#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_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_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ACVR2A	92	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	148677842	148677842	+	Missense_Mutation	SNP	G	G	T	rs111862877		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr2:148677842G>T	ENST00000241416.7	+	8	1642	c.1006G>T	c.(1006-1008)Gct>Tct	p.A336S	ACVR2A_ENST00000404590.1_Missense_Mutation_p.A336S|ACVR2A_ENST00000535787.1_Missense_Mutation_p.A228S	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	336	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.A336S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CAACCTGACAGCTTGCATTGC	0.348																																																	1	Substitution - Missense(1)	kidney(1)											93.0	97.0	96.0					2																	148677842		2203	4300	6503	SO:0001583	missense	92				CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1006G>T	2.37:g.148677842G>T	ENSP00000241416:p.Ala336Ser		B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	37	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.584944	0.86748	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	D;D;D	0.94046	-3.34;-3.34;-3.34	5.42	5.42	0.78866	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.093907	0.64402	D	0.000001	D	0.96294	0.8791	M	0.74389	2.26	0.80722	D	1	P	0.41748	0.761	P	0.57679	0.825	D	0.96153	0.9109	10	0.66056	D	0.02	.	19.586	0.95490	0.0:0.0:1.0:0.0	.	336	P27037	AVR2A_HUMAN	S	336;228;336	ENSP00000241416:A336S;ENSP00000439988:A228S;ENSP00000384338:A336S	ENSP00000241416:A336S	A	+	1	0	ACVR2A	148394312	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.957000	0.87870	2.699000	0.92147	0.655000	0.94253	GCT		0.348	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1		NM_001616	
APOH	350	broad.mit.edu;ucsc.edu	37	17	64213023	64213023	+	Missense_Mutation	SNP	T	T	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:64213023T>G	ENST00000205948.6	-	6	704	c.667A>C	c.(667-669)Aca>Cca	p.T223P		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	223	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)	p.T223P(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TAATAAAGTGTTGGTTTTGCA	0.373																																					Melanoma(155;624 1882 16869 48804 51309)												1	Substitution - Missense(1)	kidney(1)											182.0	181.0	181.0					17																	64213023		2203	4300	6503	SO:0001583	missense	350				CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.667A>C	17.37:g.64213023T>G	ENSP00000205948:p.Thr223Pro		B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	.	.	.	.	.	.	.	.	.	.	t	3.423	-0.117656	0.06838	.	.	ENSG00000091583	ENST00000205948	T	0.64991	-0.13	5.87	0.271	0.15640	Complement control module (2);Sushi/SCR/CCP (3);	1.647620	0.02841	N	0.127947	T	0.47544	0.1451	N	0.26130	0.795	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15896	-1.0421	10	0.29301	T	0.29	.	4.9609	0.14066	0.0:0.4211:0.2633:0.3156	.	223	P02749	APOH_HUMAN	P	223	ENSP00000205948:T223P	ENSP00000205948:T223P	T	-	1	0	APOH	61643485	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.088000	0.11198	-0.118000	0.11851	-0.763000	0.03452	ACA		0.373	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1		NM_000042	
ATP5G2	517	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	54063038	54063038	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:54063038C>A	ENST00000549164.1	-	4	392	c.205G>T	c.(205-207)Gac>Tac	p.D69Y	ATP5G2_ENST00000550241.1_5'Flank|ATP5G2_ENST00000602871.1_Missense_Mutation_p.D69Y|ATP5G2_ENST00000394349.3_Missense_Mutation_p.D126Y|ATP5G2_ENST00000338662.5_Missense_Mutation_p.D85Y			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	69					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.D85Y(1)		kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						GCTGCTGTGTCGATGTCCCTT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											68.0	64.0	65.0					12																	54063038		2203	4300	6503	SO:0001583	missense	517			X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	842	protein-coding gene	gene with protein product		603193	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"""			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.205G>T	12.37:g.54063038C>A	ENSP00000447317:p.Asp69Tyr		B3KQQ6	Missense_Mutation	SNP	ENST00000549164.1	37		.	.	.	.	.	.	.	.	.	.	C	29.4	4.998880	0.93227	.	.	ENSG00000135390	ENST00000394349;ENST00000549164;ENST00000338662	T;T;T	0.40476	1.03;1.03;1.03	5.26	5.26	0.73747	ATPase, F0/V0 complex, subunit C (2);	0.046351	0.85682	D	0.000000	T	0.69351	0.3101	M	0.86864	2.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.917;0.99;0.991	T	0.69647	-0.5089	10	0.39692	T	0.17	-14.6556	18.169	0.89739	0.0:1.0:0.0:0.0	.	69;85;126	Q06055;Q06055-3;Q06055-2	AT5G2_HUMAN;.;.	Y	126;69;85	ENSP00000377878:D126Y;ENSP00000447317:D69Y;ENSP00000340315:D85Y	ENSP00000340315:D85Y	D	-	1	0	ATP5G2	52349305	1.000000	0.71417	0.976000	0.42696	0.975000	0.68041	7.528000	0.81941	2.906000	0.99361	0.655000	0.94253	GAC		0.547	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1		NM_005176	
ATRX	546	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	76890185	76890185	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chrX:76890185A>C	ENST00000373344.5	-	17	4923	c.4709T>G	c.(4708-4710)tTt>tGt	p.F1570C	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.F1532C	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1570					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.F1570C(2)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ATCCCACATAAACTGAACACC	0.353			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																	Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	3	Substitution - Missense(2)|Unknown(1)	kidney(2)|bone(1)											130.0	129.0	129.0					X																	76890185		2203	4296	6499	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4709T>G	X.37:g.76890185A>C	ENSP00000362441:p.Phe1570Cys		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.225417	0.58668	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.93426	-3.22;-3.22	5.77	5.77	0.91146	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97977	0.9334	H	0.97440	4.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99285	1.0897	10	0.87932	D	0	-9.8173	15.0169	0.71594	1.0:0.0:0.0:0.0	.	1532;1570	P46100-4;P46100	.;ATRX_HUMAN	C	1570;1532	ENSP00000362441:F1570C;ENSP00000378967:F1532C	ENSP00000362441:F1570C	F	-	2	0	ATRX	76776841	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.932000	0.92897	1.929000	0.55896	0.486000	0.48141	TTT		0.353	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2		NM_000489	
BAP1	8314	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52436345	52436345	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr3:52436345delG	ENST00000460680.1	-	17	2620	c.2149delC	c.(2149-2151)cggfs	p.R718fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.R700fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CGTTTCCGCCGGTCAGGCTTC	0.662			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)			Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0													23.0	26.0	25.0					3																	52436345		2202	4294	6496	SO:0001589	frameshift_variant	8314			AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.2149delC	3.37:g.52436345delG	ENSP00000417132:p.Arg718fs		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	37	CCDS2853.1																																																																																				0.662	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			
C11orf94	143678	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	45928173	45928173	+	Missense_Mutation	SNP	G	G	A	rs540548996		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr11:45928173G>A	ENST00000449465.1	-	3	280	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	RP11-618K13.2_ENST00000533218.1_RNA	NM_001080446.2	NP_001073915.2	C9JXX5	CK094_HUMAN	chromosome 11 open reading frame 94	82						extracellular region (GO:0005576)		p.R82C(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|ovary(1)|pancreas(1)|prostate(1)	7						TCCCGCTTGCGCTGCTGGGCC	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	kidney(1)											66.0	71.0	69.0					11																	45928173		1923	4119	6042	SO:0001583	missense	143678				CCDS44577.1	11p11.2	2012-08-10			ENSG00000234776	ENSG00000234776			37213	protein-coding gene	gene with protein product							Standard	NM_001080446		Approved		uc001nbs.4	C9JXX5	OTTHUMG00000167004	ENST00000449465.1:c.244C>T	11.37:g.45928173G>A	ENSP00000401498:p.Arg82Cys			Missense_Mutation	SNP	ENST00000449465.1	37	CCDS44577.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711302	0.68730	.	.	ENSG00000234776	ENST00000449465	T	0.61392	0.11	4.66	4.66	0.58398	.	.	.	.	.	T	0.70718	0.3256	.	.	.	0.40029	D	0.9755	D	0.89917	1.0	D	0.67231	0.95	T	0.74281	-0.3716	8	0.87932	D	0	-23.401	7.9022	0.29742	0.0:0.1367:0.5187:0.3446	.	82	C9JXX5	CK094_HUMAN	C	82	ENSP00000401498:R82C	ENSP00000401498:R82C	R	-	1	0	C11orf94	45884749	1.000000	0.71417	0.999000	0.59377	0.898000	0.52572	3.397000	0.52572	2.419000	0.82065	0.655000	0.94253	CGC		0.577	C11orf94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392395.1		NM_001080446	
SHCBP1L	81626	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	182869151	182869151	+	Silent	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:182869151G>A	ENST00000367547.3	-	10	2165	c.1929C>T	c.(1927-1929)aaC>aaT	p.N643N	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Silent_p.N524N	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	715								p.N643N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						CCCCCTTGACGTTTGCTTCTA	0.308																																																	1	Substitution - coding silent(1)	kidney(1)											88.0	88.0	88.0					1																	182869151		2202	4300	6502	SO:0001819	synonymous_variant	0			AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 14"""	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.1929C>T	1.37:g.182869151G>A			Q4G195|Q9BZQ3|Q9H2B6	Silent	SNP	ENST00000367547.3	37	CCDS30955.1																																																																																				0.308	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1		NM_030933	
CNOT11	55571	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	101885856	101885856	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr2:101885856A>C	ENST00000289382.3	+	7	1677	c.1514A>C	c.(1513-1515)gAg>gCg	p.E505A	RNF149_ENST00000485752.1_5'Flank	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	505					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)		p.E505A(1)									ACACCTTCTGAGACCAAAATG	0.413																																																	1	Substitution - Missense(1)	kidney(1)											104.0	106.0	106.0					2																	101885856		2203	4300	6503	SO:0001583	missense	55571			AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 29"""	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1514A>C	2.37:g.101885856A>C	ENSP00000289382:p.Glu505Ala		Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	37	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	A	18.09	3.545787	0.65198	.	.	ENSG00000158435	ENST00000289382	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.38480	0.1042	N	0.22421	0.69	0.80722	D	1	P	0.39665	0.682	B	0.37731	0.257	T	0.23368	-1.0190	9	0.09843	T	0.71	-31.3574	16.4484	0.83959	1.0:0.0:0.0:0.0	.	505	Q9UKZ1	CB029_HUMAN	A	505	.	ENSP00000289382:E505A	E	+	2	0	C2orf29	101252288	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	9.170000	0.94795	2.285000	0.76669	0.533000	0.62120	GAG		0.413	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1		NM_017546	
C6orf62	81688	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	24706388	24706388	+	Missense_Mutation	SNP	G	G	T	rs372450488		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr6:24706388G>T	ENST00000378119.4	-	5	2834	c.667C>A	c.(667-669)Ctc>Atc	p.L223I	RP1-30M3.6_ENST00000606921.1_RNA|C6orf62_ENST00000378102.3_Missense_Mutation_p.L194I|C6orf62_ENST00000540769.1_Missense_Mutation_p.L165I	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	223						intracellular (GO:0005622)		p.L223I(2)		endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						TAAGGACGGAGGTGATCCTCT	0.443																																																	2	Substitution - Missense(2)	kidney(2)											131.0	112.0	119.0					6																	24706388		2203	4300	6503	SO:0001583	missense	81688			AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"""HBV X-transactivated protein 12"""					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.667C>A	6.37:g.24706388G>T	ENSP00000367359:p.Leu223Ile		Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	37	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.866619	0.72065	.	.	ENSG00000112308	ENST00000378119;ENST00000540769;ENST00000378102	T;T;T	0.41065	1.01;1.01;1.01	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.45915	0.1366	N	0.19112	0.55	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	T	0.49153	-0.8969	10	0.66056	D	0.02	-11.0338	20.8794	0.99867	0.0:0.0:1.0:0.0	.	223	Q9GZU0	CF062_HUMAN	I	223;165;194	ENSP00000367359:L223I;ENSP00000446225:L165I;ENSP00000367342:L194I	ENSP00000367342:L194I	L	-	1	0	C6orf62	24814367	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.772000	0.98984	2.941000	0.99782	0.655000	0.94253	CTC		0.443	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1		NM_030939	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr4:1388693C>G	ENST00000324803.4	+	1	3354	c.394C>G	c.(394-396)Cat>Gat	p.H132D		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	132					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.H132D(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACGTGCCCATGCGGAGTG	0.697													N|||	864	0.172524	0.112	0.2421	5008	,	,		13504	0.0546		0.2783	False		,,,				2504	0.2178																1	Substitution - Missense(1)	skin(1)											68.0	69.0	68.0					4																	1388693		2197	4291	6488	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.394C>G	4.37:g.1388693C>G	ENSP00000323978:p.His132Asp		Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.898|0.898	-0.723180|-0.723180	0.03158|0.03158	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.18657|.	2.2|.	0.666|0.666	-0.474|-0.474	0.12108|0.12108	.|.	.|.	.|.	.|.	.|.	T|T	0.12178|0.12178	0.0296|0.0296	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.33929|0.33929	-0.9849|-0.9849	8|5	0.28530|0.05833	T|T	0.3|0.94	.|.	2.4426|2.4426	0.04498|0.04498	0.0:0.4251:0.3263:0.2486|0.0:0.4251:0.3263:0.2486	.|.	132|.	Q8N1N5|.	CRPAK_HUMAN|.	D|R	132|115	ENSP00000323978:H132D|.	ENSP00000323978:H132D|ENSP00000372402:P115R	H|P	+|+	1|2	0|0	CRIPAK|CRIPAK	1378693|1378693	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.786000|-1.786000	0.01766|0.01766	-0.170000|-0.170000	0.10816|0.10816	-1.737000|-1.737000	0.00689|0.00689	CAT|CCA		0.697	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2		NM_175918	
CROCCP2	84809	broad.mit.edu	37	1	16946434	16946434	+	lincRNA	SNP	C	C	T	rs367060	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:16946434C>T	ENST00000412962.1	-	0	1085				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTCAGCCTTCCGCCGGGCCAG	0.672													.|||	253	0.0505192	0.115	0.0533	5008	,	,		65734	0.0119		0.0437	False		,,,				2504	0.0082																0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946434C>T			Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																					0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
CTBS	1486	broad.mit.edu	37	1	85039999	85040007	+	In_Frame_Del	DEL	GCAGCGCCA	GCAGCGCCA	-	rs142534762|rs3217269|rs199701060|rs201060055	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	GCAGCGCCA	GCAGCGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:85039999_85040007delGCAGCGCCA	ENST00000370630.5	-	1	140_148	c.92_100delTGGCGCTGC	c.(91-102)ctggcgctgcgg>cgg	p.LAL31del	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	31					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		GCCGCGAGCCgcagcgccagcagcgccag	0.718														1537	0.306909	0.5038	0.2954	5008	,	,		11352	0.0556		0.2624	False		,,,				2504	0.3538																0										865,21,1798		349,2,165,3,13,810						-3.6	0.0		dbSNP_134	4	1279,4,4361		415,1,448,1,1,1956	no	codingComplex	CTBS	NM_004388.2		764,3,613,4,14,2766	A1A1,A1A2,A1R,A2A2,A2R,RR		22.7321,33.0104,26.0447				2144,25,6159				SO:0001651	inframe_deletion	1486			M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.92_100delTGGCGCTGC	1.37:g.85040008_85040016delGCAGCGCCA	ENSP00000359664:p.Leu31_Leu33del		Q5VX50	In_Frame_Del	DEL	ENST00000370630.5	37	CCDS698.1																																																																																				0.718	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2		NM_004388	
CTCF	10664	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	67660544	67660544	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr16:67660544C>A	ENST00000264010.4	+	8	1888	c.1444C>A	c.(1444-1446)Ctc>Atc	p.L482I	CTCF_ENST00000401394.1_Missense_Mutation_p.L154I	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	482					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.L482I(1)		breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		GCGCTATGCCCTCATCCAGCA	0.453																																					Colon(175;1200 1966 6945 23069 27405)												1	Substitution - Missense(1)	kidney(1)											123.0	99.0	108.0					16																	67660544		2198	4300	6498	SO:0001583	missense	10664			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"""Zinc fingers, C2H2-type"""	13723	protein-coding gene	gene with protein product	"""11 zinc finger transcriptional repressor"""	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.1444C>A	16.37:g.67660544C>A	ENSP00000264010:p.Leu482Ile		B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	37	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	C	33	5.286348	0.95517	.	.	ENSG00000102974	ENST00000264010;ENST00000401394	T;T	0.53857	0.6;0.6	5.2	5.2	0.72013	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000026	T	0.75989	0.3925	M	0.83852	2.665	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	T	0.79738	-0.1677	10	0.87932	D	0	-2.215	19.0968	0.93255	0.0:1.0:0.0:0.0	.	482	P49711	CTCF_HUMAN	I	482;154	ENSP00000264010:L482I;ENSP00000384707:L154I	ENSP00000264010:L482I	L	+	1	0	CTCF	66218045	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.776000	0.85560	2.596000	0.87737	0.561000	0.74099	CTC		0.453	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2		NM_006565	
CWC25	54883	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	36963045	36963045	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:36963045C>T	ENST00000225428.5	-	7	1172	c.875G>A	c.(874-876)aGg>aAg	p.R292K	CWC25_ENST00000536127.1_Missense_Mutation_p.R229K	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	292								p.R292K(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						GGACCGTGACCTTCTGCCCAG	0.577																																																	1	Substitution - Missense(1)	kidney(1)											67.0	65.0	66.0					17																	36963045		1957	4151	6108	SO:0001583	missense	54883			AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"""coiled-coil domain containing 49"""	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.875G>A	17.37:g.36963045C>T	ENSP00000225428:p.Arg292Lys		A0JLM3|Q68DK5	Missense_Mutation	SNP	ENST00000225428.5	37	CCDS45663.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.240157	0.22711	.	.	ENSG00000108296	ENST00000225428;ENST00000536127	.	.	.	4.88	2.87	0.33458	.	0.125415	0.50627	N	0.000113	T	0.29588	0.0738	N	0.22421	0.69	0.36169	D	0.848622	B;B	0.10296	0.003;0.0	B;B	0.06405	0.002;0.001	T	0.25606	-1.0127	9	0.05351	T	0.99	.	7.6637	0.28417	0.0:0.806:0.0:0.194	.	229;292	B4DJK2;Q9NXE8	.;CWC25_HUMAN	K	292;229	.	ENSP00000225428:R292K	R	-	2	0	CWC25	34216571	.	.	1.000000	0.80357	0.129000	0.20672	.	.	0.656000	0.30886	-0.251000	0.11542	AGG		0.577	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6		NM_017748	
DENND2D	79961	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	111743023	111743023	+	Missense_Mutation	SNP	A	A	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:111743023A>T	ENST00000357640.4	-	1	288	c.59T>A	c.(58-60)cTc>cAc	p.L20H	CHI3L2_ENST00000445067.2_5'Flank|DENND2D_ENST00000369752.5_Intron|DENND2D_ENST00000473682.1_5'UTR	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	20					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.L20H(1)		breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		ACCTGCTCGGAGTTGAAGCAG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											92.0	72.0	79.0					1																	111743023		2203	4300	6503	SO:0001583	missense	79961				CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"""DENN/MADD domain containing"""	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.59T>A	1.37:g.111743023A>T	ENSP00000350266:p.Leu20His		Q5T5V6|Q9BSU0	Missense_Mutation	SNP	ENST00000357640.4	37	CCDS831.1	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.415147	0.01145	.	.	ENSG00000162777	ENST00000357640	T	0.14391	2.51	4.31	0.599	0.17519	.	.	.	.	.	T	0.01254	0.0041	N	0.03115	-0.41	0.20638	N	0.999875	B	0.02656	0.0	B	0.01281	0.0	T	0.47182	-0.9137	9	0.32370	T	0.25	-0.7369	1.4174	0.02305	0.5275:0.2051:0.1004:0.167	.	20	Q9H6A0	DEN2D_HUMAN	H	20	ENSP00000350266:L20H	ENSP00000350266:L20H	L	-	2	0	DENND2D	111544546	0.000000	0.05858	0.033000	0.17914	0.011000	0.07611	-0.268000	0.08607	0.092000	0.17331	-0.317000	0.08691	CTC		0.557	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1		NM_024901	
DGKK	139189	hgsc.bcm.edu	37	X	50213423	50213423	+	RNA	SNP	T	T	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chrX:50213423T>A	ENST00000376025.2	-	0	314							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					gctctgtggctggttctgggg	0.642													t|||	3	0.000794702	0.0	0.0	3775	,	,		7416	0.0		0.003	False		,,,				2504	0.0																0													80.0	93.0	89.0					X																	50213423		1867	4080	5947			139189			AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50213423T>A			B2RP91	Silent	SNP	ENST00000376025.2	37																																																																																					0.642	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1		NM_001013742	
DMKN	93099	hgsc.bcm.edu	37	19	36002423	36002423	+	Missense_Mutation	SNP	C	C	T	rs145440628		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr19:36002423C>T	ENST00000339686.3	-	5	984	c.808G>A	c.(808-810)Ggt>Agt	p.G270S	DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G270S|DMKN_ENST00000447113.2_Missense_Mutation_p.G270S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G270S|DMKN_ENST00000440396.1_Missense_Mutation_p.G270S|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.G270S	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ctgctgccaccactgctgctg	0.657																																																	0													34.0	26.0	29.0					19																	36002423		2198	4297	6495	SO:0001583	missense	93099			BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.808G>A	19.37:g.36002423C>T	ENSP00000342012:p.Gly270Ser		A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	1.760	-0.487106	0.04352	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	3.67	-1.42	0.08913	.	1.322480	0.05258	N	0.515213	T	0.18257	0.0438	N	0.04880	-0.145	0.09310	N	1	P;P;P;P;B	0.41393	0.518;0.748;0.518;0.518;0.347	B;B;B;B;B	0.32980	0.103;0.156;0.103;0.103;0.058	T	0.08086	-1.0739	10	0.05436	T	0.98	2.738	6.6997	0.23219	0.0:0.4525:0.0:0.5475	.	270;270;270;270;270	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	270	ENSP00000342012:G270S;ENSP00000394908:G270S;ENSP00000415277:G270S;ENSP00000414743:G270S;ENSP00000388404:G270S;ENSP00000409513:G270S	ENSP00000342012:G270S	G	-	1	0	DMKN	40694263	0.006000	0.16342	0.000000	0.03702	0.028000	0.11728	1.264000	0.33015	-0.150000	0.11195	0.561000	0.74099	GGT		0.657	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2		NM_033317	
COL26A1	136227	broad.mit.edu;hgsc.bcm.edu	37	7	101063346	101063346	+	RNA	SNP	T	T	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr7:101063346T>A	ENST00000397927.3	+	0	460				COL26A1_ENST00000528707.1_RNA|COL26A1_ENST00000313669.7_RNA	NM_001278563.1	NP_001265492.1	Q96A83	COQA1_HUMAN	collagen, type XXVI, alpha 1						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.C83S(1)									GTACCAGAGCTGCCGGTGGCC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											28.0	39.0	35.0					7																	101063346		2032	4175	6207			136227			AJ416091	CCDS64739.1	7q22.1	2013-01-16	2013-01-16	2013-01-16	ENSG00000160963	ENSG00000160963		"""Collagens"", ""EMI domain containing"""	18038	protein-coding gene	gene with protein product	"""Emu2 gene"""	608927	"""EMI domain containing 2"""	EMID2		12221002, 12145293	Standard	NM_001278563		Approved	Emu2, EMI6	uc003uyo.1	Q96A83	OTTHUMG00000150033		7.37:g.101063346T>A			Q32M90	Missense_Mutation	SNP	ENST00000397927.3	37		.	.	.	.	.	.	.	.	.	.	T	26.9	4.781499	0.90282	.	.	ENSG00000160963	ENST00000313669	D	0.88664	-2.41	4.95	4.95	0.65309	EMI domain (2);	0.000000	0.40728	U	0.001037	D	0.95143	0.8426	M	0.90977	3.165	0.40999	D	0.984919	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.994	D	0.96222	0.9161	10	0.87932	D	0	.	12.5981	0.56481	0.0:0.0:0.0:1.0	.	83;83	Q96A83;C9JPW4	EMID2_HUMAN;.	S	83	ENSP00000318234:C83S	ENSP00000318234:C83S	C	+	1	0	EMID2	100850066	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.368000	0.79567	1.871000	0.54225	0.456000	0.33151	TGC		0.647	COL26A1-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000315898.2		NM_133457	
ESRRA	2101	hgsc.bcm.edu	37	11	64083296	64083298	+	In_Frame_Del	DEL	GGG	GGG	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	GGG	GGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr11:64083296_64083298delGGG	ENST00000405666.1	+	7	1364_1366	c.1130_1132delGGG	c.(1129-1134)cgggcg>ccg	p.377_378RA>P	PRDX5_ENST00000265462.4_5'Flank|PRDX5_ENST00000347941.4_5'Flank|ESRRA_ENST00000406310.1_In_Frame_Del_p.376_377RA>P|ESRRA_ENST00000000442.6_In_Frame_Del_p.377_378RA>P|PRDX5_ENST00000352435.4_5'Flank	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	377	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R377_A378>P(2)		endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GAGCGGCGGCGGGCGGGCAGGCT	0.69																																																	2	Complex - deletion inframe(2)	lung(2)								51,3601		5,41,1780						2.3	1.0			19	264,7542		4,256,3643	no	coding	ESRRA	NM_004451.3		9,297,5423	A1A1,A1R,RR		3.382,1.3965,2.7492				315,11143				SO:0001651	inframe_deletion	2101			X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.1130_1132delGGG	11.37:g.64083296_64083298delGGG	ENSP00000384851:p.Arg377_Ala378delinsPro		Q14514	In_Frame_Del	DEL	ENST00000405666.1	37	CCDS41667.1																																																																																				0.690	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1		NM_004451	
FLAD1	80308	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	154962043	154962043	+	Silent	SNP	T	T	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:154962043T>G	ENST00000292180.3	+	3	1447	c.1125T>G	c.(1123-1125)tcT>tcG	p.S375S	FLAD1_ENST00000368433.1_Silent_p.S375S|FLAD1_ENST00000368428.1_5'UTR|FLAD1_ENST00000315144.10_Silent_p.S278S|FLAD1_ENST00000405236.2_Intron|FLAD1_ENST00000368432.1_Silent_p.S278S|FLAD1_ENST00000295530.2_Intron	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	375					FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)	p.S375S(1)		endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGGGTCTTCTTTGGGGAAAA	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											89.0	89.0	89.0					1																	154962043		2203	4300	6503	SO:0001819	synonymous_variant	80308				CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"""Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)"", ""FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)"", ""flavin adenine dinucleotide synthetase"""				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.1125T>G	1.37:g.154962043T>G			Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Silent	SNP	ENST00000292180.3	37	CCDS1078.1																																																																																				0.547	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1		NM_025207	
GDF3	9573	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	7842617	7842617	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:7842617G>T	ENST00000329913.3	-	2	999	c.952C>A	c.(952-954)Cat>Aat	p.H318N		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	318					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)	p.H318N(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						TCAACGGCATGCATCAGGGCT	0.507																																																	1	Substitution - Missense(1)	kidney(1)											122.0	109.0	114.0					12																	7842617		2203	4300	6503	SO:0001583	missense	9573			AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"""Endogenous ligands"""	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.952C>A	12.37:g.7842617G>T	ENSP00000331745:p.His318Asn		Q8NEJ4	Missense_Mutation	SNP	ENST00000329913.3	37	CCDS8581.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.861128	0.32884	.	.	ENSG00000184344	ENST00000329913	D	0.83673	-1.75	4.35	1.03	0.20045	Transforming growth factor-beta, C-terminal (3);	0.404207	0.31301	N	0.007900	T	0.67813	0.2933	N	0.25094	0.71	0.58432	D	0.999996	B	0.16802	0.019	B	0.29353	0.101	T	0.51926	-0.8643	10	0.07482	T	0.82	.	9.1114	0.36730	0.0:0.129:0.6725:0.1985	.	318	Q9NR23	GDF3_HUMAN	N	318	ENSP00000331745:H318N	ENSP00000331745:H318N	H	-	1	0	GDF3	7733884	1.000000	0.71417	0.565000	0.28409	0.917000	0.54804	3.101000	0.50283	0.364000	0.24374	0.561000	0.74099	CAT		0.507	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1			
GDF3	9573	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	7842665	7842665	+	Missense_Mutation	SNP	T	T	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:7842665T>C	ENST00000329913.3	-	2	951	c.904A>G	c.(904-906)Acc>Gcc	p.T302A		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	302					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)	p.T302A(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						AGAGAGATGGTCAGTGAGAAG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											121.0	109.0	113.0					12																	7842665		2203	4300	6503	SO:0001583	missense	9573			AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"""Endogenous ligands"""	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.904A>G	12.37:g.7842665T>C	ENSP00000331745:p.Thr302Ala		Q8NEJ4	Missense_Mutation	SNP	ENST00000329913.3	37	CCDS8581.1	.	.	.	.	.	.	.	.	.	.	T	12.50	1.955758	0.34471	.	.	ENSG00000184344	ENST00000329913	D	0.83335	-1.71	4.61	3.46	0.39613	Transforming growth factor-beta, C-terminal (3);	0.140867	0.64402	N	0.000006	T	0.66458	0.2791	N	0.12569	0.235	0.43593	D	0.995941	B	0.24317	0.101	B	0.33568	0.166	T	0.57277	-0.7839	10	0.09590	T	0.72	.	7.8913	0.29680	0.0:0.0993:0.0:0.9007	.	302	Q9NR23	GDF3_HUMAN	A	302	ENSP00000331745:T302A	ENSP00000331745:T302A	T	-	1	0	GDF3	7733932	0.993000	0.37304	1.000000	0.80357	0.976000	0.68499	1.018000	0.30002	1.854000	0.53819	0.459000	0.35465	ACC		0.527	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1			
GEMIN4	50628	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	649272	649272	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:649272G>C	ENST00000319004.5	-	2	2129	c.2011C>G	c.(2011-2013)Ctg>Gtg	p.L671V	GEMIN4_ENST00000576778.1_Missense_Mutation_p.L660V	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	671					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)		p.L671V(2)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		AAGATCCTCAGACTGAGGTCT	0.532																																																	2	Substitution - Missense(2)	kidney(2)											41.0	44.0	43.0					17																	649272		1965	4150	6115	SO:0001583	missense	50628			AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2011C>G	17.37:g.649272G>C	ENSP00000321706:p.Leu671Val		Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.057818	0.55325	.	.	ENSG00000179409	ENST00000319004	T	0.14266	2.52	5.57	4.6	0.57074	.	0.000000	0.64402	D	0.000001	T	0.34077	0.0885	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.06991	-1.0796	10	0.87932	D	0	-9.1078	11.773	0.51970	0.0805:0.0:0.9195:0.0	.	671	P57678	GEMI4_HUMAN	V	671	ENSP00000321706:L671V	ENSP00000321706:L671V	L	-	1	2	GEMIN4	596022	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	2.207000	0.42788	1.361000	0.45981	0.655000	0.94253	CTG		0.532	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1		NM_015721	
GGT8P	645367	broad.mit.edu	37	2	91968965	91968965	+	IGR	SNP	T	T	G	rs200616091		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr2:91968965T>G								AC027612.2 (16921 upstream) : SLC9B1P2 (111532 downstream)																							GGTGTGGGGGTTGGTCTAGCT	0.637																																																	0																																										SO:0001628	intergenic_variant	645367																															2.37:g.91968965T>G				RNA	SNP		37																																																																																				0	0.637									
GOLGA8CP	729786	broad.mit.edu	37	15	20777925	20777925	+	RNA	SNP	G	G	T	rs201114356	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr15:20777925G>T	ENST00000408427.1	+	0	83				RN7SL759P_ENST00000485130.2_RNA														p.G385V(2)									CCTGTGCAAGGAGAGACCAGG	0.617																																																	2	Substitution - Missense(2)	kidney(2)																																										0																															15.37:g.20777925G>T				Missense_Mutation	SNP	ENST00000408427.1	37																																																																																					0.617	AC131280.1-201	NOVEL	basic	miRNA	miRNA				
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377119	168377119	+	lincRNA	SNP	T	T	C	rs199867038		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr6:168377119T>C	ENST00000538528.1	-	0	500																											GTGGGGGTCATTCCCCCTGCA	0.622																																																	0													4.0	6.0	5.0					6																	168377119		621	1484	2105			100128124																															6.37:g.168377119T>C				Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
KCNN2	3781	hgsc.bcm.edu	37	5	113698631	113698632	+	In_Frame_Ins	INS	-	-	GCC	rs151038013|rs111266015|rs76852708|rs34641516		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr5:113698631_113698632insGCC	ENST00000512097.3	+	2	1177_1178	c.159_160insGCC	c.(160-162)gcc>GCCgcc	p.54_54A>AA	KCNN2_ENST00000264773.3_In_Frame_Ins_p.54_54A>AA			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	54	Poly-Ala.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	CTGCAGCCGCTGCCGCCGCCGC	0.703																																																	0										1003,2377		300,403,987						-5.9	0.0		dbSNP_126	7	2590,4184		804,982,1601	no	coding	KCNN2	NM_021614.2		1104,1385,2588	A1A1,A1R,RR		38.2344,29.6746,35.3851				3593,6561				SO:0001652	inframe_insertion	3781			AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.169_171dupGCC	5.37:g.113698638_113698640dupGCC	ENSP00000427120:p.Ala58dup		A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	In_Frame_Ins	INS	ENST00000512097.3	37	CCDS4114.1																																																																																				0.703	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2		NM_021614	
KLKB1	3818	broad.mit.edu	37	4	187172722	187172722	+	Missense_Mutation	SNP	T	T	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr4:187172722T>A	ENST00000264690.6	+	9	1137	c.950T>A	c.(949-951)gTt>gAt	p.V317D	KLKB1_ENST00000513864.1_Missense_Mutation_p.V317D	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	317	Apple 4. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.V317D(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		GGAGTGAATGTTTGCCAAGAG	0.363																																																	2	Substitution - Missense(2)	kidney(2)											103.0	110.0	107.0					4																	187172722		2203	4299	6502	SO:0001583	missense	3818			M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.950T>A	4.37:g.187172722T>A	ENSP00000264690:p.Val317Asp		A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	5.403|5.403	0.259607|0.259607	0.10239|0.10239	.|.	.|.	ENSG00000164344|ENSG00000164344	ENST00000511608|ENST00000264690;ENST00000513864;ENST00000418715	.|D;D	.|0.87966	.|-2.32;-2.32	5.27|5.27	-10.5|-10.5	0.00291|0.00291	.|Apple domain (2);PAN-1 domain (1);Apple-like (1);	.|1.961310	.|0.02328	.|N	.|0.073626	T|T	0.68229|0.68229	0.2978|0.2978	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|P;B;P	.|0.42584	.|0.784;0.003;0.491	.|B;B;B	.|0.39617	.|0.305;0.008;0.305	T|T	0.72849|0.72849	-0.4168|-0.4168	5|10	.|0.41790	.|T	.|0.15	.|.	2.9248|2.9248	0.05780|0.05780	0.1545:0.2069:0.1519:0.4866|0.1545:0.2069:0.1519:0.4866	.|.	.|279;317;317	.|E7EQA8;A8K9A9;P03952	.|.;.;KLKB1_HUMAN	I|D	365|317;317;279	.|ENSP00000264690:V317D;ENSP00000424469:V317D	.|ENSP00000264690:V317D	F|V	+|+	1|2	0|0	KLKB1|KLKB1	187409716|187409716	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.116000|0.116000	0.19942|0.19942	-3.378000|-3.378000	0.00492|0.00492	-4.009000|-4.009000	0.00082|0.00082	-0.303000|-0.303000	0.09236|0.09236	TTT|GTT		0.363	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1		NM_000892	
KLRC1	3821	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	10603588	10603588	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:10603588G>T	ENST00000359151.3	-	2	349	c.168C>A	c.(166-168)gaC>gaA	p.D56E	KLRC1_ENST00000544822.1_Missense_Mutation_p.D56E|KLRC1_ENST00000536188.1_Missense_Mutation_p.D56E|KLRC1_ENST00000347831.5_Missense_Mutation_p.D56E|KLRC1_ENST00000408006.3_Missense_Mutation_p.D56E	NM_002259.4	NP_002250	P26715	NKG2A_HUMAN	killer cell lectin-like receptor subfamily C, member 1	56					cell surface receptor signaling pathway (GO:0007166)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.D56E(1)		NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16						GATAGGTTTTGTCATTCCCTT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											168.0	169.0	169.0					12																	10603588		2202	4300	6502	SO:0001583	missense	3821			U54782	CCDS8625.1, CCDS8626.1	12p13	2010-06-30			ENSG00000134545	ENSG00000134545		"""Killer cell lectin-like receptors"", ""CD molecules"""	6374	protein-coding gene	gene with protein product	"""NKG2-1/B activating NK receptor"""	161555		NKG2		9598306	Standard	NM_002259		Approved	NKG2-A, NKG2-B, CD159a	uc001qyl.3	P26715		ENST00000359151.3:c.168C>A	12.37:g.10603588G>T	ENSP00000352064:p.Asp56Glu			Missense_Mutation	SNP	ENST00000359151.3	37	CCDS8625.1	.	.	.	.	.	.	.	.	.	.	G	8.257	0.810264	0.16537	.	.	ENSG00000134545	ENST00000536188;ENST00000359151;ENST00000408006;ENST00000347831;ENST00000544822	T;T;T;T;T	0.04406	3.63;3.63;3.63;3.63;3.63	3.96	-0.249	0.13011	.	1.394250	0.04331	N	0.352426	T	0.06416	0.0165	L	0.37507	1.11	0.09310	N	1	B;P	0.48503	0.047;0.911	B;P	0.48166	0.068;0.569	T	0.25537	-1.0129	10	0.40728	T	0.16	.	2.4422	0.04497	0.1104:0.3639:0.3396:0.1862	.	56;56	P26715-2;P26715	.;NKG2A_HUMAN	E	56	ENSP00000441432:D56E;ENSP00000352064:D56E;ENSP00000385304:D56E;ENSP00000256965:D56E;ENSP00000438038:D56E	ENSP00000256965:D56E	D	-	3	2	KLRC1	10494855	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.164000	0.03135	0.049000	0.15920	0.655000	0.94253	GAC		0.388	KLRC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400115.1		NM_002259	
KRT78	196374	hgsc.bcm.edu;ucsc.edu	37	12	53242598	53242615	+	In_Frame_Del	DEL	CCTGCTGCTGAAGCCGCC	CCTGCTGCTGAAGCCGCC	-	rs200256832|rs201230964|rs199880767	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	CCTGCTGCTGAAGCCGCC	CCTGCTGCTGAAGCCGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:53242598_53242615delCCTGCTGCTGAAGCCGCC	ENST00000304620.4	-	1	163_180	c.100_117delGGCGGCTTCAGCAGCAGG	c.(100-117)ggcggcttcagcagcaggdel	p.GGFSSR34del	KRT78_ENST00000359499.4_5'Flank	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	34	Gly-rich.|Head.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						AATTAAGGCTCCTGCTGCTGAAGCCGCCCCTGCTGCTG	0.67														25	0.00499201	0.0015	0.0317	5008	,	,		15766	0.001		0.0	False		,,,				2504	0.0																0										6,4246		2,2,2122						5.1	1.0			19	33,8189		12,9,4090	no	coding	KRT78	NM_173352.2		14,11,6212	A1A1,A1R,RR		0.4014,0.1411,0.3127				39,12435				SO:0001651	inframe_deletion	196374			AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.100_117delGGCGGCTTCAGCAGCAGG	12.37:g.53242598_53242615delCCTGCTGCTGAAGCCGCC	ENSP00000306261:p.Gly34_Arg39del		A8K4D6|Q5HYM7|Q7RTT2	In_Frame_Del	DEL	ENST00000304620.4	37	CCDS8840.1																																																																																				0.670	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1		NM_173352	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197538	39197538	+	Missense_Mutation	SNP	G	G	T	rs146863522		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:39197538G>T	ENST00000306271.4	-	1	175	c.112C>A	c.(112-114)Cgc>Agc	p.R38S		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	38			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.R38S(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TCACAGCAGCGTGGCTGGCAG	0.607																																																	1	Substitution - Missense(1)	NS(1)											54.0	68.0	63.0					17																	39197538		2019	4207	6226	SO:0001583	missense	81851			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.112C>A	17.37:g.39197538G>T	ENSP00000305975:p.Arg38Ser		A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	93	0.042582417582417584	46	0.09349593495934959	8	0.022099447513812154	30	0.05244755244755245	9	0.011873350923482849	g	0.001	-3.345547	0.00016	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.24723	1.84	2.68	-1.04	0.10068	.	.	.	.	.	T	0.00144	0.0004	N	0.00031	-2.6	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.27226	-1.0080	8	0.02654	T	1	.	0.9532	0.01380	0.2199:0.1031:0.2626:0.4145	.	38	Q07627	KRA11_HUMAN	S	38;28	ENSP00000305975:R38S	ENSP00000305975:R38S	R	-	1	0	KRTAP1-1	36451064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.060000	0.14342	-0.640000	0.05495	-3.131000	0.00060	CGC		0.607	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1		NM_030967	
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190953	39190954	+	Missense_Mutation	DNP	GG	GG	CA	rs71300033|rs78298475|rs75033421		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:39190953_39190954GG>CA	ENST00000344363.5	-	1	153_154	c.120_121CC>TG	c.(118-123)tgCCag>tgTGag	p.Q41E		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	51			Missing (in allele KAP1.1). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:12228244, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AAGCTGGTCTGGCAGCAGCTTG	0.609																																																	0																																										SO:0001583	missense	81850			AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.120_121delinsCA	17.37:g.39190953_39190954delinsCA	ENSP00000344420:p.Gln41Glu		Q07628|Q8IUG0|Q9BYS2	Missense_Mutation|Silent	SNP	ENST00000344363.5	37	CCDS42323.1																																																																																				0.609	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197549	39197549	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:39197549G>C	ENST00000306271.4	-	1	164	c.101C>G	c.(100-102)tCc>tGc	p.S34C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.S34C(6)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612																																																	6	Substitution - Missense(6)	kidney(4)|lung(1)|prostate(1)											49.0	62.0	58.0					17																	39197549		2018	4199	6217	SO:0001583	missense	81851			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.101C>G	17.37:g.39197549G>C	ENSP00000305975:p.Ser34Cys		A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	G	0.085	-1.176298	0.01646	.	.	ENSG00000188581	ENST00000306271	T	0.16196	2.36	3.91	1.65	0.23941	.	.	.	.	.	T	0.01835	0.0058	N	0.00010	-3.04	0.22552	N	0.998996	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.02654	T	1	.	7.8006	0.29172	0.1777:0.6415:0.1808:0.0	.	34	Q07627	KRA11_HUMAN	C	34	ENSP00000305975:S34C	ENSP00000305975:S34C	S	-	2	0	KRTAP1-1	36451075	1.000000	0.71417	0.987000	0.45799	0.816000	0.46133	1.227000	0.32576	0.919000	0.36945	-0.233000	0.12211	TCC		0.612	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1		NM_030967	
L1TD1	54596	hgsc.bcm.edu	37	1	62675673	62675674	+	Missense_Mutation	DNP	GC	GC	TA	rs141196718|rs532563709|rs386631745|rs200789118	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:62675673_62675674GC>TA	ENST00000498273.1	+	4	1522_1523	c.1227_1228GC>TA	c.(1225-1230)gaGCcc>gaTAcc	p.409_410EP>DT	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	409	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						aggaggaagagccctcagggct	0.554																																																	0																																										SO:0001583	missense	54596			BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	Exception_encountered	1.37:g.62675673_62675674delinsTA	ENSP00000419901:p.E409_P410delinsDT		Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1																																																																																				0.554	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1		NM_019079	
LHX1	3975	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	35297675	35297675	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:35297675A>C	ENST00000254457.5	+	2	1670	c.259A>C	c.(259-261)Aac>Cac	p.N87H	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	87	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.N87H(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				GTTTCACCTGAACTGCTTCAC	0.552																																																	1	Substitution - Missense(1)	kidney(1)											77.0	63.0	68.0					17																	35297675		2203	4300	6503	SO:0001583	missense	3975			U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"""Homeoboxes / LIM class"""	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.259A>C	17.37:g.35297675A>C	ENSP00000254457:p.Asn87His		Q3MIW0	Missense_Mutation	SNP	ENST00000254457.5	37	CCDS11316.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.981844	0.53827	.	.	ENSG00000132130	ENST00000254457	D	0.87491	-2.26	4.05	4.05	0.47172	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.88662	0.6497	L	0.35542	1.07	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86281	0.1667	10	0.25106	T	0.35	.	14.0485	0.64719	1.0:0.0:0.0:0.0	.	87	P48742	LHX1_HUMAN	H	87	ENSP00000254457:N87H	ENSP00000254457:N87H	N	+	1	0	LHX1	32371788	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.116000	0.71571	2.064000	0.61679	0.459000	0.35465	AAC		0.552	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3		NM_005568	
LIME1	54923	broad.mit.edu	37	20	62370185	62370185	+	Missense_Mutation	SNP	A	A	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr20:62370185A>G	ENST00000309546.3	+	6	907	c.820A>G	c.(820-822)Acg>Gcg	p.T274A	LIME1_ENST00000490824.1_3'UTR|RP4-583P15.14_ENST00000476221.1_3'UTR|RP4-583P15.14_ENST00000467211.1_Intron|RP4-583P15.15_ENST00000490623.2_3'UTR|SLC2A4RG_ENST00000266077.2_5'Flank	NM_017806.2	NP_060276.2	Q9H400	LIME1_HUMAN	Lck interacting transmembrane adaptor 1	274					B cell receptor signaling pathway (GO:0050853)|T cell receptor signaling pathway (GO:0050852)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T274A(1)		kidney(1)|large_intestine(1)|liver(1)	3	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CGGGGCTGGGACGCCCCCTGC	0.682																																																	1	Substitution - Missense(1)	kidney(1)											15.0	17.0	16.0					20																	62370185		2177	4290	6467	SO:0001583	missense	54923			AK000413	CCDS13536.1	20q13.33	2010-05-11			ENSG00000203896	ENSG00000203896			26016	protein-coding gene	gene with protein product		609809				12477932	Standard	NM_017806		Approved	FLJ20406, dJ583P15.4, LIME	uc002ygp.4	Q9H400	OTTHUMG00000032999	ENST00000309546.3:c.820A>G	20.37:g.62370185A>G	ENSP00000309521:p.Thr274Ala		E1P5K5|E1P5K6|Q5JWJ2|Q6XYB3|Q9NX69	Missense_Mutation	SNP	ENST00000309546.3	37	CCDS13536.1	.	.	.	.	.	.	.	.	.	.	A	4.454	0.084151	0.08583	.	.	ENSG00000203896	ENST00000309546	T	0.46063	0.88	2.16	-1.8	0.07907	.	.	.	.	.	T	0.21227	0.0511	N	0.14661	0.345	0.09310	N	0.999995	B	0.22346	0.068	B	0.14578	0.011	T	0.21143	-1.0254	9	0.22706	T	0.39	.	8.0712	0.30691	0.449:0.0:0.551:0.0	.	274	Q9H400	LIME1_HUMAN	A	274	ENSP00000309521:T274A	ENSP00000309521:T274A	T	+	1	0	LIME1	61840629	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.223000	0.01214	-0.464000	0.06963	-0.473000	0.04963	ACG		0.682	LIME1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080225.1		NM_017806	
MAGEC1	9947	hgsc.bcm.edu	37	X	140994055	140994068	+	Frame_Shift_Del	DEL	GAGAGAACTCAGAG	GAGAGAACTCAGAG	-	rs140075882	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	GAGAGAACTCAGAG	GAGAGAACTCAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chrX:140994055_140994068delGAGAGAACTCAGAG	ENST00000285879.4	+	4	1151_1164	c.865_878delGAGAGAACTCAGAG	c.(865-879)gagagaactcagagtfs	p.ERTQS289fs	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	289										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAG	0.491										HNSCC(15;0.026)																																							0																																										SO:0001589	frameshift_variant	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.865_878delGAGAGAACTCAGAG	X.37:g.140994055_140994068delGAGAGAACTCAGAG	ENSP00000285879:p.Glu289fs		A0PK03|O75451|Q8TCV4	Frame_Shift_Del	DEL	ENST00000285879.4	37	CCDS35417.1																																																																																				0.491	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1		NM_005462	
MAP1A	4130	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	43821515	43821515	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr15:43821515C>A	ENST00000300231.5	+	4	8294	c.7844C>A	c.(7843-7845)cCa>cAa	p.P2615Q	MAP1A_ENST00000382031.1_Missense_Mutation_p.P2853Q|MAP1A_ENST00000399453.1_Missense_Mutation_p.P2615Q			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2615					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.P2615Q(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AAGGCCAAGCCAGCGTCCCCT	0.662																																																	1	Substitution - Missense(1)	kidney(1)											48.0	59.0	56.0					15																	43821515		2004	4165	6169	SO:0001583	missense	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.7844C>A	15.37:g.43821515C>A	ENSP00000300231:p.Pro2615Gln		O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925627	0.52759	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01572	4.76;4.83;4.78	5.14	5.14	0.70334	.	.	.	.	.	T	0.04907	0.0132	N	0.17082	0.46	0.44409	D	0.997328	D	0.76494	0.999	D	0.67548	0.952	T	0.57335	-0.7829	9	0.72032	D	0.01	-9.9982	18.7812	0.91933	0.0:1.0:0.0:0.0	.	2615	P78559	MAP1A_HUMAN	Q	2853;2615;2615	ENSP00000371462:P2853Q;ENSP00000382380:P2615Q;ENSP00000300231:P2615Q	ENSP00000300231:P2615Q	P	+	2	0	MAP1A	41608807	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.211000	0.77933	2.660000	0.90430	0.462000	0.41574	CCA		0.662	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5		NM_002373	
MCC	4163	broad.mit.edu	37	5	112824048	112824049	+	In_Frame_Ins	INS	-	-	GCC	rs35336557|rs531679771|rs370593160	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr5:112824048_112824049insGCC	ENST00000408903.3	-	1	478_479	c.63_64insGGC	c.(61-66)ggcagc>ggcGGCagc	p.21_22insG		NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ctgctgccgctgccgccgccgc	0.738														1663	0.332069	0.0227	0.3487	5008	,	,		8489	0.5208		0.3668	False		,,,				2504	0.5082																0																																										SO:0001652	inframe_insertion	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.61_63dupGGC	5.37:g.112824055_112824057dupGCC	ENSP00000386227:p.Gly22_Gly23dup		D3DT05|Q6ZR04	In_Frame_Ins	INS	ENST00000408903.3	37	CCDS43351.1																																																																																				0.738	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1		NM_001085377	
MEX3C	51320	hgsc.bcm.edu	37	18	48723146	48723154	+	Intron	DEL	GCCGCCGCG	GCCGCCGCG	-	rs78074704|rs530394988|rs147438518|rs201868643|rs62092914|rs530602218	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	GCCGCCGCG	GCCGCCGCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr18:48723146_48723154delGCCGCCGCG	ENST00000591040.1	-	2	43				MEX3C_ENST00000592416.1_5'Flank			Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		CCccgccgccgccgccgcggccgccgccT	0.78																																																	0										429,1467		144,141,663						-0.2	0.9		dbSNP_131	4	2100,2286		804,492,897	no	coding	MEX3C	NM_016626.4		948,633,1560	A1A1,A1R,RR		47.8796,22.6266,40.2579				2529,3753				SO:0001627	intron_variant	51320			BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	28040	protein-coding gene	gene with protein product		611005	"""ring finger and KH domain containing 2"", ""mex-3 homolog C (C. elegans)"""	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.757-19200CGCGGCGGC>-	18.37:g.48723146_48723154delGCCGCCGCG			A1L022|Q9NZE3	In_Frame_Del	DEL	ENST00000591040.1	37																																																																																					0.780	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1		NM_016626	
KMT2D	8085	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	49427164	49427164	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:49427164C>T	ENST00000301067.7	-	39	11323	c.11324G>A	c.(11323-11325)gGc>gAc	p.G3775D	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3775	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.G3505D(1)|p.G3775D(1)									AGGCATAAGGCCCTGGGGCTT	0.652																																																	2	Substitution - Missense(2)	kidney(2)											19.0	24.0	23.0					12																	49427164		2117	4247	6364	SO:0001583	missense	8085			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11324G>A	12.37:g.49427164C>T	ENSP00000301067:p.Gly3775Asp		O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	3.719	-0.057996	0.07317	.	.	ENSG00000167548	ENST00000301067	T	0.78595	-1.19	5.02	4.13	0.48395	.	0.000000	0.35378	N	0.003252	T	0.74543	0.3730	N	0.14661	0.345	0.28381	N	0.919536	D	0.69078	0.997	P	0.59115	0.852	T	0.71272	-0.4642	10	0.87932	D	0	.	12.5007	0.55953	0.0:0.9162:0.0:0.0838	.	3775	O14686	MLL2_HUMAN	D	3775	ENSP00000301067:G3775D	ENSP00000301067:G3775D	G	-	2	0	MLL2	47713431	0.642000	0.27260	0.816000	0.32577	0.279000	0.26890	1.683000	0.37638	1.248000	0.43934	0.462000	0.41574	GGC		0.652	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			
MRO	83876	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	48345981	48345981	+	5'UTR	SNP	T	T	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr18:48345981T>C	ENST00000428869.2	-	0	185				MRO_ENST00000588444.1_Intron|MRO_ENST00000398439.3_5'UTR|MRO_ENST00000256425.2_5'UTR|MRO_ENST00000436348.2_Silent_p.S37S|MRO_ENST00000587291.1_5'UTR|MRO_ENST00000431965.2_Silent_p.S37S			Q9BYG7	MSTRO_HUMAN	maestro							nucleolus (GO:0005730)		p.S37S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		TGCCACGTGATGAACCGGAGC	0.602											OREG0024982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											23.0	27.0	26.0					18																	48345981		692	1591	2283	SO:0001623	5_prime_UTR_variant	83876			AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.-74A>G	18.37:g.48345981T>C		953	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Silent	SNP	ENST00000428869.2	37	CCDS11947.1																																																																																				0.602	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2		NM_031939	
MRVI1	10335	broad.mit.edu;ucsc.edu	37	11	10624763	10624763	+	Silent	SNP	C	C	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr11:10624763C>G	ENST00000436272.1	-	13	1776	c.1698G>C	c.(1696-1698)cgG>cgC	p.R566R	MRVI1_ENST00000531107.1_Silent_p.R585R|MRVI1_ENST00000424001.1_Silent_p.R278R|MRVI1_ENST00000558540.1_Silent_p.R278R|MRVI1_ENST00000423302.2_Silent_p.R593R|MRVI1_ENST00000545852.1_Silent_p.R278R|LYVE1_ENST00000531706.1_Intron|MRVI1_ENST00000534266.2_Silent_p.R278R|MRVI1_ENST00000547195.1_Silent_p.R502R|MRVI1_ENST00000527509.2_Silent_p.R502R|MRVI1_ENST00000541483.1_Silent_p.R387R|MRVI1_ENST00000421747.1_Silent_p.R584R|MRVI1_ENST00000552103.1_Silent_p.R502R			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	566					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)		p.R566R(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GGTAGGTTTCCCGGTGCTCAC	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											43.0	48.0	46.0					11																	10624763		2009	4181	6190	SO:0001819	synonymous_variant	10335			AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"""inositol 1,4,5-triphosphate-associated cGMP kinase substrate"", ""IP3R-associated cGMP kinase substrate"""	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1698G>C	11.37:g.10624763C>G			B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	37																																																																																					0.592	MRVI1-203	KNOWN	basic	protein_coding	protein_coding			NM_001098579	
MUC4	4585	hgsc.bcm.edu	37	3	195508499	195508499	+	Missense_Mutation	SNP	C	C	T	rs534369822	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr3:195508499C>T	ENST00000463781.3	-	2	10411	c.9952G>A	c.(9952-9954)Gct>Act	p.A3318T	MUC4_ENST00000475231.1_Missense_Mutation_p.A3318T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGCGTCGGTGACA	0.577													.|||	2641	0.527356	0.8306	0.33	5008	,	,		9115	0.4127		0.5388	False		,,,				2504	0.364																2	Deletion - In frame(2)	stomach(2)											9.0	12.0	11.0					3																	195508499		610	1520	2130	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9952G>A	3.37:g.195508499C>T	ENSP00000417498:p.Ala3318Thr		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	1209	0.5535714285714286	297	0.6036585365853658	169	0.46685082872928174	317	0.5541958041958042	426	0.5620052770448549	c	2.122	-0.401145	0.04865	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.48;1.47	0.423	-0.846	0.10734	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.28350	0.208	B	0.11329	0.006	T	0.44034	-0.9354	6	.	.	.	.	.	.	.	.	3190	E7ESK3	.	T	3318	ENSP00000417498:A3318T;ENSP00000420243:A3318T	.	A	-	1	0	MUC4	196993278	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-1.841000	0.01683	-2.511000	0.00503	-1.966000	0.00469	GCT		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
NCL	4691	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	232323070	232323070	+	Missense_Mutation	SNP	T	T	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr2:232323070T>C	ENST00000322723.4	-	8	1436	c.1196A>G	c.(1195-1197)aAt>aGt	p.N399S	SNORD20_ENST00000384550.1_RNA|SNORA75_ENST00000384158.1_RNA|SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	399	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)	p.N399S(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		GTAAGGGAGATTTTTAGCCAA	0.408																																																	1	Substitution - Missense(1)	kidney(1)											93.0	89.0	90.0					2																	232323070		2203	4300	6503	SO:0001583	missense	4691				CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1196A>G	2.37:g.232323070T>C	ENSP00000318195:p.Asn399Ser		Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	37	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.313633	0.81358	.	.	ENSG00000115053	ENST00000322723;ENST00000392033	T	0.27557	1.66	5.79	5.79	0.91817	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.042254	0.85682	N	0.000000	T	0.53546	0.1803	M	0.80508	2.5	0.80722	D	1	P	0.46277	0.875	P	0.57057	0.812	T	0.58685	-0.7593	10	0.87932	D	0	-30.3439	13.9068	0.63841	0.0:0.0:0.0:1.0	.	399	P19338	NUCL_HUMAN	S	399;291	ENSP00000318195:N399S	ENSP00000318195:N399S	N	-	2	0	NCL	232031314	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	6.448000	0.73469	2.221000	0.72209	0.456000	0.33151	AAT		0.408	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1		NM_005381	
NPAS4	266743	hgsc.bcm.edu	37	11	66189604	66189604	+	Silent	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr11:66189604G>A	ENST00000311034.2	+	2	365	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	63					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTCCTCTGGCGGGCCCCACGG	0.567																																																	0													36.0	40.0	39.0					11																	66189604		2200	4295	6495	SO:0001819	synonymous_variant	266743			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.189G>A	11.37:g.66189604G>A			B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	37	CCDS8138.1																																																																																				0.567	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1		NM_178864	
P2RY8	286530	broad.mit.edu	37	X	1585028	1585028	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chrX:1585028C>A	ENST00000381297.4	-	2	634	c.424G>T	c.(424-426)Gcc>Tcc	p.A142S	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.A142S(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GCACACGCGGCCACCGCGTAA	0.682			T	CRLF2	"""B-ALL, Downs associated ALL"""																																			Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	1	Substitution - Missense(1)	kidney(1)											55.0	52.0	53.0					X																	1585028		2202	4293	6495	SO:0001583	missense	286530			AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.424G>T	X.37:g.1585028C>A	ENSP00000370697:p.Ala142Ser			Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	c	5.594	0.294299	0.10567	.	.	ENSG00000182162	ENST00000381297	T	0.73152	-0.72	2.26	-0.189	0.13260	GPCR, rhodopsin-like superfamily (1);	0.969228	0.08388	U	0.953371	T	0.59838	0.2223	L	0.58510	1.815	0.09310	N	1	P	0.38677	0.642	B	0.37508	0.252	T	0.49485	-0.8935	10	0.22109	T	0.4	.	3.5594	0.07877	0.1618:0.5645:0.158:0.1157	.	142	Q86VZ1	P2RY8_HUMAN	S	142	ENSP00000370697:A142S	ENSP00000370697:A142S	A	-	1	0	P2RY8	1545028	0.995000	0.38212	0.691000	0.30163	0.147000	0.21601	2.538000	0.45710	0.740000	0.32651	0.279000	0.19357	GCC		0.682	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1		NM_178129	
PABPC1	26986	broad.mit.edu	37	8	101724606	101724606	+	Missense_Mutation	SNP	G	G	A	rs202060459		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr8:101724606G>A	ENST00000318607.5	-	7	2084	c.956C>T	c.(955-957)aCa>aTa	p.T319I	PABPC1_ENST00000519004.1_Missense_Mutation_p.T274I|PABPC1_ENST00000522387.1_Missense_Mutation_p.T287I|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	319	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)	p.T319I(2)		breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ACTAGTGATTGTACCAAATGG	0.284																																																	2	Substitution - Missense(2)	kidney(1)|endometrium(1)											154.0	166.0	162.0					8																	101724606		2203	4298	6501	SO:0001583	missense	26986			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.956C>T	8.37:g.101724606G>A	ENSP00000313007:p.Thr319Ile		Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.8|26.8	4.768189|4.768189	0.90020|0.90020	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.16196	.|2.36;2.36;2.36	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.64402	.|D	.|0.000009	.|T	.|0.37652	.|0.1011	M|M	0.62154|0.62154	1.92|1.92	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.54964	.|0.917;0.784;0.969	.|P;B;P	.|0.56916	.|0.747;0.442;0.809	.|T	.|0.03784	.|-1.1004	.|10	.|0.87932	.|D	.|0	.|.	20.0919|20.0919	0.97823|0.97823	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|287;319;319	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	X|I	188|319;319;274;287	.|ENSP00000313007:T319I;ENSP00000429594:T274I;ENSP00000429395:T287I	.|ENSP00000313007:T319I	Q|T	-|-	1|2	0|0	PABPC1|PABPC1	101793782|101793782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.776000|9.776000	0.99001|0.99001	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	CAA|ACA		0.284	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1		NM_002568	
PAK4	10298	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	39668357	39668357	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr19:39668357G>A	ENST00000593690.1	+	10	1955	c.1528G>A	c.(1528-1530)Gac>Aac	p.D510N	PAK4_ENST00000599386.1_Missense_Mutation_p.D357N|PAK4_ENST00000599470.1_Missense_Mutation_p.D357N|PAK4_ENST00000435673.2_Missense_Mutation_p.D510N|PAK4_ENST00000321944.4_Missense_Mutation_p.D420N|PAK4_ENST00000360442.3_Missense_Mutation_p.D510N|PAK4_ENST00000358301.3_Missense_Mutation_p.D510N	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	510	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D510N(1)		central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			TGAGATGGTGGACGGAGAGCC	0.602																																																	1	Substitution - Missense(1)	kidney(1)											164.0	132.0	143.0					19																	39668357		2203	4300	6503	SO:0001583	missense	10298			AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"""p21(CDKN1A)-activated kinase 4"""			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.1528G>A	19.37:g.39668357G>A	ENSP00000469413:p.Asp510Asn		B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323363	0.95708	.	.	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.13307	2.6;2.6;2.6	5.07	5.07	0.68467	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	N	0.10760	0.04	0.80722	D	1	D;P;D	0.67145	0.996;0.781;0.973	D;P;P	0.80764	0.994;0.775;0.906	T	0.24083	-1.0170	10	0.87932	D	0	.	15.9831	0.80127	0.0:0.0:1.0:0.0	.	420;357;510	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	N	510;357;314;266;510;510	ENSP00000351049:D510N;ENSP00000392753:D510N;ENSP00000353625:D510N	ENSP00000326864:D357N	D	+	1	0	PAK4	44360197	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	9.657000	0.98554	2.629000	0.89072	0.555000	0.69702	GAC		0.602	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			
PCTP	58488	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	53853436	53853436	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:53853436G>C	ENST00000268896.5	+	6	745	c.620G>C	c.(619-621)tGt>tCt	p.C207S	PCTP_ENST00000576221.1_Intron|PCTP_ENST00000576183.1_3'UTR|PCTP_ENST00000325214.6_Missense_Mutation_p.C135S|PCTP_ENST00000573500.1_Intron	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	207	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)	p.C207S(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			GCAAGAGCCTGTCAGAACTAC	0.438																																																	1	Substitution - Missense(1)	kidney(1)											100.0	90.0	94.0					17																	53853436		2203	4300	6503	SO:0001583	missense	58488			AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.620G>C	17.37:g.53853436G>C	ENSP00000268896:p.Cys207Ser		Q9BSC9|Q9UIT3|Q9UKW7	Missense_Mutation	SNP	ENST00000268896.5	37	CCDS11588.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.188938	0.78789	.	.	ENSG00000141179	ENST00000268896;ENST00000417982;ENST00000325214	T	0.78003	-1.14	6.01	5.05	0.67936	Lipid-binding START (3);START-like domain (1);	0.268891	0.43579	D	0.000555	D	0.84813	0.5555	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.83367	0.0005	10	0.32370	T	0.25	-16.1141	11.187	0.48662	0.0837:0.0:0.9163:0.0	.	207	Q9UKL6	PPCT_HUMAN	S	207;135;186	ENSP00000268896:C207S	ENSP00000268896:C207S	C	+	2	0	PCTP	51208435	1.000000	0.71417	0.936000	0.37596	0.980000	0.70556	5.899000	0.69846	1.565000	0.49641	0.650000	0.86243	TGT		0.438	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2		NM_021213	
PGR	5241	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	100933375	100933375	+	Missense_Mutation	SNP	C	C	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr11:100933375C>G	ENST00000325455.5	-	4	3468	c.2015G>C	c.(2014-2016)aGa>aCa	p.R672T	PGR_ENST00000534013.1_Missense_Mutation_p.R78T|PGR_ENST00000263463.5_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	672					cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R672T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	AAAAGTGAATCTCTGGCTTAG	0.443																																					Pancreas(124;2271 2354 21954 22882)												1	Substitution - Missense(1)	kidney(1)											194.0	172.0	179.0					11																	100933375		2203	4300	6503	SO:0001583	missense	5241			M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2015G>C	11.37:g.100933375C>G	ENSP00000325120:p.Arg672Thr		A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.257646	0.80246	.	.	ENSG00000082175	ENST00000325455;ENST00000534013	D;D	0.86432	-1.72;-2.12	5.5	5.5	0.81552	Nuclear hormone receptor, ligand-binding (1);	0.291451	0.37393	N	0.002114	D	0.89223	0.6654	M	0.65498	2.005	0.80722	D	1	P;P	0.46706	0.774;0.883	P;B	0.46758	0.526;0.4	D	0.88791	0.3278	10	0.42905	T	0.14	.	19.3866	0.94557	0.0:1.0:0.0:0.0	.	672;53	P06401;A7LQ08	PRGR_HUMAN;.	T	672;78	ENSP00000325120:R672T;ENSP00000436561:R78T	ENSP00000325120:R672T	R	-	2	0	PGR	100438585	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.825000	0.62708	2.559000	0.86315	0.655000	0.94253	AGA		0.443	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			
PLEKHG3	26030	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	65204095	65204095	+	Splice_Site	SNP	T	T	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr14:65204095T>C	ENST00000394691.1	+	14	1551		c.e14+2		PLEKHG3_ENST00000247226.7_Splice_Site|PLEKHG3_ENST00000484731.2_5'Flank|PLEKHG3_ENST00000471182.2_5'Flank			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3								Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.?(1)		endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		GGAATGAAGGTAAAGGCCAGT	0.627																																																	1	Unknown(1)	kidney(1)											35.0	32.0	33.0					14																	65204095		2202	4299	6501	SO:0001630	splice_region_variant	26030			AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.1404+2T>C	14.37:g.65204095T>C			A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Splice_Site	SNP	ENST00000394691.1	37		.	.	.	.	.	.	.	.	.	.	T	8.152	0.787700	0.16258	.	.	ENSG00000126822	ENST00000247226;ENST00000394691	.	.	.	5.13	3.97	0.46021	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.9861	0.35994	0.0:0.0:0.1874:0.8126	.	.	.	.	.	-1	.	.	.	+	.	.	PLEKHG3	64273848	1.000000	0.71417	0.928000	0.36995	0.034000	0.12701	3.891000	0.56227	0.785000	0.33685	-0.313000	0.08912	.		0.627	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1		NM_015549	Intron
RAD51AP1	10635	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	4668106	4668106	+	Missense_Mutation	SNP	T	T	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:4668106T>A	ENST00000352618.4	+	9	1005	c.955T>A	c.(955-957)Ttg>Atg	p.L319M	RAD51AP1_ENST00000228843.9_Missense_Mutation_p.L336M|RAD51AP1_ENST00000543041.1_Missense_Mutation_p.L217M|RAD51AP1_ENST00000321524.7_Missense_Mutation_p.L286M|RAD51AP1_ENST00000544927.1_3'UTR|RAD51AP1_ENST00000544931.1_3'UTR	NM_006479.4	NP_006470.1			RAD51 associated protein 1									p.L319M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			CCGCCTTGGCTTGTCCAGATT	0.493																																																	1	Substitution - Missense(1)	kidney(1)											143.0	125.0	132.0					12																	4668106		2203	4300	6503	SO:0001583	missense	10635			AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000352618.4:c.955T>A	12.37:g.4668106T>A	ENSP00000309479:p.Leu319Met			Missense_Mutation	SNP	ENST00000352618.4	37	CCDS8529.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.832272	0.50845	.	.	ENSG00000111247	ENST00000321524;ENST00000543041;ENST00000228843;ENST00000352618	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	4.32	-0.647	0.11468	.	0.000000	0.56097	D	0.000038	T	0.66107	0.2756	M	0.77103	2.36	0.39407	D	0.966681	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.998;0.999	T	0.65800	-0.6080	10	0.87932	D	0	-4.5228	7.2884	0.26352	0.0:0.5522:0.0:0.4478	.	217;336;336;319	B4DUS5;Q96B01;A8K313;Q96B01-2	.;R51A1_HUMAN;.;.	M	286;217;336;319	ENSP00000323750:L286M;ENSP00000439960:L217M;ENSP00000228843:L336M;ENSP00000309479:L319M	ENSP00000228843:L336M	L	+	1	2	RAD51AP1	4538367	0.989000	0.36119	0.998000	0.56505	0.992000	0.81027	-0.060000	0.11712	-0.025000	0.13918	0.533000	0.62120	TTG		0.493	RAD51AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398293.1		NM_006479	
RAPGEF2	9693	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	160273849	160273849	+	Missense_Mutation	SNP	C	C	T	rs546918296		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr4:160273849C>T	ENST00000264431.4	+	21	3814	c.3395C>T	c.(3394-3396)gCt>gTt	p.A1132V		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1132	Ser-rich.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.A1120V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TATACTTTGGCTCCCAGTGGT	0.373													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19567	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											95.0	89.0	91.0					4																	160273849		1878	4101	5979	SO:0001583	missense	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3395C>T	4.37:g.160273849C>T	ENSP00000264431:p.Ala1132Val		D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.80|13.80	2.346495|2.346495	0.41599|0.41599	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000264431|ENST00000510253	T|.	0.37235|.	1.21|.	6.07|6.07	5.21|5.21	0.72293|0.72293	.|.	0.101183|.	0.64402|.	D|.	0.000002|.	T|T	0.59404|0.59404	0.2191|0.2191	L|L	0.36672|0.36672	1.1|1.1	0.45272|0.45272	D|D	0.998273|0.998273	B|.	0.13145|.	0.007|.	B|.	0.12156|.	0.007|.	T|T	0.55679|0.55679	-0.8103|-0.8103	10|5	0.02654|.	T|.	1|.	.|.	17.2077|17.2077	0.86922|0.86922	0.0:0.874:0.126:0.0|0.0:0.874:0.126:0.0	.|.	1132|.	Q9Y4G8|.	RPGF2_HUMAN|.	V|F	1132|189	ENSP00000264431:A1132V|.	ENSP00000264431:A1132V|.	A|L	+|+	2|1	0|0	RAPGEF2|RAPGEF2	160493299|160493299	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.546000|1.546000	0.36179|0.36179	1.536000|1.536000	0.49237|0.49237	0.655000|0.655000	0.94253|0.94253	GCT|CTC		0.373	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2		NM_014247	
REXO4	57109	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	136279971	136279971	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr9:136279971C>T	ENST00000371942.3	-	2	585	c.386G>A	c.(385-387)aGg>aAg	p.R129K	REXO4_ENST00000478037.1_Intron|REXO4_ENST00000371935.2_Intron|ADAMTS13_ENST00000485925.1_Intron	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	129					regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R129K(1)		kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		AACAGAGCCCCTGCTGGCCTC	0.522																																																	1	Substitution - Missense(1)	kidney(1)											102.0	91.0	95.0					9																	136279971		2203	4300	6503	SO:0001583	missense	57109			AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.386G>A	9.37:g.136279971C>T	ENSP00000361010:p.Arg129Lys		B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	37	CCDS6969.1	.	.	.	.	.	.	.	.	.	.	C	1.126	-0.653956	0.03480	.	.	ENSG00000148300	ENST00000453165;ENST00000371942;ENST00000445916	T;T;T	0.19532	2.44;2.44;2.14	4.77	-0.0677	0.13759	.	4.823880	0.00166	N	0.000005	T	0.09512	0.0234	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	10	0.02654	T	1	-0.7608	0.8281	0.01125	0.171:0.2286:0.3376:0.2628	.	129	Q9GZR2	REXO4_HUMAN	K	114;129;36	ENSP00000403272:R114K;ENSP00000361010:R129K;ENSP00000391534:R36K	ENSP00000361010:R129K	R	-	2	0	REXO4	135269792	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.058000	0.11750	0.074000	0.16767	-0.305000	0.09177	AGG		0.522	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1			
SNX29	92017	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	12136831	12136831	+	Missense_Mutation	SNP	G	G	T	rs200498279	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr16:12136831G>T	ENST00000566228.1	+	5	394	c.325G>T	c.(325-327)Gcc>Tcc	p.A109S	SNX29_ENST00000568359.1_3'UTR	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	109	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.A109S(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GCGCCACATCGCCTCAGACGT	0.657																																																	1	Substitution - Missense(1)	kidney(1)											43.0	36.0	38.0					16																	12136831		2197	4300	6497	SO:0001583	missense	0			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.325G>T	16.37:g.12136831G>T	ENSP00000456480:p.Ala109Ser		B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	G	8.219	0.801987	0.16397	.	.	ENSG00000140660	ENST00000268271	.	.	.	4.64	-1.3	0.09259	.	0.486656	0.20636	N	0.088489	T	0.07683	0.0193	N	0.00368	-1.59	0.80722	D	1	.	.	.	.	.	.	T	0.15694	-1.0428	7	0.10636	T	0.68	3.6012	2.7979	0.05406	0.4239:0.0:0.2267:0.3493	.	.	.	.	S	109	.	ENSP00000268271:A109S	A	+	1	0	RUNDC2A	12044332	0.534000	0.26362	0.792000	0.32020	0.953000	0.61014	0.807000	0.27140	-0.060000	0.13132	-0.521000	0.04368	GCC		0.657	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			
SALL1	6299	broad.mit.edu;ucsc.edu|broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	51173118	51173119	+	Missense_Mutation	DNP	AA	AA	CT			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx|Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr16:51173118_51173119AA>CT	ENST00000251020.4	-	2	3047_3048	c.3014_3015TT>AG	c.(3013-3015)aTT>aAG	p.I1005K	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.I908K	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1005					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I1005N(1)|p.I1005M(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TTTTGCCACAAATGTCACAAGC	0.396																																					GBM(103;1352 1446 1855 4775 8890)												2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3014_3015delinsCT	16.37:g.51173118_51173119delinsCT	ENSP00000251020:p.Ile1005Lys		Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																				0.396	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2		NM_002968	
SCOC	60592	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	141302257	141302257	+	Silent	SNP	A	A	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr4:141302257A>G	ENST00000608372.1	+	4	506	c.479A>G	c.(478-480)tAa>tGa	p.*160*	SCOC_ENST00000512749.1_Silent_p.*83*|SCOC_ENST00000394205.3_Silent_p.*123*|SCOC_ENST00000506322.1_Silent_p.*83*|SCOC_ENST00000502535.1_Silent_p.*83*|SCOC_ENST00000338517.4_Silent_p.*123*|SCOC_ENST00000510586.1_Silent_p.*83*|SCOC_ENST00000506597.1_Silent_p.*132*|SCOC_ENST00000394203.3_Silent_p.*123*|SCOC_ENST00000394201.4_Silent_p.*83*			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	0					positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.*160*(1)|p.*123*(1)		kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					AAAAGAAAGTAAGGGATTGAC	0.333																																																	2	Substitution - coding silent(2)	kidney(2)											37.0	37.0	37.0					4																	141302257		2203	4295	6498	SO:0001819	synonymous_variant	60592			AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"""short coiled coil protein"""			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.479A>G	4.37:g.141302257A>G			B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Silent	SNP	ENST00000608372.1	37	CCDS54806.1																																																																																				0.333	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2			
SFSWAP	6433	hgsc.bcm.edu;ucsc.edu	37	12	132211499	132211506	+	Frame_Shift_Del	DEL	TCTGACAA	TCTGACAA	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	TCTGACAA	TCTGACAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:132211499_132211506delTCTGACAA	ENST00000261674.4	+	6	988_995	c.847_854delTCTGACAA	c.(847-855)tctgacaatfs	p.SDN283fs	SFSWAP_ENST00000541286.1_Frame_Shift_Del_p.SDN283fs	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	283					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						AGGAGTCAGCTCTGACAATGAAGATGAT	0.37																																																	0																																										SO:0001589	frameshift_variant	6433			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.847_854delTCTGACAA	12.37:g.132211499_132211506delTCTGACAA	ENSP00000261674:p.Ser283fs		B2RN45|B7ZM97|F5H6B8|Q6PJF7	Frame_Shift_Del	DEL	ENST00000261674.4	37	CCDS9273.1																																																																																				0.370	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1		NM_004592	
SLC44A3	126969	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	95357883	95357883	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:95357883A>C	ENST00000271227.6	+	14	1769	c.1667A>C	c.(1666-1668)aAc>aCc	p.N556T	SLC44A3_ENST00000527077.1_Missense_Mutation_p.N488T|SLC44A3_ENST00000529450.1_Missense_Mutation_p.N523T|SLC44A3_ENST00000532427.1_Missense_Mutation_p.N476T|SLC44A3_ENST00000446120.2_Missense_Mutation_p.N520T|SLC44A3_ENST00000467909.1_Missense_Mutation_p.N508T	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	556					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N508T(1)|p.N556T(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	ATGGCTTTTAACTACAATCGG	0.393																																																	2	Substitution - Missense(2)	kidney(2)											290.0	282.0	285.0					1																	95357883		2203	4300	6503	SO:0001583	missense	126969			BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1667A>C	1.37:g.95357883A>C	ENSP00000271227:p.Asn556Thr		B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.128706	0.77549	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04;2.04	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000002	T	0.23886	0.0578	L	0.39898	1.24	0.43137	D	0.994888	D;P;D;D;D	0.76494	0.999;0.86;0.999;0.999;0.999	D;P;D;D;D	0.85130	0.961;0.561;0.961;0.997;0.997	T	0.03231	-1.1058	10	0.18276	T	0.48	-13.1471	15.2398	0.73461	1.0:0.0:0.0:0.0	.	476;520;488;523;556	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	T	520;556;488;523;508;476	ENSP00000389143:N520T;ENSP00000271227:N556T;ENSP00000433641:N488T;ENSP00000431836:N523T;ENSP00000432789:N508T;ENSP00000436661:N476T	ENSP00000271227:N556T	N	+	2	0	SLC44A3	95130471	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.052000	0.89448	2.054000	0.61138	0.402000	0.26972	AAC		0.393	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3		NM_152369	
SLC6A8	6535	broad.mit.edu;hgsc.bcm.edu	37	X	152956789	152956789	+	Missense_Mutation	SNP	T	T	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chrX:152956789T>A	ENST00000253122.5	+	3	901	c.425T>A	c.(424-426)tTc>tAc	p.F142Y	SLC6A8_ENST00000430077.2_Missense_Mutation_p.F27Y	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	142					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)	p.F142Y(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	GTGATCGTCTTCTACTGCAAC	0.597																																																	1	Substitution - Missense(1)	kidney(1)											43.0	37.0	39.0					X																	152956789		2197	4295	6492	SO:0001583	missense	6535				CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"""Solute carriers"""	11055	protein-coding gene	gene with protein product	"""creatine transporter"""	300036	"""solute carrier family 6 (neurotransmitter transporter, creatine), member 8"""			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.425T>A	X.37:g.152956789T>A	ENSP00000253122:p.Phe142Tyr		B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Missense_Mutation	SNP	ENST00000253122.5	37	CCDS14726.1	.	.	.	.	.	.	.	.	.	.	t	14.45	2.537900	0.45176	.	.	ENSG00000130821	ENST00000253122;ENST00000430077	T;T	0.76448	-1.02;-1.02	3.76	3.76	0.43208	.	.	.	.	.	T	0.79167	0.4400	M	0.80332	2.49	0.53688	D	0.999973	B;P;P	0.47962	0.335;0.903;0.774	B;B;P	0.48089	0.261;0.348;0.566	T	0.76664	-0.2876	9	0.12103	T	0.63	.	10.8615	0.46829	0.0:0.0:0.0:1.0	.	142;161;142	D3DWV2;Q59EV7;P48029	.;.;SC6A8_HUMAN	Y	142;27	ENSP00000253122:F142Y;ENSP00000403041:F27Y	ENSP00000253122:F142Y	F	+	2	0	SLC6A8	152609983	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	1.675000	0.37555	1.390000	0.46547	0.356000	0.21956	TTC		0.597	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			
SP140	11262	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	231090582	231090582	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr2:231090582G>A	ENST00000392045.3	+	1	137	c.23G>A	c.(22-24)gGg>gAg	p.G8E	SP110_ENST00000540870.1_5'Flank|SP140_ENST00000373645.3_Missense_Mutation_p.G8E|SP140_ENST00000420434.3_Missense_Mutation_p.G8E|SP140_ENST00000417495.3_Missense_Mutation_p.G8E|SP140_ENST00000343805.6_Missense_Mutation_p.G8E|SP140_ENST00000486687.2_Missense_Mutation_p.G8E|SP140_ENST00000350136.5_5'UTR	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	8					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G8E(2)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GGCCAGCAGGGGCAGATGGCA	0.552																																																	2	Substitution - Missense(2)	kidney(2)											159.0	130.0	140.0					2																	231090582		2203	4300	6503	SO:0001583	missense	11262			U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.23G>A	2.37:g.231090582G>A	ENSP00000375899:p.Gly8Glu		E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.368351	0.42003	.	.	ENSG00000079263	ENST00000537563;ENST00000486687;ENST00000392044;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434;ENST00000373645	T;T;T;T;T	0.61392	0.33;0.4;0.11;0.37;0.48	2.87	0.688	0.18027	.	.	.	.	.	T	0.32315	0.0825	N	0.08118	0	0.20638	N	0.999878	B;B;B;B;B;B	0.22346	0.005;0.005;0.009;0.012;0.068;0.004	B;B;B;B;B;B	0.12837	0.002;0.002;0.006;0.002;0.008;0.002	T	0.22138	-1.0225	9	0.87932	D	0	.	4.9125	0.13829	0.3476:0.0:0.6524:0.0	.	8;8;8;8;8;8	E7EUR5;E7ESH9;E9PFJ6;Q13342;E7EX75;Q6NSG4	.;.;.;LY10_HUMAN;.;.	E	8	ENSP00000440107:G8E;ENSP00000375899:G8E;ENSP00000342096:G8E;ENSP00000398210:G8E;ENSP00000362749:G8E	ENSP00000342096:G8E	G	+	2	0	SP140	230798826	0.000000	0.05858	0.016000	0.15963	0.592000	0.36648	-0.831000	0.04405	0.160000	0.19432	0.585000	0.79938	GGG		0.552	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1		NM_007237	
SSSCA1	10534	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	65338194	65338194	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr11:65338194C>T	ENST00000309328.3	+	2	201	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	FAM89B_ENST00000449319.2_5'Flank|SSSCA1_ENST00000531405.1_Missense_Mutation_p.R10C|FAM89B_ENST00000316409.2_5'Flank|SSSCA1_ENST00000527920.1_Missense_Mutation_p.R10C|SSSCA1_ENST00000526877.1_Missense_Mutation_p.R47C|SSSCA1-AS1_ENST00000567594.1_RNA|FAM89B_ENST00000530349.1_5'Flank	NM_006396.1	NP_006387.1	O60232	SSA27_HUMAN	Sjogren syndrome/scleroderma autoantigen 1	47					mitotic nuclear division (GO:0007067)			p.R47C(1)		kidney(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8						GCGCGGTTACCGCATGCTGGG	0.711																																																	1	Substitution - Missense(1)	kidney(1)											30.0	35.0	33.0					11																	65338194		2201	4295	6496	SO:0001583	missense	10534			AB001740	CCDS8104.1	11q13.1	2007-10-04	2007-10-04			ENSG00000173465			11328	protein-coding gene	gene with protein product		606044	"""Sjogren's syndrome/scleroderma autoantigen 1"""			9486406	Standard	NM_006396		Approved	p27	uc001oek.3	O60232		ENST00000309328.3:c.139C>T	11.37:g.65338194C>T	ENSP00000312318:p.Arg47Cys			Missense_Mutation	SNP	ENST00000309328.3	37	CCDS8104.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.435929	0.83885	.	.	ENSG00000173465	ENST00000309328;ENST00000531405;ENST00000527920;ENST00000526877;ENST00000533115	T;T;T	0.56444	0.84;0.46;0.84	5.64	5.64	0.86602	.	0.112233	0.56097	D	0.000030	T	0.60945	0.2308	L	0.36672	1.1	0.58432	D	0.999997	D	0.89917	1.0	D	0.66847	0.947	T	0.63093	-0.6714	10	0.87932	D	0	-15.4619	12.1925	0.54278	0.1705:0.8295:0.0:0.0	.	47	O60232	SSA27_HUMAN	C	47;10;10;47;41	ENSP00000312318:R47C;ENSP00000431666:R47C;ENSP00000435432:R41C	ENSP00000312318:R47C	R	+	1	0	SSSCA1	65094770	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.173000	0.65010	2.654000	0.90174	0.555000	0.69702	CGC		0.711	SSSCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389511.1		NM_006396	
TAC3	6866	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	57409489	57409489	+	Silent	SNP	A	A	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr12:57409489A>T	ENST00000458521.2	-	2	252	c.93T>A	c.(91-93)gtT>gtA	p.V31V	TAC3_ENST00000415231.1_Silent_p.V31V|TAC3_ENST00000441881.1_Silent_p.V31V	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	31					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)	p.V31V(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						CCCCGCCAGGAACCACCTCCT	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											77.0	75.0	76.0					12																	57409489		2203	4300	6503	SO:0001819	synonymous_variant	6866			AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"""Endogenous ligands"""	11521	protein-coding gene	gene with protein product	"""preprotachykinin-B"""	162330	"""neuromedin K"", ""neurokinin beta"""	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.93T>A	12.37:g.57409489A>T			Q6IAG2|Q71BC6|Q71BC9	Silent	SNP	ENST00000458521.2	37	CCDS8928.1																																																																																				0.587	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1		NM_001006667	
TBC1D9B	23061	hgsc.bcm.edu;ucsc.edu	37	5	179299981	179299981	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr5:179299981delT	ENST00000356834.3	-	14	2363	c.2326delA	c.(2326-2328)agcfs	p.S776fs	TBC1D9B_ENST00000519746.1_5'Flank|TBC1D9B_ENST00000355235.3_Frame_Shift_Del_p.S776fs|TBC1D9B_ENST00000444477.2_5'Flank	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	776						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCCTCAGGCTGCTGAATTTC	0.562																																																	0													106.0	101.0	103.0					5																	179299981		2203	4300	6503	SO:0001589	frameshift_variant	23061			AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2326delA	5.37:g.179299981delT	ENSP00000349291:p.Ser776fs		D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Frame_Shift_Del	DEL	ENST00000356834.3	37	CCDS43408.1																																																																																				0.562	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3		NM_015043	
TBP	6908	hgsc.bcm.edu	37	6	170871061	170871061	+	Silent	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr6:170871061G>A	ENST00000392092.2	+	3	516	c.237G>A	c.(235-237)caG>caA	p.Q79Q	TBP_ENST00000230354.6_Silent_p.Q79Q|TBP_ENST00000540980.1_Silent_p.Q59Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	79	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q79Q(2)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.582																																																	2	Substitution - coding silent(2)	prostate(1)|endometrium(1)											12.0	17.0	15.0					6																	170871061		1930	3791	5721	SO:0001819	synonymous_variant	6908			M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.237G>A	6.37:g.170871061G>A			B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																				0.582	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2		NM_003194	
TBP	6908	broad.mit.edu;hgsc.bcm.edu	37	6	170871067	170871067	+	Silent	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr6:170871067G>A	ENST00000392092.2	+	3	522	c.243G>A	c.(241-243)caG>caA	p.Q81Q	TBP_ENST00000230354.6_Silent_p.Q81Q|TBP_ENST00000540980.1_Silent_p.Q61Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	81	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q81Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											11.0	17.0	15.0					6																	170871067		1946	3814	5760	SO:0001819	synonymous_variant	6908			M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.243G>A	6.37:g.170871067G>A			B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																				0.587	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2		NM_003194	
TCHH	7062	hgsc.bcm.edu	37	1	152084175	152084176	+	In_Frame_Ins	INS	-	-	TGCTGCTCGCGCCTCTCC			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:152084175_152084176insTGCTGCTCGCGCCTCTCC	ENST00000368804.1	-	2	1516_1517	c.1517_1518insGGAGAGGCGCGAGCAGCA	c.(1516-1518)caa>caGGAGAGGCGCGAGCAGCAa	p.506_506Q>QERREQQ		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	506	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCGCCTTAGTTGCTGCTCGCG	0.644																																																	0																																										SO:0001652	inframe_insertion	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1500_1517dupGGAGAGGCGCGAGCAGCA	1.37:g.152084175_152084176insTGCTGCTCGCGCCTCTCC	ENSP00000357794:p.GluArgArgGluGlnGln506dup		Q5VUI3	In_Frame_Ins	INS	ENST00000368804.1	37	CCDS41396.1																																																																																				0.644	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2		NM_007113	
TRIM55	84675	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	67047249	67047249	+	Silent	SNP	C	C	A	rs151067178		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr8:67047249C>A	ENST00000315962.4	+	3	739	c.366C>A	c.(364-366)ccC>ccA	p.P122P	TRIM55_ENST00000350034.4_Silent_p.P122P|TRIM55_ENST00000276573.7_Silent_p.P122P|TRIM55_ENST00000353317.5_Silent_p.P122P	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	122					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.P122P(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			CCGACCAGCCCATGTGCGAGG	0.517																																																	1	Substitution - coding silent(1)	kidney(1)											143.0	116.0	125.0					8																	67047249		2203	4300	6503	SO:0001819	synonymous_variant	84675			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	14215	protein-coding gene	gene with protein product		606469	"""ring finger protein 29"", ""tripartite motif-containing 55"""	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.366C>A	8.37:g.67047249C>A			B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Silent	SNP	ENST00000315962.4	37	CCDS6184.1																																																																																				0.517	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1		NM_184085	
TRIM62	55223	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	33612870	33612870	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:33612870G>A	ENST00000291416.5	-	5	1569	c.1336C>T	c.(1336-1338)Cct>Tct	p.P446S	TRIM62_ENST00000543586.1_Missense_Mutation_p.P325S	NM_018207.2	NP_060677.2	Q9BVG3	TRI62_HUMAN	tripartite motif containing 62	446	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P446S(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)				AGCTTGCCAGGGAACTTCTCG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											107.0	94.0	98.0					1																	33612870		2203	4300	6503	SO:0001583	missense	55223			BC007999	CCDS376.1	1p35.1	2013-10-11	2011-01-25		ENSG00000116525	ENSG00000116525		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	25574	protein-coding gene	gene with protein product	"""ductal epithelium-associated RING Chromosome 1"""		"""tripartite motif-containing 62"""			19536326	Standard	NM_018207		Approved	FLJ10759, DEAR1	uc001bxb.3	Q9BVG3	OTTHUMG00000004132	ENST00000291416.5:c.1336C>T	1.37:g.33612870G>A	ENSP00000291416:p.Pro446Ser		B3KVH5|B4DTE4|D3DPR1|Q9NVG0	Missense_Mutation	SNP	ENST00000291416.5	37	CCDS376.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.901980	0.33535	.	.	ENSG00000116525	ENST00000291416;ENST00000543586	T;T	0.57752	0.38;0.38	5.6	4.66	0.58398	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.056364	0.64402	D	0.000001	T	0.32941	0.0846	N	0.00355	-1.605	0.58432	D	0.99999	D	0.89917	1.0	D	0.91635	0.999	T	0.50215	-0.8854	10	0.02654	T	1	.	13.4719	0.61287	0.0:0.0:0.8423:0.1577	.	446	Q9BVG3	TRI62_HUMAN	S	446;325	ENSP00000291416:P446S;ENSP00000441173:P325S	ENSP00000291416:P446S	P	-	1	0	TRIM62	33385457	1.000000	0.71417	0.687000	0.30102	0.933000	0.57130	2.859000	0.48364	1.318000	0.45170	0.491000	0.48974	CCT		0.557	TRIM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011890.1		NM_018207	
TUBGCP6	85378	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	50657163	50657163	+	Missense_Mutation	SNP	T	T	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr22:50657163T>C	ENST00000248846.5	-	21	4894	c.4790A>G	c.(4789-4791)gAt>gGt	p.D1597G	TUBGCP6_ENST00000439308.2_3'UTR|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1597					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.D1597G(1)		breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GCTCAGCACATCCGGGGCGTT	0.677																																																	1	Substitution - Missense(1)	kidney(1)											49.0	46.0	47.0					22																	50657163		2203	4300	6503	SO:0001583	missense	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.4790A>G	22.37:g.50657163T>C	ENSP00000248846:p.Asp1597Gly		Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.027336	0.75390	.	.	ENSG00000128159	ENST00000248846;ENST00000425018	T;T	0.08984	3.03;3.03	4.63	4.63	0.57726	.	0.095514	0.64402	D	0.000001	T	0.25717	0.0626	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.995	T	0.00920	-1.1514	10	0.72032	D	0.01	.	13.8622	0.63569	0.0:0.0:0.0:1.0	.	1589;1597;1597	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	G	1597;283	ENSP00000248846:D1597G;ENSP00000405979:D283G	ENSP00000248846:D1597G	D	-	2	0	TUBGCP6	48999290	1.000000	0.71417	0.472000	0.27241	0.581000	0.36288	7.633000	0.83260	1.945000	0.56424	0.482000	0.46254	GAT		0.677	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3		NM_020461	
SMG1P4	100507526	broad.mit.edu	37	16	21902089	21902089	+	RNA	SNP	A	A	G	rs56214519		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr16:21902089A>G	ENST00000540706.1	-	0	0				snoU13_ENST00000459388.1_RNA														p.A694A(7)									TCTTACTGTCAGCTAAAAGGC	0.373																																																	7	Substitution - coding silent(7)	endometrium(4)|kidney(3)																																										0																															16.37:g.21902089A>G				RNA	SNP	ENST00000540706.1	37																																																																																					0.373	RP11-645C24.2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000402428.1			
KRTAP2-3	730755	broad.mit.edu	37	17	39216302	39216303	+	Start_Codon_Ins	INS	-	-	G	rs201832186|rs369140188|rs369908545|rs370014641|rs113441706	byFrequency	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr17:39216302_39216303insG	ENST00000391418.2	-	0	41_42					NM_001165252.1	NP_001158724.1	P0C7H8	KRA23_HUMAN	keratin associated protein 2-3							keratin filament (GO:0045095)											GAGCCGGTCATGGTGGTGTCTG	0.634																																																	0										720,2376		135,450,963						4.5	1.0		dbSNP_132	8	423,4813		81,261,2276	no	frameshift	LOC730755	NM_001165252.1		216,711,3239	A1A1,A1R,RR		8.0787,23.2558,13.7182				1143,7189				SO:0001582	initiator_codon_variant	0			BC012486	CCDS54123.1	17q21.2	2012-08-03			ENSG00000212724	ENSG00000212724		"""Keratin associated proteins"""	18906	protein-coding gene	gene with protein product							Standard	NM_001165252		Approved	KAP2.3	uc002hvx.3	P0C7H8	OTTHUMG00000133655	ENST00000391418.2:c.2dupC	17.37:g.39216304_39216304dupG				Translation_Start_Site	INS	ENST00000391418.2	37	CCDS54123.1																																																																																				0.634	KRTAP2-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257692.1		NM_001165252	
USH2A	7399	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	216166458	216166458	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:216166458C>A	ENST00000307340.3	-	35	7095	c.6709G>T	c.(6709-6711)Gac>Tac	p.D2237Y	USH2A_ENST00000366943.2_Missense_Mutation_p.D2237Y	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2237	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.D2237Y(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATGTCCTCGTCAGTTAGGGCC	0.507										HNSCC(13;0.011)	OREG0014251	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											182.0	163.0	169.0					1																	216166458		2203	4300	6503	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.6709G>T	1.37:g.216166458C>A	ENSP00000305941:p.Asp2237Tyr	2234	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739341	0.89573	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53857	0.6;0.6	6.17	5.26	0.73747	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.547689	0.14977	N	0.287475	T	0.47746	0.1462	L	0.51422	1.61	0.09310	N	0.999999	P	0.43169	0.8	B	0.39185	0.293	T	0.51458	-0.8703	10	0.62326	D	0.03	.	12.1962	0.54298	0.0:0.8715:0.0:0.1285	.	2237	O75445	USH2A_HUMAN	Y	2237	ENSP00000305941:D2237Y;ENSP00000355910:D2237Y	ENSP00000305941:D2237Y	D	-	1	0	USH2A	214233081	0.891000	0.30450	0.049000	0.19019	0.932000	0.56968	2.267000	0.43329	2.941000	0.99782	0.655000	0.94253	GAC		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1		NM_007123	
VHL	7428	hgsc.bcm.edu	37	3	10183804	10183805	+	Frame_Shift_Del	DEL	CG	CG	-	rs587780731		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01W-1244-10	CG	CG	CG	-	CG	CG	Unknown	Valid	Somatic	Phase_I	WXS	PacBio	.		Illumina MiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	099df9a3-e2e2-4441-b88d-a83da347cbae	g.chr3:10183804_10183805delCG	ENST00000256474.2	+	1	1113_1114	c.273_274delCG	c.(271-276)ttcgacfs	p.FD91fs	VHL_ENST00000345392.2_Frame_Shift_Del_p.FD91fs|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	91			F -> L (in cerebellar hemangioblastoma). {ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.D92fs*38(1)|p.F91fs*68(1)|p.F91fs*64(1)|p.R60fs*35(1)|p.N90fs*67(1)|p.D92Y(1)|p.V84_E94>E(1)|p.L89fs*67(1)|p.N90fs*38(1)|p.F91_E94del(1)|p.D92N(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GGCTCAACTTCGACGGCGAGCC	0.718		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	11	Deletion - Frameshift(7)|Substitution - Missense(2)|Complex - deletion inframe(1)|Deletion - In frame(1)	kidney(11)	GRCh37	CM042500	VHL	M																																				SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.273_274delCG	3.37:g.10183804_10183805delCG	ENSP00000256474:p.Phe91fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.718	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VSIG8	391123	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	159827560	159827560	+	Silent	SNP	C	C	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr1:159827560C>T	ENST00000368100.1	-	4	762	c.627G>A	c.(625-627)gaG>gaA	p.E209E	C1orf204_ENST00000368102.1_5'Flank|C1orf204_ENST00000491974.1_5'Flank	NM_001013661.1	NP_001013683.1	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	209	Ig-like V-type 2.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	poly(A) RNA binding (GO:0044822)	p.E209E(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	8	all_hematologic(112;0.0597)					TGTGGAAGGACTCCTGGTAGG	0.572																																																	1	Substitution - coding silent(1)	kidney(1)											57.0	58.0	58.0					1																	159827560		2203	4300	6503	SO:0001819	synonymous_variant	391123				CCDS30913.1	1q23.2	2013-01-11			ENSG00000243284	ENSG00000243284		"""Immunoglobulin superfamily / V-set domain containing"""	32063	protein-coding gene	gene with protein product							Standard	NM_001013661		Approved		uc001fuh.3	Q5VU13	OTTHUMG00000168834	ENST00000368100.1:c.627G>A	1.37:g.159827560C>T			Q5VU14	Silent	SNP	ENST00000368100.1	37	CCDS30913.1																																																																																				0.572	VSIG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085978.8		NM_001013661	
ZBTB33	10009	hgsc.bcm.edu	37	X	119387833	119387834	+	In_Frame_Ins	INS	-	-	TGA	rs201958171|rs77815464|rs59686094		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chrX:119387833_119387834insTGA	ENST00000326624.2	+	2	791_792	c.563_564insTGA	c.(562-567)tctgat>tcTGAtgat	p.194_195insD	ZBTB33_ENST00000557385.1_In_Frame_Ins_p.194_195insD	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	194					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						GTTACCGATTCtgatgatgatg	0.396														1942	0.514437	0.2065	0.4078	3775	,	,		15520	0.4494		0.5328	False		,,,				2504	0.4059																0																																										SO:0001652	inframe_insertion	10009			BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.579_581dupTGA	X.37:g.119387840_119387842dupTGA	ENSP00000314153:p.Asp194_Asp194dup		B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	In_Frame_Ins	INS	ENST00000326624.2	37	CCDS14596.1																																																																																				0.396	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2		NM_006777	
ZNF12	7559	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	6731954	6731954	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr7:6731954delA	ENST00000405858.1	-	5	1160	c.619delT	c.(619-621)tatfs	p.Y207fs	AC073343.13_ENST00000366167.2_RNA|AC073343.2_ENST00000577401.1_RNA|ZNF12_ENST00000342651.5_Frame_Shift_Del_p.Y169fs|ZNF12_ENST00000404360.1_Frame_Shift_Del_p.Y133fs	NM_006956.2|NM_016265.3	NP_008887.2|NP_057349.2	P17014	ZNF12_HUMAN	zinc finger protein 12	207					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(3)	16		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		ATTTTCTGATAAAGACTTTCT	0.338																																																	0													40.0	38.0	39.0					7																	6731954		1819	4085	5904	SO:0001589	frameshift_variant	7559			X52334, AB021643	CCDS47538.1, CCDS47539.1	7p21.1	2013-01-08	2005-06-09		ENSG00000164631	ENSG00000164631		"""Zinc fingers, C2H2-type"", ""-"""	12902	protein-coding gene	gene with protein product		194536	"""zinc finger protein 325"""	ZNF325			Standard	NM_016265		Approved	KOX3, GIOT-3	uc003sqt.1	P17014	OTTHUMG00000151910	ENST00000405858.1:c.619delT	7.37:g.6731954delA	ENSP00000385939:p.Tyr207fs		A8MYC4|A8WFQ8|B2RNQ7|B4DF45|Q6N016|Q8NHZ0|Q9H9P0|Q9ULZ6	Frame_Shift_Del	DEL	ENST00000405858.1	37	CCDS47538.1																																																																																				0.338	ZNF12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324373.2		NM_016265	
ZNF208	7757	broad.mit.edu	37	19	22154068	22154068	+	Silent	SNP	T	T	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr19:22154068T>C	ENST00000397126.4	-	4	3916	c.3768A>G	c.(3766-3768)gaA>gaG	p.E1256E	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	1256					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E1128E(2)|p.E1256E(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TGCCACATTCTTCACATTTGT	0.383																																																	3	Substitution - coding silent(3)	kidney(3)											41.0	44.0	43.0					19																	22154068		2101	4236	6337	SO:0001819	synonymous_variant	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.3768A>G	19.37:g.22154068T>C				Silent	SNP	ENST00000397126.4	37	CCDS54240.1																																																																																				0.383	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1		NM_007153	
ZNF841	284371	broad.mit.edu;hgsc.bcm.edu	37	19	52568835	52568835	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr19:52568835C>T	ENST00000426391.2	-	5	2503	c.1952G>A	c.(1951-1953)tGt>tAt	p.C651Y	ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.C767Y|ZNF841_ENST00000594295.1_Missense_Mutation_p.C767Y|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000359973.2_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	651					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C767Y(2)|p.C208Y(1)		breast(1)|endometrium(4)|kidney(3)|lung(3)	11						ACATTCATTACATTTGTAAGG	0.428																																																	3	Substitution - Missense(3)	kidney(3)											66.0	61.0	62.0					19																	52568835		692	1591	2283	SO:0001583	missense	284371			AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1952G>A	19.37:g.52568835C>T	ENSP00000415453:p.Cys651Tyr		B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	37		.	.	.	.	.	.	.	.	.	.	C	22.2	4.264015	0.80358	.	.	ENSG00000197608	ENST00000389534;ENST00000426391	D;D	0.85088	-1.94;-1.94	1.97	1.97	0.26223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93628	0.7965	H	0.95328	3.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.93957	0.7237	9	0.87932	D	0	.	10.95	0.47323	0.0:1.0:0.0:0.0	.	767;651	Q6ZN19-3;Q6ZN19	.;ZN841_HUMAN	Y	767;651	ENSP00000374185:C767Y;ENSP00000415453:C651Y	ENSP00000374185:C767Y	C	-	2	0	ZNF841	57260647	0.056000	0.20664	0.005000	0.12908	0.883000	0.51084	1.741000	0.38238	1.082000	0.41137	0.313000	0.20887	TGT		0.428	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1		XM_209155	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60822215	60822215	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3f847558-8bc7-49b0-899d-2a7b8f0e3d1a	41213977-65aa-487a-9d3e-c5cfc7c0ceed	g.chr5:60822215delA	ENST00000252744.5	+	7	1829	c.1829delA	c.(1828-1830)caafs	p.Q610fs		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	610					neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						TTCCGAACCCAAAAAAAAGGT	0.408																																																	0													144.0	131.0	135.0					5																	60822215		692	1591	2283	SO:0001589	frameshift_variant	57688			BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.1829delA	5.37:g.60822215delA	ENSP00000252744:p.Gln610fs			Frame_Shift_Del	DEL	ENST00000252744.5	37	CCDS47215.1																																																																																				0.408	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1		NM_020928	
