23;1.91	5.39	2.73	0.32206	.	0.999424	0.08094	N	0.998897	T	0.20251	0.0487	L	0.29908	0.895	0.09310	N	1	B;B;B;B;B	0.32203	0.037;0.168;0.36;0.105;0.037	B;B;B;B;B	0.33750	0.043;0.039;0.169;0.04;0.058	T	0.27123	-1.0083	10	0.42905	T	0.14	.	7.8449	0.29421	0.7962:0.0:0.2038:0.0	.	853;1811;1764;1843;1237	Q5JTU8;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;CK5P2_HUMAN;.	R	1811;1802;1843;1764;1237;853	ENSP00000354065:M1811R;ENSP00000352258:M1802R;ENSP00000343818:M1843R;ENSP00000353317:M1764R;ENSP00000400395:M1237R;ENSP00000409941:M853R	ENSP00000343818:M1843R	M	-	2	0	CDK5RAP2	122196661	0.098000	0.21812	0.178000	0.23040	0.862000	0.49288	1.603000	0.36794	0.910000	0.36722	0.533000	0.62120	ATG		0.428	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
OR1J1	347168	broad.mit.edu	37	9	125239745	125239745	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chr9:125239745G>A	ENST00000259357.2	-	1	490	c.461C>T	c.(460-462)gCg>gTg	p.A154V	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, member 1	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						AAGAGCACACGCACAAGCGAT	0.542																																						uc011lyu.1																			0				skin(2)	2						c.(460-462)GCG>GTG		olfactory receptor, family 1, subfamily J,							90.0	78.0	82.0					9																	125239745		2203	4300	6503	SO:0001583	missense	347168				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr9:125239745G>A	AL353767	CCDS35120.1	9q33.2	2013-09-20			ENSG00000136834	ENSG00000136834		"""GPCR / Class A : Olfactory receptors"""	8208	protein-coding gene	gene with protein product							Standard	NM_001004451		Approved	hg32	uc011lyu.2	Q8NGS3	OTTHUMG00000020603	ENST00000259357.2:c.461C>T	9.37:g.125239745G>A	ENSP00000259357:p.Ala154Val					OR1J2_uc004bmj.1_Intron	p.A154V	NM_001004451	NP_001004451	Q8NGS3	OR1J1_HUMAN			1	461	-			154			Helical; Name=4; (Potential).		A3KFL8|Q6IF10|Q96R88	Missense_Mutation	SNP	ENST00000259357.2	37	c.461C>T	CCDS35120.1	.	.	.	.	.	.	.	.	.	.	g	0.058	-1.231824	0.01505	.	.	ENSG00000136834	ENST00000259357	T	0.35605	1.3	4.57	1.74	0.24563	GPCR, rhodopsin-like superfamily (1);	0.344126	0.25178	N	0.032547	T	0.17534	0.0421	N	0.16307	0.4	0.22127	N	0.999346	P	0.35959	0.53	B	0.31245	0.126	T	0.10776	-1.0615	10	0.52906	T	0.07	.	5.3894	0.16236	0.2498:0.146:0.6042:0.0	.	154	Q8NGS3	OR1J1_HUMAN	V	154	ENSP00000259357:A154V	ENSP00000259357:A154V	A	-	2	0	OR1J1	124279566	0.000000	0.05858	0.422000	0.26621	0.005000	0.04900	0.782000	0.26788	0.294000	0.22547	-0.267000	0.10333	GCG		0.542	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1		
PCDH11Y	83259	broad.mit.edu	37	Y	5605524	5605524	+	Silent	SNP	C	C	A			TCGA-06-0747-01A-01W-0348-08	TCGA-06-0747-10A-01W-0348-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	7773738f-f5dd-48ae-870c-aa89aea77450	edc2c7dd-acde-4bbc-ae3a-4f3ccdcf712d	g.chrY:5605524C>A	ENST00000215473.6	+	6	3564	c.3564C>A	c.(3562-3564)ctC>ctA	p.L1188L				Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	1188					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CCATTGTTCTCTGCCACAGCC	0.582																																						uc004fqo.2																			0					0						c.(3562-3564)CTC>CTA		protocadherin 11 Y-linked isoform c																																				SO:0001819	synonymous_variant	83259				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chrY:5605524C>A	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"""Cadherins / Protocadherins : Non-clustered"""	15813	protein-coding gene	gene with protein product		400022	"""protocadherin 22"""	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000215473.6:c.3564C>A	Y.37:g.5605524C>A							p.L1188L	NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN			5	4298	+			1188			Cytoplasmic (Potential).		Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Silent	SNP	ENST00000215473.6	37	c.3564C>A																																																																																					0.582	PCDH11Y-201	KNOWN	basic	protein_coding	protein_coding		NM_032973	
