#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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
ARID1A	8289	hgsc.bcm.edu	37	1	27105570	27105571	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr1:27105570_27105571insT	ENST00000324856.7	+	20	5552_5553	c.5181_5182insT	c.(5182-5184)tttfs	p.F1728fs	ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.F56fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.F1345fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.F1511fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1728					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.G1729fs*7(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TGATTGAGATCTTTGGCATTTT	0.475			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.I1510fs			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.4530_4531insT	1						.																																			26978158	SO:0001589	frameshift_variant	8289	exon20			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5184dupT	1.37:g.27105573_27105573dupT	ENSP00000320485:p.Phe1728fs		26978157	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	37	CCDS285.1																																																																																				0.475	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
TAX1BP1	8887	hgsc.bcm.edu	37	7	27868361	27868361	+	Silent	SNP	C	C	T	rs534866304		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr7:27868361C>T	ENST00000396319.2	+	17	2371	c.2283C>T	c.(2281-2283)agC>agT	p.S761S	TAX1BP1_ENST00000409980.1_Silent_p.S785S|TAX1BP1_ENST00000543117.1_Silent_p.S719S|TAX1BP1_ENST00000265393.6_Silent_p.S719S|TAX1BP1_ENST00000433216.2_Silent_p.S562S	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	761					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.S761S(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			CGATGTGCAGCGAGCAGTTCC	0.418													C|||	1	0.000199681	0.0	0.0	5008	,	,		17086	0.001		0.0	False		,,,				2504	0.0				p.S761S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2283T	7						.						150.0	140.0	143.0					7																	27868361		2203	4300	6503	27834886	SO:0001819	synonymous_variant	8887	exon17			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.2283C>T	7.37:g.27868361C>T			27834886	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Silent	SNP	ENST00000396319.2	37	CCDS5415.1																																																																																				0.418	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
IGFBP3	3486	hgsc.bcm.edu	37	7	45956967	45956967	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr7:45956967G>A	ENST00000275521.6	-	2	608	c.475C>T	c.(475-477)Cgg>Tgg	p.R159W	IGFBP3_ENST00000381086.5_Missense_Mutation_p.R62W|IGFBP3_ENST00000465642.1_5'UTR|IGFBP3_ENST00000381083.4_Missense_Mutation_p.R165W	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	159	Ser/Thr-rich.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)	p.R159W(1)		large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	TCAGACACCCGGTGCGTGCTG	0.532											OREG0018049	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R159W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C475T	7						.						85.0	80.0	82.0					7																	45956967		2203	4300	6503	45923492	SO:0001583	missense	3486	exon2				CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"""growth hormone-dependent binding protein"", ""acid stable subunit of the 140 K IGF complex"", ""binding protein 53"", ""binding protein 29"", ""IGF-binding protein 3"""	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.475C>T	7.37:g.45956967G>A	ENSP00000275521:p.Arg159Trp	935	45923492	NM_000598	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Missense_Mutation	SNP	ENST00000275521.6	37	CCDS5505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.28|13.28	2.191392|2.191392	0.38707|0.38707	.|.	.|.	ENSG00000146674|ENSG00000146674	ENST00000417621|ENST00000545032;ENST00000275521;ENST00000381086;ENST00000438491;ENST00000442142;ENST00000381083;ENST00000433047;ENST00000448817	.|T;T;T;T	.|0.27402	.|2.32;1.67;2.33;1.76	5.55|5.55	-2.77|-2.77	0.05877|0.05877	.|.	.|0.888278	.|0.09850	.|N	.|0.747650	T|T	0.28433|0.28433	0.0703|0.0703	M|M	0.80183|0.80183	2.485|2.485	0.09310|0.09310	N|N	1|1	.|B;P;P	.|0.42692	.|0.239;0.787;0.646	.|B;B;B	.|0.36464	.|0.035;0.225;0.072	T|T	0.28902|0.28902	-1.0029|-1.0029	5|10	.|0.72032	.|D	.|0.01	-22.1882|-22.1882	4.6062|4.6062	0.12378|0.12378	0.228:0.0:0.3159:0.456|0.228:0.0:0.3159:0.456	.|.	.|62;159;144	.|B3KWK7;P17936;B4DN53	.|.;IBP3_HUMAN;.	L|W	20|136;159;62;145;57;165;131;49	.|ENSP00000275521:R159W;ENSP00000370476:R62W;ENSP00000370473:R165W;ENSP00000389668:R49W	.|ENSP00000275521:R159W	P|R	-|-	2|1	0|2	IGFBP3|IGFBP3	45923492|45923492	0.998000|0.998000	0.40836|0.40836	0.002000|0.002000	0.10522|0.10522	0.048000|0.048000	0.14542|0.14542	0.652000|0.652000	0.24888|0.24888	-0.172000|-0.172000	0.10779|0.10779	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.532	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398	
RAE1	8480	hgsc.bcm.edu	37	20	55948631	55948631	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr20:55948631C>T	ENST00000395841.2	+	9	1163	c.743C>T	c.(742-744)cCg>cTg	p.P248L	RAE1_ENST00000395840.2_Missense_Mutation_p.P248L|RAE1_ENST00000527947.1_Missense_Mutation_p.P248L|RAE1_ENST00000371242.2_Missense_Mutation_p.P248L	NM_003610.3	NP_003601.1	P78406	RAE1L_HUMAN	ribonucleic acid export 1	248					carbohydrate metabolic process (GO:0005975)|cellular response to organic cyclic compound (GO:0071407)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|nuclear pore (GO:0005643)|nucleolus (GO:0005730)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|RNA binding (GO:0003723)	p.P248L(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(6)|prostate(3)|skin(2)	21	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			ATCAACCCCCCGAACCCGTAA	0.438																																					p.P248L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C743T	20						.						107.0	109.0	108.0					20																	55948631		2203	4300	6503	55382038	SO:0001583	missense	8480	exon9			U84720	CCDS13458.1	20q13.31	2013-08-28	2013-08-28		ENSG00000101146	ENSG00000101146		"""WD repeat domain containing"""	9828	protein-coding gene	gene with protein product		603343	"""RAE1 (RNA export 1, S.pombe) homolog"", ""RAE1 RNA export 1 homolog (S. pombe)"""			9370289, 9256445	Standard	XM_005260582		Approved	Mnrp41	uc002xyi.3	P78406	OTTHUMG00000032819	ENST00000395841.2:c.743C>T	20.37:g.55948631C>T	ENSP00000379182:p.Pro248Leu		55382038	NM_003610	A8K882|O15306|Q3SYL7|Q5TCH8|Q6V708|Q9H100|Q9NQM6	Missense_Mutation	SNP	ENST00000395841.2	37	CCDS13458.1	.	.	.	.	.	.	.	.	.	.	c	12.42	1.933081	0.34096	.	.	ENSG00000101146	ENST00000395841;ENST00000371242;ENST00000527947;ENST00000395840	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.66	4.71	0.59529	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.161535	0.56097	D	0.000026	T	0.42268	0.1195	N	0.02539	-0.55	0.80722	D	1	P;B;B	0.46912	0.886;0.003;0.003	B;B;B	0.35510	0.204;0.003;0.003	T	0.51426	-0.8707	10	0.34782	T	0.22	.	14.3391	0.66614	0.1484:0.8516:0.0:0.0	.	248;248;248	E9PQ57;A8K882;P78406	.;.;RAE1L_HUMAN	L	248	ENSP00000379182:P248L;ENSP00000360286:P248L;ENSP00000432609:P248L;ENSP00000379181:P248L	ENSP00000360286:P248L	P	+	2	0	RAE1	55382038	1.000000	0.71417	0.978000	0.43139	0.437000	0.31866	5.486000	0.66856	1.374000	0.46228	-0.182000	0.12963	CCG		0.438	RAE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079842.2		
TCF20	6942	hgsc.bcm.edu	37	22	42606146	42606146	+	Silent	SNP	T	T	G			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr22:42606146T>G	ENST00000359486.3	-	1	5302	c.5166A>C	c.(5164-5166)ggA>ggC	p.G1722G	TCF20_ENST00000404876.1_Silent_p.G23G|TCF20_ENST00000335626.4_Silent_p.G1722G	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1722					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.G1722G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GATAAAAAGGTCCAAAGAGGT	0.517																																					p.G1722G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A5166C	22						.						79.0	80.0	80.0					22																	42606146		2203	4300	6503	40936090	SO:0001819	synonymous_variant	6942	exon1			U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.5166A>C	22.37:g.42606146T>G			40936090	NM_005650	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																				0.517	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
BLVRB	645	hgsc.bcm.edu	37	19	40957334	40957334	+	Missense_Mutation	SNP	G	G	A	rs200072753		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr19:40957334G>A	ENST00000263368.4	-	4	551	c.400C>T	c.(400-402)Cgg>Tgg	p.R134W	BLVRB_ENST00000595483.1_Intron	NM_000713.2	NP_000704.1	P30043	BLVRB_HUMAN	biliverdin reductase B (flavin reductase (NADPH))	134					heme catabolic process (GO:0042167)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	biliverdin reductase activity (GO:0004074)|riboflavin reductase (NADPH) activity (GO:0042602)	p.R134W(1)		large_intestine(3)|lung(3)	6			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Riboflavin(DB00140)	TTGTGCATCCGGATGTGGTCA	0.612																																					p.R134W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C400T	19						.						97.0	64.0	75.0					19																	40957334		2203	4300	6503	45649174	SO:0001583	missense	645	exon4			D26308	CCDS33029.1	19q13.1-q13.2	2011-09-14				ENSG00000090013	1.3.1.24, 1.5.1.30	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	1063	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 43U, member 1"""	600941	"""Flavin reductase"""	FLR		7656592, 19027726	Standard	NM_000713		Approved	SDR43U1	uc002onw.2	P30043		ENST00000263368.4:c.400C>T	19.37:g.40957334G>A	ENSP00000263368:p.Arg134Trp		45649174	NM_000713	A6NKD8|B2R5C6|P32078|P53005|Q32LZ2	Missense_Mutation	SNP	ENST00000263368.4	37	CCDS33029.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181604	0.78677	.	.	ENSG00000090013	ENST00000263368	T	0.31510	1.49	5.37	5.37	0.77165	NAD(P)-binding domain (1);NmrA-like (1);	0.000000	0.85682	D	0.000000	T	0.66597	0.2805	M	0.93062	3.375	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75199	-0.3402	10	0.87932	D	0	-30.402	18.2503	0.90000	0.0:0.0:1.0:0.0	.	134	P30043	BLVRB_HUMAN	W	134	ENSP00000263368:R134W	ENSP00000263368:R134W	R	-	1	2	BLVRB	45649174	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.757000	0.55212	2.682000	0.91365	0.467000	0.42956	CGG		0.612	BLVRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462563.1		
CSGALNACT1	55790	hgsc.bcm.edu	37	8	19363229	19363229	+	Silent	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr8:19363229G>A	ENST00000454498.2	-	4	1130	c.117C>T	c.(115-117)gaC>gaT	p.D39D	CSGALNACT1_ENST00000332246.6_Silent_p.D39D|CSGALNACT1_ENST00000544602.1_Silent_p.D39D|CSGALNACT1_ENST00000522854.1_Silent_p.D39D|CSGALNACT1_ENST00000311540.4_Silent_p.D39D	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	39					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)	p.D39D(1)|p.D39E(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		GCTGCTCCTCGTCACCTTTTG	0.627																																					p.D39D												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|NS(1)	c.C117T	8						.						87.0	85.0	86.0					8																	19363229		2203	4300	6503	19407509	SO:0001819	synonymous_variant	55790	exon4			AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"""Beta 4-glycosyltransferases"""	24290	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase"""					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.117C>T	8.37:g.19363229G>A			19407509	NM_018371	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Silent	SNP	ENST00000454498.2	37	CCDS6010.1																																																																																				0.627	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371	
CSMD3	114788	hgsc.bcm.edu	37	8	113277692	113277692	+	Silent	SNP	G	G	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr8:113277692G>T	ENST00000297405.5	-	60	9880	c.9636C>A	c.(9634-9636)atC>atA	p.I3212I	CSMD3_ENST00000343508.3_Silent_p.I3172I|CSMD3_ENST00000455883.2_Silent_p.I3043I|CSMD3_ENST00000352409.3_Silent_p.I3142I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3212	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I3212I(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TACAAGTCCTGATTCTGGAGC	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.I3212I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9636A	8						.						177.0	154.0	162.0					8																	113277692		2203	4300	6503	113346868	SO:0001819	synonymous_variant	114788	exon60			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9636C>A	8.37:g.113277692G>T			113346868	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
IVL	3713	hgsc.bcm.edu	37	1	152882328	152882328	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr1:152882328C>A	ENST00000368764.3	+	2	119	c.55C>A	c.(55-57)Ctc>Atc	p.L19I	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	19					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.L19I(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGTCAGGAGCTCCTCAAGAC	0.552																																					p.L19I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C55A	1						.						90.0	77.0	81.0					1																	152882328		2203	4300	6503	151148952	SO:0001583	missense	3713	exon2			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.55C>A	1.37:g.152882328C>A	ENSP00000357753:p.Leu19Ile		151148952	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	9.769	1.172163	0.21704	.	.	ENSG00000163207	ENST00000368764	T	0.09350	2.99	4.5	-4.9	0.03094	Involucrin, N-terminal (1);	.	.	.	.	T	0.02193	0.0068	L	0.50333	1.59	0.18873	N	0.999986	B	0.23377	0.084	B	0.24006	0.05	T	0.44314	-0.9336	9	0.21540	T	0.41	6.3575	4.2226	0.10565	0.2566:0.2842:0.0:0.4593	.	19	P07476	INVO_HUMAN	I	19	ENSP00000357753:L19I	ENSP00000357753:L19I	L	+	1	0	IVL	151148952	0.000000	0.05858	0.002000	0.10522	0.535000	0.34838	-0.794000	0.04584	-1.234000	0.02548	0.561000	0.74099	CTC		0.552	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517142	158517142	+	Missense_Mutation	SNP	C	C	T	rs41273491	byFrequency	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr1:158517142C>T	ENST00000302617.3	-	1	753	c.754G>A	c.(754-756)Gtc>Atc	p.V252I		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	252						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V252I(1)		NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					AGAATTACGACGGTCAGGTGG	0.507													C|||	1009	0.201478	0.0537	0.219	5008	,	,		23681	0.377		0.2416	False		,,,				2504	0.1667				p.V252I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G754A	1						.	C	ILE/VAL	396,4010	197.1+/-221.3	24,348,1831	179.0	172.0	175.0		754	3.5	0.9	1	dbSNP_127	175	1985,6615	347.0+/-326.4	252,1481,2567	yes	missense	OR6Y1	NM_001005189.1	29	276,1829,4398	TT,TC,CC		23.0814,8.9877,18.3069	possibly-damaging	252/326	158517142	2381,10625	2203	4300	6503	156783766	SO:0001583	missense	391112	exon1			BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"""GPCR / Class A : Olfactory receptors"""	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.754G>A	1.37:g.158517142C>T	ENSP00000304807:p.Val252Ile		156783766	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	510	0.23351648351648352	29	0.05894308943089431	74	0.20441988950276244	221	0.38636363636363635	186	0.24538258575197888	C	15.12	2.737955	0.49045	0.089877	0.230814	ENSG00000197532	ENST00000302617	T	0.00253	8.43	5.34	3.5	0.40072	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38005	N	0.001848	T	0.00144	0.0004	M	0.89030	3	0.80722	P	0.0	D	0.58620	0.983	P	0.46659	0.523	T	0.38286	-0.9668	9	0.39692	T	0.17	.	6.2283	0.20720	0.1489:0.6944:0.0:0.1567	rs41273491	252	Q8NGX8	OR6Y1_HUMAN	I	252	ENSP00000304807:V252I	ENSP00000304807:V252I	V	-	1	0	OR6Y1	156783766	0.000000	0.05858	0.894000	0.35097	0.910000	0.53928	0.454000	0.21827	0.827000	0.34685	-0.137000	0.14449	GTC		0.507	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189	
NME7	29922	hgsc.bcm.edu	37	1	169279275	169279275	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr1:169279275C>A	ENST00000367811.3	-	4	578	c.322G>T	c.(322-324)Gaa>Taa	p.E108*	NME7_ENST00000472647.1_Nonsense_Mutation_p.E72*|NME7_ENST00000469474.1_5'UTR|RP4-800F24.1_ENST00000432081.1_RNA	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	108					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.E108*(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					TCAATTATTTCTCCAGCCTTT	0.264																																					p.E72X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G214T	1						.						88.0	92.0	91.0					1																	169279275		2200	4289	6489	167545899	SO:0001587	stop_gained	29922	exon4			AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 67"""	613465	"""non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"""			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.322G>T	1.37:g.169279275C>A	ENSP00000356785:p.Glu108*		167545899	NM_197972	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Nonsense_Mutation	SNP	ENST00000367811.3	37	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	C	40	7.964266	0.98585	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	.	.	.	5.34	5.34	0.76211	.	0.209119	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-33.107	15.77	0.78162	0.0:1.0:0.0:0.0	.	.	.	.	X	72;108	.	ENSP00000356785:E108X	E	-	1	0	NME7	167545899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.664000	0.46783	2.513000	0.84729	0.650000	0.86243	GAA		0.264	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330	
ZNF202	7753	hgsc.bcm.edu	37	11	123601446	123601446	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr11:123601446G>A	ENST00000529691.1	-	2	370	c.151C>T	c.(151-153)Cgc>Tgc	p.R51C	ZNF202_ENST00000530393.1_Missense_Mutation_p.R51C|ZNF202_ENST00000336139.4_Missense_Mutation_p.R51C			O95125	ZN202_HUMAN	zinc finger protein 202	51	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R51C(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		TAGCGGAAGCGTCGGAAGTTC	0.542																																					p.R51C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C151T	11						.						104.0	103.0	103.0					11																	123601446		2202	4299	6501	123106656	SO:0001583	missense	7753	exon4			AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.151C>T	11.37:g.123601446G>A	ENSP00000433881:p.Arg51Cys		123106656	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	37	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	G	5.341	0.248254	0.10130	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691;ENST00000533463	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	4.7	-3.61	0.04556	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.641780	0.12664	N	0.449374	T	0.03827	0.0108	L	0.41961	1.31	0.20074	N	0.999938	B	0.06786	0.001	B	0.06405	0.002	T	0.36553	-0.9743	10	0.46703	T	0.11	-2.5298	4.7731	0.13166	0.3452:0.0:0.4094:0.2454	.	51	O95125	ZN202_HUMAN	C	51	ENSP00000337724:R51C;ENSP00000432504:R51C;ENSP00000433881:R51C;ENSP00000431223:R51C	ENSP00000337724:R51C	R	-	1	0	ZNF202	123106656	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	-2.698000	0.00826	-0.454000	0.07066	-1.130000	0.01982	CGC		0.542	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
OPCML	4978	hgsc.bcm.edu	37	11	132306121	132306121	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr11:132306121C>A	ENST00000331898.7	-	6	1374	c.796G>T	c.(796-798)Ggt>Tgt	p.G266C	OPCML_ENST00000541867.1_Missense_Mutation_p.G266C|OPCML_ENST00000374778.4_Missense_Mutation_p.G225C|OPCML_ENST00000524381.1_Missense_Mutation_p.G259C|OPCML_ENST00000529038.1_5'UTR	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	266	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.G266C(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CCATCCAGACCAGTGGCTAAC	0.443																																					p.G259C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G775T	11						.						139.0	129.0	132.0					11																	132306121		2201	4297	6498	131811331	SO:0001583	missense	4978	exon7			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"""Immunoglobulin superfamily / I-set domain containing"""	8143	protein-coding gene	gene with protein product	"""IgLON family member 1"""	600632	"""opioid-binding protein/cell adhesion molecule-like"""			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.796G>T	11.37:g.132306121C>A	ENSP00000330862:p.Gly266Cys		131811331	NM_001012393	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.637795	0.67130	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90669	0.7073	M	0.94142	3.5	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.995;0.992;0.992	D	0.92381	0.5913	10	0.87932	D	0	-22.5285	19.8961	0.96958	0.0:1.0:0.0:0.0	.	266;259;265;266	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	C	266;259;225;233;266	ENSP00000330862:G266C;ENSP00000434750:G259C;ENSP00000363910:G225C;ENSP00000445496:G266C	ENSP00000330862:G266C	G	-	1	0	OPCML	131811331	1.000000	0.71417	0.998000	0.56505	0.313000	0.28021	7.480000	0.81109	2.803000	0.96430	0.650000	0.86243	GGT		0.443	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393	
AGPAT1	10554	hgsc.bcm.edu	37	6	32137800	32137800	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr6:32137800T>C	ENST00000395499.1	-	6	1201	c.622A>G	c.(622-624)Ata>Gta	p.I208V	AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000395497.1_Missense_Mutation_p.I208V|PPT2-EGFL8_ENST00000422437.1_Intron|AGPAT1_ENST00000375104.2_Missense_Mutation_p.I208V|AGPAT1_ENST00000412465.2_Missense_Mutation_p.I96V|AGPAT1_ENST00000375107.3_Missense_Mutation_p.I208V|AGPAT1_ENST00000395496.1_Missense_Mutation_p.I208V|AGPAT1_ENST00000336984.6_Missense_Mutation_p.I208V			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	208					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.I208V(1)		central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						GACATGACTATGGGGACAATG	0.552																																					p.I208V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A622G	6						.						84.0	78.0	80.0					6																	32137800		1511	2709	4220	32245778	SO:0001583	missense	10554	exon6			U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	324	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, alpha"""	603099	"""1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"""			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.622A>G	6.37:g.32137800T>C	ENSP00000378877:p.Ile208Val		32245778	NM_032741	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	37	CCDS4744.1	.	.	.	.	.	.	.	.	.	.	T	4.735	0.136739	0.09032	.	.	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984;ENST00000412465	D;D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	5.99	5.99	0.97316	Phospholipid/glycerol acyltransferase (2);1-acyl-sn-glycerol-3-phosphate acyltransferase (1);	0.054086	0.85682	D	0.000000	T	0.54382	0.1855	N	0.01086	-1.025	0.40947	D	0.984511	B;B;B	0.24132	0.065;0.098;0.015	B;B;B	0.31101	0.054;0.124;0.011	T	0.61686	-0.7012	10	0.02654	T	1	-16.5371	8.8876	0.35414	0.0:0.0819:0.0:0.9181	.	172;98;208	B4DRH1;B3KPH3;Q99943	.;.;PLCA_HUMAN	V	208;208;208;208;208;208;96	ENSP00000378874:I208V;ENSP00000364248:I208V;ENSP00000378877:I208V;ENSP00000364245:I208V;ENSP00000378875:I208V;ENSP00000337463:I208V;ENSP00000410473:I96V	ENSP00000337463:I208V	I	-	1	0	AGPAT1	32245778	0.973000	0.33851	1.000000	0.80357	0.999000	0.98932	0.468000	0.22051	2.291000	0.77112	0.533000	0.62120	ATA		0.552	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411	
MAPK13	5603	hgsc.bcm.edu	37	6	36103814	36103814	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr6:36103814G>A	ENST00000211287.4	+	5	698	c.436G>A	c.(436-438)Gtc>Atc	p.V146I	MAPK13_ENST00000373761.6_Intron|MAPK13_ENST00000490334.1_3'UTR|MAPK13_ENST00000373759.1_Missense_Mutation_p.V68I|MAPK13_ENST00000373766.5_Missense_Mutation_p.V146I	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	146	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.V146I(1)		breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						CTCTGCTGGGGTCGTGCACAG	0.587																																					p.V146I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G436A	6						.						133.0	117.0	122.0					6																	36103814		2203	4300	6503	36211792	SO:0001583	missense	5603	exon5			Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.436G>A	6.37:g.36103814G>A	ENSP00000211287:p.Val146Ile		36211792	NM_002754	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Missense_Mutation	SNP	ENST00000211287.4	37	CCDS4818.1	.	.	.	.	.	.	.	.	.	.	G	3.288	-0.145572	0.06627	.	.	ENSG00000156711	ENST00000211287;ENST00000373770;ENST00000373766;ENST00000373759	T;T;T	0.61392	0.11;0.11;0.11	4.88	2.74	0.32292	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.272209	0.26136	N	0.026122	T	0.08626	0.0214	N	0.04132	-0.27	0.23386	N	0.99779	B	0.02656	0.0	B	0.10450	0.005	T	0.40720	-0.9548	10	0.02654	T	1	-22.5091	6.3362	0.21296	0.4583:0.0:0.5417:0.0	.	146	O15264	MK13_HUMAN	I	146;146;146;68	ENSP00000211287:V146I;ENSP00000362871:V146I;ENSP00000362864:V68I	ENSP00000211287:V146I	V	+	1	0	MAPK13	36211792	0.995000	0.38212	0.995000	0.50966	0.857000	0.48899	2.762000	0.47597	0.293000	0.22520	0.555000	0.69702	GTC		0.587	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1		
TFAP2D	83741	hgsc.bcm.edu	37	6	50683108	50683108	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr6:50683108C>T	ENST00000008391.3	+	2	547	c.319C>T	c.(319-321)Cac>Tac	p.H107Y		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.H107Y(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GCAGATCCACCACGGGGAGCC	0.612																																					p.H107Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C319T	6						.						119.0	106.0	111.0					6																	50683108		2203	4300	6503	50791067	SO:0001583	missense	83741	exon2			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.319C>T	6.37:g.50683108C>T	ENSP00000008391:p.His107Tyr		50791067	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	4.333	0.061241	0.08339	.	.	ENSG00000008197	ENST00000008391	D	0.97114	-4.25	5.21	5.21	0.72293	.	0.100353	0.64402	D	0.000002	D	0.94663	0.8279	N	0.08118	0	0.80722	D	1	P	0.45126	0.851	P	0.55391	0.775	D	0.96344	0.9253	10	0.62326	D	0.03	-16.7743	19.1268	0.93388	0.0:1.0:0.0:0.0	.	107	Q7Z6R9	AP2D_HUMAN	Y	107	ENSP00000008391:H107Y	ENSP00000008391:H107Y	H	+	1	0	TFAP2D	50791067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.604000	0.82830	2.590000	0.87494	0.655000	0.94253	CAC		0.612	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
NR2E1	7101	hgsc.bcm.edu	37	6	108502832	108502832	+	Silent	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr6:108502832G>A	ENST00000368986.4	+	8	1680	c.972G>A	c.(970-972)acG>acA	p.T324T	NR2E1_ENST00000368983.3_Silent_p.T361T	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	324	Ligand-binding. {ECO:0000250}.				aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	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 (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.T324T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		CTCAGCTAACGCTCAACAGCT	0.478																																					p.T324T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G972A	6						.						136.0	118.0	124.0					6																	108502832		2203	4300	6503	108609525	SO:0001819	synonymous_variant	7101	exon8			Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"""Nuclear hormone receptors"""	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.972G>A	6.37:g.108502832G>A			108609525	NM_003269	Q6ZMP8	Silent	SNP	ENST00000368986.4	37	CCDS5063.1																																																																																				0.478	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2		
DNAH9	1770	hgsc.bcm.edu	37	17	11656242	11656242	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr17:11656242A>T	ENST00000262442.4	+	33	6771	c.6703A>T	c.(6703-6705)Att>Ttt	p.I2235F	DNAH9_ENST00000454412.2_Missense_Mutation_p.I2235F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2235	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.I2235F(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TCCAATGTGGATTGAATCCCT	0.453																																					p.I2235F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6703T	17						.						137.0	119.0	125.0					17																	11656242		2203	4300	6503	11596967	SO:0001583	missense	1770	exon33			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6703A>T	17.37:g.11656242A>T	ENSP00000262442:p.Ile2235Phe		11596967	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.850476	0.91277	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	D;D	0.92348	-3.02;-3.02	5.56	5.56	0.83823	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	D	0.98046	0.9356	H	0.99535	4.615	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99780	1.1027	10	0.87932	D	0	.	16.0147	0.80427	1.0:0.0:0.0:0.0	.	2235	Q9NYC9	DYH9_HUMAN	F	2235;2235;817	ENSP00000262442:I2235F;ENSP00000414874:I2235F	ENSP00000262442:I2235F	I	+	1	0	DNAH9	11596967	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	9.287000	0.95975	2.237000	0.73441	0.460000	0.39030	ATT		0.453	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
TRPV2	51393	hgsc.bcm.edu	37	17	16330137	16330137	+	Silent	SNP	G	G	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr17:16330137G>T	ENST00000338560.7	+	7	1596	c.1197G>T	c.(1195-1197)ctG>ctT	p.L399L	AC093484.4_ENST00000441875.1_RNA|TRPV2_ENST00000577397.1_Intron	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	399					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.L399L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TGTGTAATCTGATCTACATGT	0.532																																					p.L399L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1197T	17						.						125.0	94.0	104.0					17																	16330137		2203	4300	6503	16270862	SO:0001819	synonymous_variant	51393	exon7			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1197G>T	17.37:g.16330137G>T			16270862	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1																																																																																				0.532	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
ACACA	31	hgsc.bcm.edu	37	17	35486332	35486332	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr17:35486332G>A	ENST00000394406.2	-	47	5982	c.5792C>T	c.(5791-5793)cCa>cTa	p.P1931L	ACACA_ENST00000361253.5_Missense_Mutation_p.P57L|ACACA_ENST00000335166.5_Missense_Mutation_p.P1853L|ACACA_ENST00000353139.5_Missense_Mutation_p.P1968L|ACACA_ENST00000360679.3_Missense_Mutation_p.P1873L	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1931	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.P1873L(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGGATCGTATGGGGTCTTTGT	0.463																																					p.P1968L	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5903T	17						.						154.0	127.0	136.0					17																	35486332		2203	4300	6503	32560445	SO:0001583	missense	31	exon47			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5792C>T	17.37:g.35486332G>A	ENSP00000377928:p.Pro1931Leu		32560445	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178107	0.94846	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330;ENST00000361253	D;D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78;-4.78	5.08	5.08	0.68730	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.000000	0.85682	D	0.000000	D	0.99171	0.9713	M	0.91510	3.215	0.80722	D	1	D;D;D;D	0.89917	0.995;1.0;0.998;0.998	D;D;D;D	0.79784	0.931;0.993;0.92;0.95	D	0.99383	1.0923	10	0.87932	D	0	-9.7775	18.46	0.90735	0.0:0.0:1.0:0.0	.	630;1968;1931;1873	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	L	1968;1873;1931;1955;1853;630;57	ENSP00000344789:P1968L;ENSP00000353898:P1873L;ENSP00000377928:P1931L;ENSP00000335323:P1853L;ENSP00000354565:P57L	ENSP00000335323:P1853L	P	-	2	0	ACACA	32560445	1.000000	0.71417	0.400000	0.26346	0.890000	0.51754	9.578000	0.98200	2.345000	0.79718	0.655000	0.94253	CCA		0.463	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
AMZ2	51321	hgsc.bcm.edu	37	17	66250663	66250663	+	Silent	SNP	T	T	C			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr17:66250663T>C	ENST00000359904.3	+	5	1837	c.705T>C	c.(703-705)taT>taC	p.Y235Y	AMZ2_ENST00000577273.1_Intron|AMZ2_ENST00000577985.1_Silent_p.Y235Y|AMZ2_ENST00000580753.1_Silent_p.Y235Y|AMZ2_ENST00000359783.4_Silent_p.Y177Y|AMZ2_ENST00000392720.2_Silent_p.Y235Y|AMZ2_ENST00000577866.1_Silent_p.Y235Y|AMZ2_ENST00000585050.1_Intron	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	235							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Y177Y(1)|p.Y235Y(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			TCGACAACTATTATATTCCAG	0.338																																					p.Y235Y												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T705C	17						.						75.0	73.0	74.0					17																	66250663		2203	4300	6503	63762258	SO:0001819	synonymous_variant	51321	exon6			CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"""archaemetzincin-2"""	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.705T>C	17.37:g.66250663T>C			63762258	NM_001033570	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Silent	SNP	ENST00000359904.3	37	CCDS11674.1																																																																																				0.338	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627	
ETS2	2114	hgsc.bcm.edu	37	21	40194713	40194713	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr21:40194713G>A	ENST00000360214.3	+	11	1770	c.1310G>A	c.(1309-1311)cGc>cAc	p.R437H	ETS2_ENST00000360938.3_Missense_Mutation_p.R437H	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	437					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R437H(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TCGGGGAAGCGCTACGTGTAC	0.567																																					p.R437H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1310A	21						.						113.0	87.0	96.0					21																	40194713		2203	4300	6503	39116583	SO:0001583	missense	2114	exon10				CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.1310G>A	21.37:g.40194713G>A	ENSP00000353344:p.Arg437His		39116583	NM_005239	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	37	CCDS13659.1	.	.	.	.	.	.	.	.	.	.	G	36	5.950681	0.97139	.	.	ENSG00000157557	ENST00000360214;ENST00000360938	T;T	0.30448	1.53;1.53	5.62	5.62	0.85841	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.049344	0.85682	D	0.000000	T	0.65439	0.2691	H	0.94925	3.6	0.80722	D	1	D	0.55385	0.971	P	0.58820	0.846	T	0.76022	-0.3111	10	0.87932	D	0	.	19.2718	0.94013	0.0:0.0:1.0:0.0	.	437	P15036	ETS2_HUMAN	H	437	ENSP00000353344:R437H;ENSP00000354194:R437H	ENSP00000353344:R437H	R	+	2	0	ETS2	39116583	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.706000	0.98722	2.634000	0.89283	0.655000	0.94253	CGC		0.567	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
ATP2B2	491	hgsc.bcm.edu	37	3	10370566	10370566	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr3:10370566C>T	ENST00000352432.4	-	22	3733	c.3664G>A	c.(3664-3666)Gac>Aac	p.D1222N	ATP2B2_ENST00000360273.2_Missense_Mutation_p.D1222N|ATP2B2_ENST00000343816.4_Missense_Mutation_p.D1208N|MIR378B_ENST00000578876.1_RNA|ATP2B2_ENST00000397077.1_Missense_Mutation_p.D1177N|ATP2B2_ENST00000383800.4_Missense_Mutation_p.D1177N|ATP2B2_ENST00000467702.2_5'UTR			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1222					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)	p.D1177N(1)		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						TTGCTTGTGTCGGTCGTCAGG	0.607																																					p.D1177N	Ovarian(125;1619 1709 15675 19819 38835)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3529A	3						.						117.0	102.0	107.0					3																	10370566		2203	4300	6503	10345566	SO:0001583	missense	491	exon20			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.3664G>A	3.37:g.10370566C>T	ENSP00000324172:p.Asp1222Asn		10345566	NM_001683	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	37	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830701	0.50845	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124	D;D;D;D;D;D	0.92299	-3.0;-2.99;-2.99;-3.0;-3.01;-2.99	5.97	5.97	0.96955	.	0.146053	0.64402	D	0.000013	D	0.90397	0.6994	L	0.50333	1.59	0.80722	D	1	B;B;B	0.19331	0.035;0.008;0.004	B;B;B	0.15052	0.012;0.005;0.002	D	0.85029	0.0916	10	0.34782	T	0.22	-28.1009	20.4171	0.99027	0.0:1.0:0.0:0.0	.	1157;1189;1222	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	N	1222;1177;1177;1222;1208;1157;411;1078	ENSP00000324172:D1222N;ENSP00000373311:D1177N;ENSP00000380267:D1177N;ENSP00000353414:D1222N;ENSP00000344677:D1208N;ENSP00000414854:D1078N	ENSP00000344677:D1208N	D	-	1	0	ATP2B2	10345566	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.994000	0.70623	2.832000	0.97577	0.585000	0.79938	GAC		0.607	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
GLT8D1	55830	hgsc.bcm.edu	37	3	52728926	52728926	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr3:52728926T>A	ENST00000407584.3	-	11	1901	c.1051A>T	c.(1051-1053)Att>Ttt	p.I351F	GLT8D1_ENST00000463827.1_5'UTR|GLT8D1_ENST00000394783.3_Missense_Mutation_p.I351F|GLT8D1_ENST00000491606.1_Missense_Mutation_p.I351F|GLT8D1_ENST00000266014.5_Missense_Mutation_p.I351F|SNORD69_ENST00000391150.1_RNA|GLT8D1_ENST00000478968.2_Missense_Mutation_p.I351F	NM_001010983.1|NM_001278280.1	NP_001010983.1|NP_001265209.1	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	351						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.I351F(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(3)	8				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GGGTCTGGAATATACCATTTT	0.403																																					p.I351F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1051T	3						.						176.0	158.0	164.0					3																	52728926		2203	4300	6503	52703966	SO:0001583	missense	55830	exon11			AY358579	CCDS2862.1	3p21.1	2013-02-22			ENSG00000016864	ENSG00000016864		"""Glycosyltransferase family 8 domain containing"""	24870	protein-coding gene	gene with protein product						12975309	Standard	NM_152932		Approved	AD-017, FLJ14611	uc003dfi.4	Q68CQ7	OTTHUMG00000158759	ENST00000407584.3:c.1051A>T	3.37:g.52728926T>A	ENSP00000385730:p.Ile351Phe		52703966	NM_001010983	Q7Z4D1|Q8N2J6|Q9P0I5	Missense_Mutation	SNP	ENST00000407584.3	37	CCDS2862.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.94|17.94	3.511868|3.511868	0.64522|0.64522	.|.	.|.	ENSG00000016864|ENSG00000016864	ENST00000478968;ENST00000394783;ENST00000407584;ENST00000266014;ENST00000491606|ENST00000394786	T;T;T;T;T|.	0.21932|.	1.98;1.98;1.98;1.98;1.98|.	5.63|5.63	4.46|4.46	0.54185|0.54185	.|.	0.149392|.	0.64402|.	D|.	0.000013|.	T|T	0.64616|0.64616	0.2614|0.2614	M|M	0.69823|0.69823	2.125|2.125	0.58432|0.58432	D|D	0.999997|0.999997	P|.	0.43477|.	0.808|.	B|.	0.41860|.	0.368|.	T|T	0.62996|0.62996	-0.6735|-0.6735	10|5	0.46703|.	T|.	0.11|.	-14.4877|-14.4877	8.6744|8.6744	0.34170|0.34170	0.0:0.1773:0.0:0.8227|0.0:0.1773:0.0:0.8227	.|.	351|.	Q68CQ7|.	GL8D1_HUMAN|.	F|F	351|180	ENSP00000419612:I351F;ENSP00000378263:I351F;ENSP00000385730:I351F;ENSP00000266014:I351F;ENSP00000418853:I351F|.	ENSP00000266014:I351F|.	I|Y	-|-	1|2	0|0	GLT8D1|GLT8D1	52703966|52703966	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.382000|1.382000	0.34374|0.34374	1.048000|1.048000	0.40298|0.40298	0.533000|0.533000	0.62120|0.62120	ATT|TAT		0.403	GLT8D1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352065.3	NM_152932	
WNK1	65125	hgsc.bcm.edu	37	12	1017949	1017949	+	Silent	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr12:1017949G>A	ENST00000315939.6	+	28	7783	c.7140G>A	c.(7138-7140)cgG>cgA	p.R2380R	WNK1_ENST00000530271.2_Silent_p.R2878R|WNK1_ENST00000537687.1_Silent_p.R2640R|WNK1_ENST00000535572.1_Silent_p.R2132R|WNK1_ENST00000340908.4_Silent_p.R1973R	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	2380			R -> W (in dbSNP:rs56262445). {ECO:0000269|PubMed:17344846}.		intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.R2380R(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CCAACCTGCGGACCACTTAGA	0.517																																					p.R2640R	Colon(19;451 567 6672 12618 28860)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G7920A	12						.						41.0	45.0	44.0					12																	1017949		2203	4300	6503	888210	SO:0001819	synonymous_variant	65125	exon28			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.7140G>A	12.37:g.1017949G>A			888210	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																				0.517	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
LIMA1	51474	hgsc.bcm.edu	37	12	50594644	50594644	+	Silent	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr12:50594644G>A	ENST00000341247.4	-	7	1037	c.888C>T	c.(886-888)ggC>ggT	p.G296G	LIMA1_ENST00000552008.1_5'UTR|LIMA1_ENST00000552491.1_5'Flank|LIMA1_ENST00000552909.1_Silent_p.G136G|LIMA1_ENST00000552783.1_Silent_p.G136G|LIMA1_ENST00000394943.3_Silent_p.G296G|LIMA1_ENST00000552823.1_Silent_p.G136G|LIMA1_ENST00000547825.1_5'UTR	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	296					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)	p.G296G(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						TTTTGATTTCGCCACCACTGG	0.383																																					p.G296G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C888T	12						.						175.0	175.0	175.0					12																	50594644		2203	4300	6503	48880911	SO:0001819	synonymous_variant	51474	exon7			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.888C>T	12.37:g.50594644G>A			48880911	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Silent	SNP	ENST00000341247.4	37	CCDS8802.1																																																																																				0.383	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
ZBTB39	9880	hgsc.bcm.edu	37	12	57397042	57397042	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr12:57397042G>A	ENST00000300101.2	-	2	1745	c.1660C>T	c.(1660-1662)Cgc>Tgc	p.R554C		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	554					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R554C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1)	16						ACGTGGTAGCGATAGGCAGCC	0.577																																					p.R554C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1660T	12						.						43.0	41.0	42.0					12																	57397042		2203	4300	6503	55683309	SO:0001583	missense	9880	exon2			AB002350	CCDS31839.1	12q13.3	2013-01-09				ENSG00000166860		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	29014	protein-coding gene	gene with protein product						9205841	Standard	NM_014830		Approved	KIAA0352, ZNF922	uc001sml.2	O15060		ENST00000300101.2:c.1660C>T	12.37:g.57397042G>A	ENSP00000300101:p.Arg554Cys		55683309	NM_014830	A7MD38|Q9UD98	Missense_Mutation	SNP	ENST00000300101.2	37	CCDS31839.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234742	0.58886	.	.	ENSG00000166860	ENST00000300101	T	0.61510	0.1	5.7	5.7	0.88788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.065623	0.64402	D	0.000010	T	0.76190	0.3953	M	0.87900	2.915	0.52099	D	0.999947	D	0.89917	1.0	D	0.64687	0.928	T	0.78612	-0.2136	10	0.51188	T	0.08	-24.3591	12.2924	0.54825	0.0:0.0:0.8308:0.1692	.	554	O15060	ZBT39_HUMAN	C	554	ENSP00000300101:R554C	ENSP00000300101:R554C	R	-	1	0	ZBTB39	55683309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.889000	0.69766	2.694000	0.91930	0.650000	0.86243	CGC		0.577	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830	
LACTB	114294	hgsc.bcm.edu	37	15	63433510	63433510	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr15:63433510G>T	ENST00000261893.4	+	6	1222	c.1150G>T	c.(1150-1152)Gtc>Ttc	p.V384F	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	384						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.V384F(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						GAAACGTCTTGTCAACACACC	0.353																																					p.V384F	Melanoma(85;443 1381 6215 27308 35583)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1150T	15						.						115.0	111.0	112.0					15																	63433510		2203	4300	6503	61220563	SO:0001583	missense	114294	exon6			AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.1150G>T	15.37:g.63433510G>T	ENSP00000261893:p.Val384Phe		61220563	NM_032857	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.905164	0.33628	.	.	ENSG00000103642	ENST00000261893	T	0.44083	0.93	5.64	2.78	0.32641	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.166042	0.53938	D	0.000058	T	0.40322	0.1112	M	0.65975	2.015	0.80722	D	1	P	0.37423	0.594	B	0.38921	0.285	T	0.18650	-1.0330	10	0.46703	T	0.11	-4.2337	8.6444	0.33996	0.2867:0.0:0.7133:0.0	.	384	P83111	LACTB_HUMAN	F	384	ENSP00000261893:V384F	ENSP00000261893:V384F	V	+	1	0	LACTB	61220563	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	4.670000	0.61583	0.430000	0.26230	-0.253000	0.11424	GTC		0.353	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
GAK	2580	hgsc.bcm.edu	37	4	844781	844781	+	Silent	SNP	G	G	A	rs75072999	byFrequency	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr4:844781G>A	ENST00000314167.4	-	26	3710	c.3600C>T	c.(3598-3600)acC>acT	p.T1200T	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.T1121T	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1200					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T1200T(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		TCTCTGCAATGGTCTTTGGCC	0.522													G|||	134	0.0267572	0.0015	0.036	5008	,	,		16676	0.0		0.0835	False		,,,				2504	0.0235				p.T1200T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3600T	4						.	G		92,4314	74.1+/-112.3	2,88,2113	213.0	192.0	199.0		3600	2.3	1.0	4	dbSNP_132	199	802,7798	187.4+/-234.7	48,706,3546	no	coding-synonymous	GAK	NM_005255.2		50,794,5659	AA,AG,GG		9.3256,2.0881,6.8738		1200/1312	844781	894,12112	2203	4300	6503	834781	SO:0001819	synonymous_variant	2580	exon26			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3600C>T	4.37:g.844781G>A			834781	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	70	0.03205128205128205	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	55	0.07255936675461741	G	12.15	1.852878	0.32699	0.020881	0.093256	ENSG00000178950	ENST00000511980	.	.	.	5.41	2.33	0.28932	.	.	.	.	.	T	0.08447	0.0210	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41627	-0.9498	5	0.87932	D	0	-52.9883	11.0372	0.47808	0.0:0.2378:0.6265:0.1357	.	.	.	.	L	356	.	ENSP00000424553:P66L	P	-	2	0	GAK	834781	1.000000	0.71417	0.998000	0.56505	0.856000	0.48823	0.666000	0.25097	0.625000	0.30304	0.655000	0.94253	CCA		0.522	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
SH3TC1	54436	hgsc.bcm.edu	37	4	8235213	8235213	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr4:8235213G>C	ENST00000245105.3	+	14	3322	c.3255G>C	c.(3253-3255)caG>caC	p.Q1085H	SH3TC1_ENST00000539824.1_Missense_Mutation_p.Q1009H	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	1085										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						TCTTGCGGCAGAGCGAGCTGG	0.527																																					p.Q1085H	NSCLC(145;2298 2623 35616 37297)											.	.	0			c.G3255C	4						.						83.0	77.0	79.0					4																	8235213		2203	4300	6503	8286113	SO:0001583	missense	54436	exon14			AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.3255G>C	4.37:g.8235213G>C	ENSP00000245105:p.Gln1085His		8286113	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.825390	0.32237	.	.	ENSG00000125089	ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.77620	-1.01;-1.11	3.49	1.73	0.24493	Tetratricopeptide-like helical (1);	0.084755	0.49916	D	0.000128	T	0.73783	0.3631	L	0.52364	1.645	0.44619	D	0.997598	P	0.36959	0.575	B	0.43052	0.406	T	0.71027	-0.4711	10	0.72032	D	0.01	-21.8299	8.9853	0.35990	0.1851:0.0:0.8149:0.0	.	1085	Q8TE82	S3TC1_HUMAN	H	1085;1009;914	ENSP00000245105:Q1085H;ENSP00000441045:Q1009H	ENSP00000245105:Q1085H	Q	+	3	2	SH3TC1	8286113	1.000000	0.71417	0.204000	0.23530	0.396000	0.30629	1.785000	0.38684	0.225000	0.20959	-0.298000	0.09462	CAG		0.527	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
ZMAT1	84460	hgsc.bcm.edu	37	X	101138645	101138645	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chrX:101138645C>A	ENST00000372782.3	-	7	1801	c.1754G>T	c.(1753-1755)aGa>aTa	p.R585I	ZMAT1_ENST00000458570.1_Missense_Mutation_p.R414I|ZMAT1_ENST00000540921.1_Missense_Mutation_p.R585I|ZMAT1_ENST00000494068.1_5'UTR	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	585						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R414I(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GACCTTGACTCTATCCTCCTC	0.393																																					p.R585I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1754T	X						.						233.0	195.0	208.0					X																	101138645		2203	4300	6503	101025301	SO:0001583	missense	84460	exon7			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"""Zinc fingers, matrin-type"""	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1754G>T	X.37:g.101138645C>A	ENSP00000361868:p.Arg585Ile		101025301	NM_001011657	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	C	7.412	0.634885	0.14322	.	.	ENSG00000166432	ENST00000372782;ENST00000540921;ENST00000458570	T;T;T	0.23552	2.48;2.48;1.9	4.27	1.58	0.23477	.	1.576670	0.03473	N	0.213973	T	0.11793	0.0287	N	0.08118	0	0.22803	N	0.998718	P	0.35363	0.497	B	0.23018	0.043	T	0.16719	-1.0393	10	0.52906	T	0.07	-4.693	4.1531	0.10247	0.0:0.1308:0.2007:0.6685	.	585	Q5H9K5	ZMAT1_HUMAN	I	585;585;414	ENSP00000361868:R585I;ENSP00000437529:R585I;ENSP00000413044:R414I	ENSP00000361868:R585I	R	-	2	0	ZMAT1	101025301	0.005000	0.15991	0.553000	0.28255	0.372000	0.29890	-0.006000	0.12833	0.210000	0.20664	-0.380000	0.06706	AGA		0.393	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1		
GRIA3	2892	hgsc.bcm.edu	37	X	122538640	122538640	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chrX:122538640G>T	ENST00000371251.1	+	10	1427	c.1375G>T	c.(1375-1377)Gcc>Tcc	p.A459S	GRIA3_ENST00000264357.5_Missense_Mutation_p.A459S|GRIA3_ENST00000541091.1_Missense_Mutation_p.A443S|GRIA3_ENST00000542149.1_Missense_Mutation_p.A459S|GRIA3_ENST00000371256.5_Missense_Mutation_p.A459S			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	459					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)	p.A459S(2)		breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	TGTAGACCTAGCCTATGAAAT	0.413																																					p.A459S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1375T	X						.						178.0	141.0	154.0					X																	122538640		2203	4300	6503	122366321	SO:0001583	missense	2892	exon10			U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1375G>T	X.37:g.122538640G>T	ENSP00000360297:p.Ala459Ser		122366321	NM_007325	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	37	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231590	0.79688	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251;ENST00000541091	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.7	5.7	0.88788	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.88385	0.6422	M	0.79475	2.455	0.80722	D	1	P;D;D	0.69078	0.875;0.997;0.996	P;D;D	0.79108	0.627;0.992;0.987	D	0.89366	0.3671	10	0.66056	D	0.02	.	17.6357	0.88121	0.0:0.0:1.0:0.0	.	443;459;459	B7Z4C0;P42263;P42263-2	.;GRIA3_HUMAN;.	S	459;459;459;459;443	ENSP00000264357:A459S;ENSP00000446146:A459S;ENSP00000360302:A459S;ENSP00000360297:A459S;ENSP00000446440:A443S	ENSP00000264357:A459S	A	+	1	0	GRIA3	122366321	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.381000	0.81170	0.506000	0.49869	GCC		0.413	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
FAM47B	170062	hgsc.bcm.edu	37	X	34961583	34961583	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chrX:34961583G>A	ENST00000329357.5	+	1	671	c.635G>A	c.(634-636)cGc>cAc	p.R212H		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	212	Pro-rich.							p.R212H(1)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TCCAGTCGCCGCCCAGAGCCT	0.647																																					p.R212H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G635A	X						.						36.0	39.0	38.0					X																	34961583		2202	4298	6500	34871504	SO:0001583	missense	170062	exon1			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.635G>A	X.37:g.34961583G>A	ENSP00000328307:p.Arg212His		34871504	NM_152631	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	G	0.063	-1.218590	0.01542	.	.	ENSG00000189132	ENST00000329357	T	0.21191	2.02	0.217	-0.433	0.12287	.	.	.	.	.	T	0.10294	0.0252	N	0.15975	0.35	0.09310	N	0.999993	B	0.15473	0.013	B	0.06405	0.002	T	0.28933	-1.0028	9	0.38643	T	0.18	.	4.5853	0.12279	0.3225:0.0:0.6775:0.0	.	212	Q8NA70	FA47B_HUMAN	H	212	ENSP00000328307:R212H	ENSP00000328307:R212H	R	+	2	0	FAM47B	34871504	0.086000	0.21541	0.001000	0.08648	0.001000	0.01503	-2.031000	0.01427	-0.777000	0.04572	-0.766000	0.03442	CGC		0.647	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
MAGEC2	51438	hgsc.bcm.edu	37	X	141291466	141291466	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chrX:141291466C>A	ENST00000247452.3	-	3	655	c.308G>T	c.(307-309)tGc>tTc	p.C103F		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	103	Ser-rich.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.C103F(1)		NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGAGCAGCAGGAGCTCAg	0.567										HNSCC(46;0.14)																											p.C103F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G308T	X						.						72.0	68.0	70.0					X																	141291466		2203	4300	6503	141119132	SO:0001583	missense	51438	exon3			AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"""cancer/testis antigen 10"""	300468	"""melanoma antigen, family E, 1, cancer/testis specific"""	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.308G>T	X.37:g.141291466C>A	ENSP00000354660:p.Cys103Phe		141119132	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	37	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	6.124	0.391135	0.11581	.	.	ENSG00000046774	ENST00000247452	T	0.04194	3.68	1.16	-1.27	0.09347	Melanoma associated antigen, MAGE, N-terminal (1);	1.205610	0.06722	U	0.775049	T	0.03959	0.0111	N	0.24115	0.695	0.09310	N	1	D	0.55385	0.971	B	0.43838	0.433	T	0.43750	-0.9372	10	0.26408	T	0.33	.	6.4755	0.22033	0.0:0.4006:0.5994:0.0	.	103	Q9UBF1	MAGC2_HUMAN	F	103	ENSP00000354660:C103F	ENSP00000354660:C103F	C	-	2	0	MAGEC2	141119132	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.915000	0.01578	-0.518000	0.06452	-0.478000	0.04885	TGC		0.567	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249	
LRP1B	53353	hgsc.bcm.edu	37	2	141816607	141816607	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr2:141816607C>A	ENST00000389484.3	-	9	2224	c.1253G>T	c.(1252-1254)gGt>gTt	p.G418V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	418					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.G418V(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CACAGTTATACCATAAAGATG	0.289										TSP Lung(27;0.18)																											p.G418V	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1253T	2						.						80.0	83.0	82.0					2																	141816607		2202	4296	6498	141533077	SO:0001583	missense	53353	exon9			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1253G>T	2.37:g.141816607C>A	ENSP00000374135:p.Gly418Val		141533077	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.830517	0.71258	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.94280	-3.39	5.83	4.95	0.65309	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.071450	0.53938	U	0.000044	D	0.96247	0.8776	M	0.89715	3.055	0.80722	D	1	D	0.54047	0.964	P	0.55055	0.767	D	0.96645	0.9477	10	0.87932	D	0	.	14.3481	0.66680	0.0:0.9293:0.0:0.0707	.	418	Q9NZR2	LRP1B_HUMAN	V	418;356	ENSP00000374135:G418V	ENSP00000374135:G418V	G	-	2	0	LRP1B	141533077	0.996000	0.38824	0.998000	0.56505	0.991000	0.79684	2.994000	0.49433	2.757000	0.94681	0.563000	0.77884	GGT		0.289	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SCN2A	6326	hgsc.bcm.edu	37	2	166223786	166223786	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr2:166223786T>C	ENST00000375437.2	+	19	3870	c.3580T>C	c.(3580-3582)Tgg>Cgg	p.W1194R	SCN2A_ENST00000283256.6_Missense_Mutation_p.W1194R|SCN2A_ENST00000357398.3_Missense_Mutation_p.W1194R|SCN2A_ENST00000375427.2_Missense_Mutation_p.W1194R	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1194					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.W1194R(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGGGAAACTCTGGTGGAATTT	0.398																																					p.W1194R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3580C	2						.						167.0	158.0	161.0					2																	166223786		2203	4300	6503	165932032	SO:0001583	missense	6326	exon18			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3580T>C	2.37:g.166223786T>C	ENSP00000364586:p.Trp1194Arg		165932032	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.703925	0.88924	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.92699	-3.09;-3.09;-3.09;-3.09	6.07	6.07	0.98685	Sodium ion transport-associated (1);	0.193849	0.38111	N	0.001818	D	0.97489	0.9178	H	0.96111	3.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.98635	1.0673	10	0.87932	D	0	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	1194;1194	Q99250-2;Q99250	.;SCN2A_HUMAN	R	1194	ENSP00000364586:W1194R;ENSP00000349973:W1194R;ENSP00000283256:W1194R;ENSP00000364576:W1194R	ENSP00000283256:W1194R	W	+	1	0	SCN2A	165932032	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	TGG		0.398	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
CNRIP1	25927	hgsc.bcm.edu	37	2	68546426	68546426	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr2:68546426C>T	ENST00000263655.3	-	1	712	c.107G>A	c.(106-108)cGc>cAc	p.R36H	CNRIP1_ENST00000409559.3_Missense_Mutation_p.R36H|CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409862.1_Missense_Mutation_p.R36H	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	36								p.R36H(2)		kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						CTTGATGGTGCGGTTCTGGCC	0.642																																					p.R36H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G107A	2						.						51.0	40.0	44.0					2																	68546426		2154	4235	6389	68399930	SO:0001583	missense	25927	exon1			AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 32"""	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.107G>A	2.37:g.68546426C>T	ENSP00000263655:p.Arg36His		68399930	NM_015463	B2R4D0|Q49AN4|Q9UFZ0	Missense_Mutation	SNP	ENST00000263655.3	37	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.841864	0.91197	.	.	ENSG00000119865	ENST00000409559;ENST00000263655;ENST00000409862	.	.	.	4.83	3.94	0.45596	.	0.000000	0.85682	D	0.000000	T	0.68384	0.2995	L	0.58810	1.83	0.54753	D	0.999989	D;D;D	0.76494	0.999;0.997;0.999	P;P;P	0.60886	0.88;0.799;0.855	T	0.72154	-0.4376	9	0.72032	D	0.01	-9.4359	13.6096	0.62068	0.0:0.8447:0.1553:0.0	.	36;36;36	B8ZZB8;Q96F85;Q96F85-2	.;CNRP1_HUMAN;.	H	36	.	ENSP00000263655:R36H	R	-	2	0	CNRIP1	68399930	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.058000	0.76676	1.231000	0.43661	0.491000	0.48974	CGC		0.642	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463	
NDUFS1	4719	hgsc.bcm.edu	37	2	206997720	206997720	+	Missense_Mutation	SNP	C	C	T	rs141196622		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr2:206997720C>T	ENST00000233190.6	-	14	1768	c.1502G>A	c.(1501-1503)cGg>cAg	p.R501Q	NDUFS1_ENST00000457011.1_Missense_Mutation_p.R385Q|NDUFS1_ENST00000432169.1_Missense_Mutation_p.R390Q|NDUFS1_ENST00000423725.1_Missense_Mutation_p.R444Q|NDUFS1_ENST00000455934.2_Missense_Mutation_p.R515Q|NDUFS1_ENST00000440274.1_Missense_Mutation_p.R465Q|NDUFS1_ENST00000449699.1_Missense_Mutation_p.R501Q	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	501					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R501Q(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACTAGTCATCCGAATCTTTTG	0.363																																					p.R501Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1502A	2						.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	116.0	107.0	110.0		1394,1169,1331,1544,1502	5.9	0.3	2	dbSNP_134	110	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	NDUFS1	NM_001199981.1,NM_001199982.1,NM_001199983.1,NM_001199984.1,NM_005006.6	43,43,43,43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	465/692,390/617,444/671,515/742,501/728	206997720	1,13005	2203	4300	6503	206705965	SO:0001583	missense	4719	exon14				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1502G>A	2.37:g.206997720C>T	ENSP00000233190:p.Arg501Gln		206705965	NM_005006	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	37	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199892	0.58126	2.27E-4	0.0	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	5.91	5.91	0.95273	Molybdopterin oxidoreductase (1);	0.108901	0.64402	D	0.000016	D	0.86489	0.5945	L	0.45698	1.435	0.80722	D	1	B;B;B;B	0.15930	0.008;0.014;0.015;0.015	B;B;B;B	0.28011	0.085;0.017;0.017;0.017	T	0.80830	-0.1207	10	0.49607	T	0.09	-31.8348	20.2946	0.98546	0.0:1.0:0.0:0.0	.	390;465;515;501	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	Q	501;444;385;465;515;501;390	ENSP00000233190:R501Q;ENSP00000397760:R444Q;ENSP00000400976:R385Q;ENSP00000409766:R465Q;ENSP00000392709:R515Q;ENSP00000399912:R501Q;ENSP00000409689:R390Q	ENSP00000233190:R501Q	R	-	2	0	NDUFS1	206705965	0.998000	0.40836	0.333000	0.25482	0.991000	0.79684	5.493000	0.66899	2.804000	0.96469	0.462000	0.41574	CGG		0.363	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
RNF6	6049	hgsc.bcm.edu	37	13	26788610	26788610	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr13:26788610T>C	ENST00000381588.4	-	5	2161	c.1409A>G	c.(1408-1410)aAt>aGt	p.N470S	RNF6_ENST00000381570.3_Missense_Mutation_p.N470S|RNF6_ENST00000346166.3_Missense_Mutation_p.N470S|RNF6_ENST00000399762.2_Missense_Mutation_p.N114S|RNF6_ENST00000468480.1_Intron	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	470					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N470S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		AACAAGCTCATTCTCAGAAAT	0.458																																					p.N470S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1409G	13						.						92.0	88.0	89.0					13																	26788610		2203	4300	6503	25686610	SO:0001583	missense	6049	exon5			AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"""RING-type (C3HC4) zinc fingers"""	10069	protein-coding gene	gene with protein product	"""RING-H2 protein RNF-6"""	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1409A>G	13.37:g.26788610T>C	ENSP00000371000:p.Asn470Ser		25686610	NM_005977	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Missense_Mutation	SNP	ENST00000381588.4	37	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.857993	0.32791	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570;ENST00000399762	T;T;T;T	0.13657	3.15;3.15;3.15;2.57	4.5	3.28	0.37604	.	0.268186	0.35739	N	0.003012	T	0.13243	0.0321	L	0.51422	1.61	0.30634	N	0.757192	B;B	0.30406	0.06;0.278	B;B	0.25987	0.065;0.057	T	0.05801	-1.0863	10	0.59425	D	0.04	-5.103	11.0917	0.48119	0.0:0.0:0.5124:0.4876	.	114;470	B4DDP0;Q9Y252	.;RNF6_HUMAN	S	470;470;470;114	ENSP00000342121:N470S;ENSP00000371000:N470S;ENSP00000370982:N470S;ENSP00000382665:N114S	ENSP00000342121:N470S	N	-	2	0	RNF6	25686610	1.000000	0.71417	0.970000	0.41538	0.990000	0.78478	4.291000	0.59025	0.834000	0.34852	0.374000	0.22700	AAT		0.458	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977	
FREM2	341640	hgsc.bcm.edu	37	13	39264109	39264109	+	Silent	SNP	C	C	T			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr13:39264109C>T	ENST00000280481.7	+	1	2844	c.2628C>T	c.(2626-2628)caC>caT	p.H876H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	876					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H876H(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACATGGCCACATGAGAGTGT	0.507																																					p.H876H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2628T	13						.						93.0	79.0	84.0					13																	39264109		2203	4300	6503	38162109	SO:0001819	synonymous_variant	341640	exon1			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2628C>T	13.37:g.39264109C>T			38162109	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																				0.507	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
MYO16	23026	hgsc.bcm.edu	37	13	109445885	109445885	+	Missense_Mutation	SNP	G	G	A	rs537057276	byFrequency	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr13:109445885G>A	ENST00000357550.2	+	5	613	c.572G>A	c.(571-573)cGc>cAc	p.R191H	MYO16_ENST00000251041.5_Missense_Mutation_p.R191H|MYO16_ENST00000356711.2_Missense_Mutation_p.R191H	NM_001198950.1	NP_001185879.1			myosin XVI									p.R191H(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			ACCTCACTGCGCCAGATGAAG	0.443																																					p.R213H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G638A	13						.						129.0	122.0	125.0					13																	109445885		2203	4300	6503	108243886	SO:0001583	missense	23026	exon6				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.572G>A	13.37:g.109445885G>A	ENSP00000350160:p.Arg191His		108243886	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.613625	0.28712	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041	T;T;T	0.53206	0.63;0.63;0.63	5.76	3.13	0.36017	Ankyrin repeat-containing domain (3);	0.173228	0.27447	U	0.019329	T	0.29882	0.0747	L	0.28014	0.82	0.80722	D	1	B;B	0.27951	0.08;0.195	B;B	0.21708	0.017;0.036	T	0.04522	-1.0945	9	.	.	.	.	9.1214	0.36788	0.2372:0.0:0.7628:0.0	.	191;191	Q9Y6X6-2;Q9Y6X6	.;MYO16_HUMAN	H	191	ENSP00000349145:R191H;ENSP00000350160:R191H;ENSP00000251041:R191H	.	R	+	2	0	MYO16	108243886	0.996000	0.38824	0.993000	0.49108	0.761000	0.43186	1.317000	0.33631	0.373000	0.24621	-0.218000	0.12543	CGC		0.443	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
PCDHA8	56140	hgsc.bcm.edu	37	5	140221377	140221377	+	Silent	SNP	G	G	A			TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr5:140221377G>A	ENST00000531613.1	+	1	471	c.471G>A	c.(469-471)gcG>gcA	p.A157A	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.A157A	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	157	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A157A(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAGAGGGCGCGTCCGATGCAG	0.458																																					p.A157A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G471A	5						.						80.0	86.0	84.0					5																	140221377		2203	4300	6503	140201561	SO:0001819	synonymous_variant	56140	exon1			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.471G>A	5.37:g.140221377G>A			140201561	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																				0.458	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
RASA1	5921	hgsc.bcm.edu	37	5	86629108	86629108	+	Nonsense_Mutation	SNP	C	C	T	rs137853218		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr5:86629108C>T	ENST00000274376.6	+	4	1417	c.853C>T	c.(853-855)Cga>Tga	p.R285*	RASA1_ENST00000456692.2_Nonsense_Mutation_p.R108*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.R119*|RASA1_ENST00000512763.1_Nonsense_Mutation_p.R118*	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	285	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.R285*(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AAGGCGTGTACGAGCTATTCT	0.313																																					p.R285X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C853T	5	GRCh37	CM081410	RASA1	M	rs137853218	.						67.0	72.0	71.0					5																	86629108		2203	4300	6503	86664864	SO:0001587	stop_gained	5921	exon4				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.853C>T	5.37:g.86629108C>T	ENSP00000274376:p.Arg285*		86664864	NM_002890	B2R6W3|Q9UDI1	Nonsense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	C	42	9.693761	0.99240	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	15.7476	0.77958	0.1368:0.8631:0.0:0.0	.	.	.	.	X	285;318;108;118;119	.	ENSP00000274376:R285X	R	+	1	2	RASA1	86664864	0.998000	0.40836	0.990000	0.47175	0.957000	0.61999	3.659000	0.54489	2.587000	0.87381	0.650000	0.86243	CGA		0.313	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
PPP2R2B	5521	hgsc.bcm.edu	37	5	145980011	145980011	+	Missense_Mutation	SNP	G	G	A	rs148423117		TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3574-01A-01W-0831-10	TCGA-AG-3574-10A-01W-0831-10	g.chr5:145980011G>A	ENST00000394413.3	-	7	1373	c.803C>T	c.(802-804)cCg>cTg	p.P268L	PPP2R2B_ENST00000356826.3_Missense_Mutation_p.P268L|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.P268L|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.P326L|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.P268L|PPP2R2B_ENST00000508545.2_Missense_Mutation_p.P257L|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.P257L|CTB-99A3.1_ENST00000512730.1_RNA|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.P334L|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.P274L|PPP2R2B_ENST00000336640.6_Missense_Mutation_p.P271L			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	268					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.P271L(3)|p.P326L(2)|p.P268L(1)|p.P257L(1)		endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGATCTTCCGGCTCTTCAAA	0.413																																					p.P268L												.	.	7	Substitution - Missense(7)	kidney(4)|large_intestine(3)	c.C803T	5						.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	56.0	56.0	56.0		803,803,803,803,812,743,770	5.8	1.0	5	dbSNP_134	56	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	PPP2R2B	NM_001127381.1,NM_004576.2,NM_181674.2,NM_181675.2,NM_181676.2,NM_181677.2,NM_181678.2	98,98,98,98,98,98,98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	268/444,268/444,268/444,268/444,271/447,248/424,257/433	145980011	1,13005	2203	4300	6503	145960204	SO:0001583	missense	5521	exon8			M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.803C>T	5.37:g.145980011G>A	ENSP00000377935:p.Pro268Leu		145960204	NM_001127381	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928122	0.73327	2.27E-4	0.0	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	M	0.79475	2.455	0.80722	D	1	P;P;P;P;P;P	0.43750	0.816;0.816;0.816;0.664;0.705;0.816	B;B;B;B;B;B	0.34590	0.13;0.186;0.134;0.13;0.035;0.186	T	0.43637	-0.9379	10	0.51188	T	0.08	-22.597	20.0467	0.97609	0.0:0.0:1.0:0.0	.	326;274;257;334;271;268	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	L	268;257;334;268;268;268;257;271;274;326	ENSP00000377935:P268L;ENSP00000431320:P257L;ENSP00000377936:P334L;ENSP00000377933:P268L;ENSP00000349283:P268L;ENSP00000398779:P268L;ENSP00000377932:P257L;ENSP00000336591:P271L;ENSP00000421396:P274L;ENSP00000377931:P326L	ENSP00000336591:P271L	P	-	2	0	AC011357.1	145960204	1.000000	0.71417	0.977000	0.42913	0.992000	0.81027	9.869000	0.99810	2.749000	0.94314	0.655000	0.94253	CCG		0.413	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678	
